Thu Jul 14 10:49:22 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base /opt/share/freesurfer/bin/recon-all -base CA149base -tp CA149T1 -tp CA149T2 -all subjid CA149base setenv SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Actual FREESURFER_HOME /opt/share/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux magma 2.6.34.10-0.6-desktop #1 SMP PREEMPT 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 56191628 kbytes vmemoryuse 59593840 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 515842 total used free shared buffers cached Mem: 66107712 11288924 54818788 0 731800 5475432 -/+ buffers/cache: 5081692 61026020 Swap: 8384508 4546544 3837964 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-14:49:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/share/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/share/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Thu Jul 14 10:49:38 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz --lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --template /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz --average 1 --sat 4.685 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz'... Will use TP 1 as random initial target (seed 7899 ). MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) to TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::computeMultiresRegistration - Gaussian Pyramid - Gaussian Pyramid - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.2611422594622 0 1.0000000000000 0 -11.6287113640282 0 0 1.0000000000000 4.1228113649287 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 12.3901 Iteration(f): 2 -- diff. to prev. transform: 4.03977 Iteration(f): 3 -- diff. to prev. transform: 3.55419 Iteration(f): 4 -- diff. to prev. transform: 1.84896 Iteration(f): 5 -- diff. to prev. transform: 2.14165 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 6.96327 Iteration(f): 2 -- diff. to prev. transform: 5.74141 Iteration(f): 3 -- diff. to prev. transform: 5.55055 Iteration(f): 4 -- diff. to prev. transform: 5.6916 Iteration(f): 5 -- diff. to prev. transform: 1.14683 max it: 5 reached! Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 7.52911 Iteration(f): 2 -- diff. to prev. transform: 1.02864 Iteration(f): 3 -- diff. to prev. transform: 0.303 Iteration(f): 4 -- diff. to prev. transform: 0.0716646 Iteration(f): 5 -- diff. to prev. transform: 0.0915364 max it: 5 reached! Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 9.18169 Iteration(f): 2 -- diff. to prev. transform: 2.6423 Iteration(f): 3 -- diff. to prev. transform: 0.211904 Iteration(f): 4 -- diff. to prev. transform: 0.0198634 Iteration(f): 5 -- diff. to prev. transform: 0.00149082 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.233751 Iteration(f): 2 -- diff. to prev. transform: 0.0179814 Iteration(f): 3 -- diff. to prev. transform: 0.0014246 < 0.01 :-) - final transform: Tf = [ ... 0.9993262848404 0.0082085076700 0.0357714527092 -4.9039929491302 -0.0117454481286 0.9949365083652 0.0998167759964 -18.9631218587834 -0.0347709774863 -0.1001696796635 0.9943626171577 19.6990204039638 0 0 0 1.0000000000000 ] - final iscale: If = 1 computing coord of TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) wrt to TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) computing mean coord of TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) mapping back to rot, err = 2.23594e-08 computing mean coord of TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) mapping back to rot, err = 2.3132e-08 warping movs and creating initial template... using median Writing final template: /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 2 minutes and 2 seconds. mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz --average 1 --ixforms /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --noit --template /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --template: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz as template output volume. reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz'... warping movs and creating initial template... using median Writing final template: /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 18 seconds. /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms mri_concatenate_lta -invert1 CA149T1_to_CA149base.lta identity.nofile CA149base_to_CA149T1.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file CA149base_to_CA149T1.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 CA149T2_to_CA149base.lta identity.nofile CA149base_to_CA149T2.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file CA149base_to_CA149T2.lta... mri_concatenate_lta successful. #-------------------------------------------- #@# MotionCor Thu Jul 14 10:52:00 EDT 2016 Found 1 runs /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms mri_convert /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz --conform mri_convert /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz... TR=1950.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, -1.86265e-08, -6.70552e-08) j_ras = (-7.45058e-09, 1.32713e-08, -1) k_ras = (-7.45058e-09, 1, 2.58442e-08) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz... mri_add_xform_to_header -c /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/talairach.xfm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Jul 14 10:52:30 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 14 10:54:24 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7007, pval=0.4932 >= threshold=0.0050) awk -f /opt/share/freesurfer/bin/extract_talairach_avi_QA.awk /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/talairach_avi.log TalAviQA: 0.98581 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 14 10:54:25 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri /opt/share/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 2011/03/02 20:16:39 nicks Exp $ Linux magma 2.6.34.10-0.6-desktop #1 SMP PREEMPT 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 14 10:54:26 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.16858 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16858/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16858/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=1950.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, -1.77636e-15, 4.81386e-16) j_ras = (0, 1.32713e-08, -1) k_ras = (-1.77636e-15, 1, 2.58442e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.16858/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jul 14 10:54:38 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.16858/nu0.mnc ./tmp.mri_nu_correct.mni.16858/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16858/0/ [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 10:54:39] running: /opt/share/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.16858/0/ ./tmp.mri_nu_correct.mni.16858/nu0.mnc ./tmp.mri_nu_correct.mni.16858/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.00098552 [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 10:57:47] running: /opt/share/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16858/nu0.mnc ./tmp.mri_nu_correct.mni.16858/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Jul 14 10:58:02 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.16858/nu1.mnc ./tmp.mri_nu_correct.mni.16858/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.16858/1/ [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 10:58:02] running: /opt/share/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.16858/1/ ./tmp.mri_nu_correct.mni.16858/nu1.mnc ./tmp.mri_nu_correct.mni.16858/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000988571 [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 10:59:48] running: /opt/share/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16858/nu1.mnc ./tmp.mri_nu_correct.mni.16858/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.16858/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16858/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.16858/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16858/ones.mgz sysname Linux hostname magma machine x86_64 user ncorriveau input ./tmp.mri_nu_correct.mni.16858/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.16858/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.16858/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16858/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16858/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16858/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16858/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16858/input.mean.dat sysname Linux hostname magma machine x86_64 user ncorriveau Loading ./tmp.mri_nu_correct.mni.16858/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.16858/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16858/ones.mgz --i ./tmp.mri_nu_correct.mni.16858/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16858/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16858/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16858/ones.mgz --i ./tmp.mri_nu_correct.mni.16858/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16858/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16858/output.mean.dat sysname Linux hostname magma machine x86_64 user ncorriveau Loading ./tmp.mri_nu_correct.mni.16858/ones.mgz Loading ./tmp.mri_nu_correct.mni.16858/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.16858/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.16858/nu2.mnc ./tmp.mri_nu_correct.mni.16858/nu2.mnc mul 1.02532602449051766058 Saving result to './tmp.mri_nu_correct.mni.16858/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.16858/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.16858/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.16858/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, 4.81386e-16) j_ras = (0, 1.32713e-08, -1) k_ras = (-1.77636e-15, 1, 2.58442e-08) 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 21 seconds. mapping (24, 142) to ( 3, 110) Thu Jul 14 11:02:13 EDT 2016 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Thu Jul 14 11:02:13 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_normalize -g 1 -W ctrl_vol.mgz bias_vol.mgz nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.119 0.048 -0.089 -4.130; -0.024 1.068 0.389 -26.198; 0.112 -0.339 1.157 6.346; 0.000 0.000 0.000 1.000; writing ctrl pts to ctrl_vol.mgz writing bias field to bias_vol.mgz INFO: Modifying talairach volume c_(r,a,s) based on average_305 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 4 minutes and 38 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 109 gm peak at 69 (69), valley at 58 (58) csf peak at 39, setting threshold to 59 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 61 (61) csf peak at 38, setting threshold to 60 writing bias field to bias_vol.mgz.... #-------------------------------------------- #@# Skull Stripping Thu Jul 14 11:06:54 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz --average 0 --ixforms /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --noit --finalnearest --template brainmask_template.mgz $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz as movable/source volume. Total: 2 input volumes --average: Using method 0 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --finalnearest: Use nearest neighbor interpolation for final average! --template: Using brainmask_template.mgz as template output volume. reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz'... warping movs and creating initial template... using mean Writing final template: brainmask_template.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 15 seconds. mri_mask -keep_mask_deletion_edits T1.mgz brainmask_template.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_template.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Jul 14 11:07:25 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_em_register -mask brainmask.mgz norm_template.mgz /opt/share/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'norm_template.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, 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=22.1 skull bounding box = (67, 75, 59) --> (190, 203, 209) using (108, 118, 134) as brain centroid... mean wm in atlas = 107, using box (93,102,116) --> (123, 133,152) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -6181.3 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.3, -13.4, -24.1): log p = -5970.789 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-5501.1, old_max_log_p =-5970.8 (thresh=-5964.8) 1.226 -0.156 -0.042 -2.951; 0.161 1.184 0.317 -91.749; 0.000 -0.298 1.111 0.858; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-5501.1, old_max_log_p =-5501.1 (thresh=-5495.6) 1.226 -0.156 -0.042 -2.951; 0.161 1.184 0.317 -91.749; 0.000 -0.298 1.111 0.858; 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=-5351.5, old_max_log_p =-5501.1 (thresh=-5495.6) 1.162 -0.100 -0.061 -3.095; 0.131 1.222 0.367 -100.878; 0.035 -0.336 1.077 5.749; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-5351.5, old_max_log_p =-5351.5 (thresh=-5346.2) 1.162 -0.100 -0.061 -3.095; 0.131 1.222 0.367 -100.878; 0.035 -0.336 1.077 5.749; 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=-5321.0, old_max_log_p =-5351.5 (thresh=-5346.2) 1.159 -0.125 -0.087 4.789; 0.160 1.222 0.356 -102.686; 0.055 -0.327 1.075 1.752; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5320.0, old_max_log_p =-5321.0 (thresh=-5315.6) 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 5315.8 after pass:transform: ( 1.16, -0.13, -0.08, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.33, 1.08, 3.10) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 5315.8 tol 0.000010 Resulting transform: 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -5320.0 (old=-6181.3) transform before final EM align: 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 664615.6 after pass:transform: ( 1.16, -0.13, -0.08, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.33, 1.08, 3.10) dfp_em_step_func: 011: -log(p) = 663240.2 after pass:transform: ( 1.17, -0.12, -0.07, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.32, 1.08, 3.10) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 663240.2 tol 0.000000 final transform: 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 26 minutes and 36 seconds. #-------------------------------------- #@# CA Normalize Thu Jul 14 11:34:02 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz norm_template.mgz /opt/share/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 volumes reading atlas from '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from norm_template.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=22.1 skull bounding box = (67, 75, 59) --> (190, 203, 209) using (108, 118, 134) as brain centroid... mean wm in atlas = 107, using box (93,102,116) --> (123, 133,152) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 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 (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 125.0 0 of 1687 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 0 of 2067 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 125.0 0 of 29 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 125.0 0 of 40 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) Brain_Stem: limiting intensities to 85.0 --> 125.0 9 of 39 (23.1%) samples deleted using 3862 total control points for intensity normalization... bias field = 1.001 +- 0.023 2 of 3853 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 1 of 1690 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 125.0 0 of 2043 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 125.0 0 of 58 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 125.0 0 of 76 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) Brain_Stem: limiting intensities to 84.0 --> 125.0 29 of 92 (31.5%) samples deleted using 3959 total control points for intensity normalization... bias field = 0.998 +- 0.022 2 of 3929 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 2 of 1739 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 7 of 2085 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 125.0 0 of 95 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 125.0 0 of 82 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) Brain_Stem: limiting intensities to 69.0 --> 125.0 0 of 210 (0.0%) samples deleted using 4211 total control points for intensity normalization... bias field = 0.997 +- 0.024 5 of 4202 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 3 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Thu Jul 14 11:37:07 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/share/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.70 (predicted orig area = 4.7) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87502.227 ms 0001: dt=129.472000, rms=0.678 (7.650%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 86599.797 ms 0002: dt=129.472000, rms=0.664 (1.997%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66214.266 ms 0003: dt=129.472000, rms=0.652 (1.829%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93247.812 ms 0004: dt=110.976000, rms=0.649 (0.475%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71137.242 ms 0005: dt=221.952000, rms=0.641 (1.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73789.031 ms 0006: dt=55.488000, rms=0.639 (0.293%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79514.484 ms 0007: dt=369.920000, rms=0.636 (0.446%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87593.359 ms 0008: dt=110.976000, rms=0.632 (0.729%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 92042.469 ms 0009: dt=55.488000, rms=0.631 (0.111%), neg=0, invalid=766 0010: dt=55.488000, rms=0.631 (0.056%), neg=0, invalid=766 0011: dt=55.488000, rms=0.630 (0.120%), neg=0, invalid=766 0012: dt=55.488000, rms=0.629 (0.205%), neg=0, invalid=766 0013: dt=55.488000, rms=0.627 (0.293%), neg=0, invalid=766 0014: dt=55.488000, rms=0.625 (0.307%), neg=0, invalid=766 0015: dt=55.488000, rms=0.623 (0.288%), neg=0, invalid=766 0016: dt=55.488000, rms=0.622 (0.264%), neg=0, invalid=766 0017: dt=55.488000, rms=0.620 (0.229%), neg=0, invalid=766 0018: dt=55.488000, rms=0.619 (0.226%), neg=0, invalid=766 0019: dt=55.488000, rms=0.617 (0.233%), neg=0, invalid=766 0020: dt=55.488000, rms=0.616 (0.229%), neg=0, invalid=766 0021: dt=55.488000, rms=0.615 (0.208%), neg=0, invalid=766 0022: dt=55.488000, rms=0.613 (0.200%), neg=0, invalid=766 0023: dt=55.488000, rms=0.612 (0.189%), neg=0, invalid=766 0024: dt=55.488000, rms=0.611 (0.185%), neg=0, invalid=766 0025: dt=55.488000, rms=0.610 (0.187%), neg=0, invalid=766 0026: dt=55.488000, rms=0.609 (0.196%), neg=0, invalid=766 0027: dt=55.488000, rms=0.608 (0.189%), neg=0, invalid=766 0028: dt=55.488000, rms=0.607 (0.161%), neg=0, invalid=766 0029: dt=55.488000, rms=0.606 (0.148%), neg=0, invalid=766 0030: dt=55.488000, rms=0.605 (0.132%), neg=0, invalid=766 0031: dt=55.488000, rms=0.604 (0.133%), neg=0, invalid=766 0032: dt=55.488000, rms=0.603 (0.147%), neg=0, invalid=766 0033: dt=55.488000, rms=0.602 (0.133%), neg=0, invalid=766 0034: dt=55.488000, rms=0.602 (0.118%), neg=0, invalid=766 0035: dt=55.488000, rms=0.601 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 122160.859 ms 0036: dt=1479.680000, rms=0.600 (0.124%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 95494.141 ms 0037: dt=129.472000, rms=0.599 (0.165%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126850.094 ms 0038: dt=8.092000, rms=0.599 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94591.625 ms 0039: dt=73.984000, rms=0.599 (0.032%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 112423.023 ms 0040: dt=517.888000, rms=0.598 (0.267%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96702.102 ms 0041: dt=32.368000, rms=0.597 (0.016%), neg=0, invalid=766 0042: dt=32.368000, rms=0.597 (0.004%), neg=0, invalid=766 0043: dt=32.368000, rms=0.597 (-0.006%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87363.656 ms 0044: dt=145.152000, rms=0.594 (1.238%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71131.188 ms 0045: dt=103.680000, rms=0.585 (1.489%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81857.188 ms 0046: dt=25.920000, rms=0.583 (0.375%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96512.898 ms 0047: dt=124.416000, rms=0.579 (0.587%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70990.055 ms 0048: dt=31.104000, rms=0.577 (0.430%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 91354.320 ms 0049: dt=62.208000, rms=0.575 (0.387%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81031.211 ms 0050: dt=31.104000, rms=0.573 (0.215%), neg=0, invalid=766 0051: dt=31.104000, rms=0.572 (0.203%), neg=0, invalid=766 0052: dt=31.104000, rms=0.571 (0.261%), neg=0, invalid=766 0053: dt=31.104000, rms=0.568 (0.424%), neg=0, invalid=766 0054: dt=31.104000, rms=0.566 (0.448%), neg=0, invalid=766 0055: dt=31.104000, rms=0.563 (0.509%), neg=0, invalid=766 0056: dt=31.104000, rms=0.560 (0.495%), neg=0, invalid=766 0057: dt=31.104000, rms=0.557 (0.497%), neg=0, invalid=766 0058: dt=31.104000, rms=0.555 (0.476%), neg=0, invalid=766 0059: dt=31.104000, rms=0.552 (0.417%), neg=0, invalid=766 0060: dt=31.104000, rms=0.550 (0.396%), neg=0, invalid=766 0061: dt=31.104000, rms=0.548 (0.329%), neg=0, invalid=766 0062: dt=31.104000, rms=0.547 (0.352%), neg=0, invalid=766 0063: dt=31.104000, rms=0.545 (0.293%), neg=0, invalid=766 0064: dt=31.104000, rms=0.544 (0.243%), neg=0, invalid=766 0065: dt=31.104000, rms=0.542 (0.248%), neg=0, invalid=766 0066: dt=31.104000, rms=0.541 (0.237%), neg=0, invalid=766 0067: dt=31.104000, rms=0.540 (0.235%), neg=0, invalid=766 0068: dt=31.104000, rms=0.539 (0.199%), neg=0, invalid=766 0069: dt=31.104000, rms=0.538 (0.172%), neg=0, invalid=766 0070: dt=31.104000, rms=0.537 (0.150%), neg=0, invalid=766 0071: dt=31.104000, rms=0.536 (0.154%), neg=0, invalid=766 0072: dt=31.104000, rms=0.535 (0.147%), neg=0, invalid=766 0073: dt=31.104000, rms=0.535 (0.118%), neg=0, invalid=766 0074: dt=31.104000, rms=0.534 (0.123%), neg=0, invalid=766 0075: dt=31.104000, rms=0.533 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81443.148 ms 0076: dt=25.920000, rms=0.533 (0.010%), neg=0, invalid=766 0077: dt=25.920000, rms=0.533 (0.015%), neg=0, invalid=766 0078: dt=25.920000, rms=0.533 (0.013%), neg=0, invalid=766 0079: dt=25.920000, rms=0.533 (0.006%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77165.805 ms 0080: dt=103.680000, rms=0.532 (0.279%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101471.922 ms 0081: dt=36.288000, rms=0.531 (0.128%), neg=0, invalid=766 0082: dt=36.288000, rms=0.531 (0.059%), neg=0, invalid=766 0083: dt=36.288000, rms=0.530 (0.076%), neg=0, invalid=766 0084: dt=36.288000, rms=0.530 (0.100%), neg=0, invalid=766 0085: dt=36.288000, rms=0.529 (0.095%), neg=0, invalid=766 0086: dt=36.288000, rms=0.529 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71284.305 ms 0087: dt=82.944000, rms=0.529 (0.020%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.550, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 104226.172 ms 0088: dt=1.600000, rms=0.550 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100549.047 ms 0089: dt=0.125000, rms=0.550 (0.001%), neg=0, invalid=766 0090: dt=0.125000, rms=0.550 (0.000%), neg=0, invalid=766 0091: dt=0.125000, rms=0.550 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.550, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87614.422 ms 0092: dt=1.600000, rms=0.550 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70140.273 ms 0093: dt=0.001953, rms=0.550 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.610, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75788.555 ms 0094: dt=4.794872, rms=0.592 (2.840%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 67940.500 ms 0095: dt=1.872340, rms=0.592 (0.071%), neg=0, invalid=766 0096: dt=1.872340, rms=0.592 (-0.022%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 67180.797 ms 0097: dt=0.252000, rms=0.592 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100189.633 ms 0098: dt=0.144000, rms=0.592 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 104416.516 ms 0099: dt=0.015750, rms=0.592 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.648, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87108.336 ms 0100: dt=1.189904, rms=0.643 (0.712%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 110594.641 ms 0101: dt=1.876543, rms=0.639 (0.685%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81844.172 ms 0102: dt=0.448000, rms=0.639 (0.047%), neg=0, invalid=766 0103: dt=0.448000, rms=0.639 (0.020%), neg=0, invalid=766 0104: dt=0.448000, rms=0.639 (0.008%), neg=0, invalid=766 0105: dt=0.448000, rms=0.639 (-0.046%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 90919.703 ms 0106: dt=1.536000, rms=0.637 (0.178%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78600.477 ms 0107: dt=0.000000, rms=0.637 (0.002%), neg=0, invalid=766 0108: dt=0.100000, rms=0.637 (-0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77624.672 ms 0109: dt=0.143037, rms=0.596 (0.882%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87827.664 ms 0110: dt=0.239726, rms=0.596 (0.080%), neg=0, invalid=766 0111: dt=0.239726, rms=0.592 (0.598%), neg=0, invalid=766 0112: dt=0.119863, rms=0.592 (-0.258%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 83346.891 ms 0113: dt=0.000000, rms=0.592 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68492.586 ms 0114: dt=0.028000, rms=0.592 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66231.492 ms 0115: dt=0.019975, rms=0.592 (0.002%), neg=0, invalid=766 0116: dt=0.019975, rms=0.592 (0.002%), neg=0, invalid=766 0117: dt=0.019975, rms=0.592 (-0.007%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12067 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (985 voxels, overlap=0.355) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (985 voxels, peak = 20), gca=19.8 gca peak = 0.14022 (22) mri peak = 0.13083 (23) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (940 voxels, overlap=0.584) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (940 voxels, peak = 20), gca=19.8 gca peak = 0.24234 (100) mri peak = 0.18069 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (317 voxels, overlap=0.255) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (317 voxels, peak = 108), gca=107.5 gca peak = 0.19192 (97) mri peak = 0.15241 (106) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (287 voxels, overlap=0.244) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (287 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.08374 (73) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (619 voxels, overlap=0.070) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (619 voxels, peak = 72), gca=72.4 gca peak = 0.29892 (64) mri peak = 0.07620 (72) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (435 voxels, overlap=0.177) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (435 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.09928 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (51455 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (51455 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.09567 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (51365 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (51365 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03437 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (20819 voxels, overlap=0.389) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (20819 voxels, peak = 72), gca=72.4 gca peak = 0.13270 (63) mri peak = 0.03158 (68) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22252 voxels, overlap=0.596) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22252 voxels, peak = 69), gca=69.3 gca peak = 0.15182 (70) mri peak = 0.08373 (83) Right_Caudate (50): linear fit = 1.20 x + 0.0 (418 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.20 x + 0.0 (418 voxels, peak = 84), gca=84.0 gca peak = 0.14251 (76) mri peak = 0.10560 (85) Left_Caudate (11): linear fit = 1.08 x + 0.0 (469 voxels, overlap=0.488) Left_Caudate (11): linear fit = 1.08 x + 0.0 (469 voxels, peak = 82), gca=81.7 gca peak = 0.12116 (60) mri peak = 0.04738 (65) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22074 voxels, overlap=0.712) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22074 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04579 (63) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25814 voxels, overlap=0.907) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25814 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.10267 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7052 voxels, overlap=0.687) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7052 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.11077 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6085 voxels, overlap=0.806) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6085 voxels, peak = 91), gca=91.3 gca peak = 0.25455 (62) mri peak = 0.14050 (71) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (233 voxels, overlap=0.141) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (233 voxels, peak = 70), gca=69.8 gca peak = 0.39668 (62) mri peak = 0.14410 (71) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (229 voxels, overlap=0.242) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (229 voxels, peak = 68), gca=68.2 gca peak = 0.10129 (93) mri peak = 0.07422 (98) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3372 voxels, overlap=0.904) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3372 voxels, peak = 95), gca=95.3 gca peak = 0.12071 (89) mri peak = 0.07394 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3339 voxels, overlap=0.476) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3339 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.06836 (97) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1813 voxels, overlap=0.176) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1813 voxels, peak = 94), gca=94.3 gca peak = 0.15214 (84) mri peak = 0.06240 (89) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1793 voxels, overlap=0.852) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1793 voxels, peak = 92), gca=92.4 gca peak = 0.08983 (85) mri peak = 0.06529 (93) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9393 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9393 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.09786 (104) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (772 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (772 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07683 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (908 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (908 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.09568 (24) gca peak = 0.13542 (27) mri peak = 0.08153 (24) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (264 voxels, overlap=0.468) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (264 voxels, peak = 23), gca=23.0 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) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Right_Pallidum too bright - rescaling by 0.985 (from 1.075) to 105.9 (was 107.5) saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.620, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 92091.703 ms 0118: dt=92.480000, rms=0.615 (0.789%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87573.297 ms 0119: dt=129.472000, rms=0.613 (0.288%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76903.883 ms 0120: dt=129.472000, rms=0.610 (0.428%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79614.789 ms 0121: dt=129.472000, rms=0.609 (0.173%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85271.016 ms 0122: dt=110.976000, rms=0.608 (0.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100889.977 ms 0123: dt=92.480000, rms=0.607 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 88616.906 ms 0124: dt=129.472000, rms=0.605 (0.224%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 109960.172 ms 0125: dt=73.984000, rms=0.605 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101211.828 ms 0126: dt=295.936000, rms=0.603 (0.268%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93077.766 ms 0127: dt=55.488000, rms=0.602 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126177.523 ms 0128: dt=2071.552000, rms=0.595 (1.126%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93327.234 ms 0129: dt=55.488000, rms=0.592 (0.458%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81443.961 ms 0130: dt=887.808000, rms=0.589 (0.479%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 86651.992 ms 0131: dt=73.984000, rms=0.589 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96874.781 ms 0132: dt=129.472000, rms=0.588 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101861.195 ms 0133: dt=129.472000, rms=0.588 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 108352.453 ms 0134: dt=110.976000, rms=0.588 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84303.188 ms 0135: dt=92.480000, rms=0.587 (0.040%), neg=0, invalid=766 0136: dt=92.480000, rms=0.587 (0.051%), neg=0, invalid=766 0137: dt=92.480000, rms=0.587 (0.067%), neg=0, invalid=766 0138: dt=92.480000, rms=0.586 (0.102%), neg=0, invalid=766 0139: dt=92.480000, rms=0.585 (0.110%), neg=0, invalid=766 0140: dt=92.480000, rms=0.585 (0.144%), neg=0, invalid=766 0141: dt=92.480000, rms=0.584 (0.134%), neg=0, invalid=766 0142: dt=92.480000, rms=0.583 (0.145%), neg=0, invalid=766 0143: dt=92.480000, rms=0.582 (0.136%), neg=0, invalid=766 0144: dt=92.480000, rms=0.581 (0.151%), neg=0, invalid=766 0145: dt=92.480000, rms=0.580 (0.139%), neg=0, invalid=766 0146: dt=92.480000, rms=0.580 (0.139%), neg=0, invalid=766 0147: dt=92.480000, rms=0.579 (0.130%), neg=0, invalid=766 0148: dt=92.480000, rms=0.578 (0.134%), neg=0, invalid=766 0149: dt=92.480000, rms=0.577 (0.129%), neg=0, invalid=766 0150: dt=92.480000, rms=0.577 (0.117%), neg=0, invalid=766 0151: dt=92.480000, rms=0.576 (0.116%), neg=0, invalid=766 0152: dt=92.480000, rms=0.575 (0.114%), neg=0, invalid=766 0153: dt=92.480000, rms=0.575 (0.118%), neg=0, invalid=766 0154: dt=92.480000, rms=0.574 (0.108%), neg=0, invalid=766 0155: dt=92.480000, rms=0.573 (0.103%), neg=0, invalid=766 0156: dt=92.480000, rms=0.573 (0.096%), neg=0, invalid=766 0157: dt=92.480000, rms=0.572 (0.090%), neg=0, invalid=766 0158: dt=92.480000, rms=0.572 (0.087%), neg=0, invalid=766 0159: dt=92.480000, rms=0.571 (0.087%), neg=0, invalid=766 0160: dt=92.480000, rms=0.571 (0.086%), neg=0, invalid=766 0161: dt=92.480000, rms=0.570 (0.081%), neg=0, invalid=766 0162: dt=92.480000, rms=0.570 (0.080%), neg=0, invalid=766 0163: dt=92.480000, rms=0.570 (0.077%), neg=0, invalid=766 0164: dt=92.480000, rms=0.569 (0.072%), neg=0, invalid=766 0165: dt=92.480000, rms=0.569 (0.071%), neg=0, invalid=766 0166: dt=92.480000, rms=0.568 (0.068%), neg=0, invalid=766 0167: dt=92.480000, rms=0.568 (0.064%), neg=0, invalid=766 0168: dt=92.480000, rms=0.568 (0.064%), neg=0, invalid=766 0169: dt=92.480000, rms=0.567 (0.061%), neg=0, invalid=766 0170: dt=92.480000, rms=0.567 (0.057%), neg=0, invalid=766 0171: dt=92.480000, rms=0.567 (0.053%), neg=0, invalid=766 0172: dt=92.480000, rms=0.566 (0.050%), neg=0, invalid=766 0173: dt=92.480000, rms=0.566 (0.046%), neg=0, invalid=766 0174: dt=92.480000, rms=0.566 (0.048%), neg=0, invalid=766 0175: dt=92.480000, rms=0.566 (0.046%), neg=0, invalid=766 0176: dt=92.480000, rms=0.565 (0.047%), neg=0, invalid=766 0177: dt=92.480000, rms=0.565 (0.046%), neg=0, invalid=766 0178: dt=92.480000, rms=0.565 (0.045%), neg=0, invalid=766 0179: dt=92.480000, rms=0.565 (0.038%), neg=0, invalid=766 0180: dt=92.480000, rms=0.564 (0.037%), neg=0, invalid=766 0181: dt=92.480000, rms=0.564 (0.038%), neg=0, invalid=766 0182: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 0183: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 0184: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 0185: dt=92.480000, rms=0.563 (0.034%), neg=0, invalid=766 0186: dt=92.480000, rms=0.563 (0.033%), neg=0, invalid=766 0187: dt=92.480000, rms=0.563 (0.033%), neg=0, invalid=766 0188: dt=92.480000, rms=0.563 (0.032%), neg=0, invalid=766 0189: dt=92.480000, rms=0.563 (0.031%), neg=0, invalid=766 0190: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 0191: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 0192: dt=92.480000, rms=0.562 (0.029%), neg=0, invalid=766 0193: dt=92.480000, rms=0.562 (0.028%), neg=0, invalid=766 0194: dt=92.480000, rms=0.562 (0.029%), neg=0, invalid=766 0195: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 0196: dt=92.480000, rms=0.561 (0.032%), neg=0, invalid=766 0197: dt=92.480000, rms=0.561 (0.029%), neg=0, invalid=766 0198: dt=92.480000, rms=0.561 (0.028%), neg=0, invalid=766 0199: dt=92.480000, rms=0.561 (0.024%), neg=0, invalid=766 0200: dt=92.480000, rms=0.561 (0.026%), neg=0, invalid=766 0201: dt=92.480000, rms=0.561 (0.026%), neg=0, invalid=766 0202: dt=92.480000, rms=0.561 (0.029%), neg=0, invalid=766 0203: dt=92.480000, rms=0.560 (0.024%), neg=0, invalid=766 0204: dt=92.480000, rms=0.560 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 112931.984 ms 0205: dt=129.472000, rms=0.560 (0.003%), neg=0, invalid=766 0206: dt=129.472000, rms=0.560 (0.003%), neg=0, invalid=766 0207: dt=129.472000, rms=0.560 (0.006%), neg=0, invalid=766 0208: dt=129.472000, rms=0.560 (0.008%), neg=0, invalid=766 0209: dt=129.472000, rms=0.560 (0.012%), neg=0, invalid=766 0210: dt=129.472000, rms=0.560 (0.011%), neg=0, invalid=766 0211: dt=129.472000, rms=0.560 (0.016%), neg=0, invalid=766 0212: dt=129.472000, rms=0.560 (0.016%), neg=0, invalid=766 0213: dt=129.472000, rms=0.560 (0.015%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 117745.602 ms 0214: dt=129.472000, rms=0.559 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 103247.500 ms 0215: dt=369.920000, rms=0.558 (0.110%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 107582.523 ms 0216: dt=32.368000, rms=0.558 (0.034%), neg=0, invalid=766 0217: dt=32.368000, rms=0.558 (0.007%), neg=0, invalid=766 0218: dt=32.368000, rms=0.558 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.560, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 127856.289 ms 0219: dt=145.152000, rms=0.556 (0.757%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 99217.461 ms 0220: dt=82.944000, rms=0.551 (0.776%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 87736.266 ms 0221: dt=20.736000, rms=0.549 (0.392%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 97923.445 ms 0222: dt=145.152000, rms=0.546 (0.594%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 90565.875 ms 0223: dt=31.104000, rms=0.544 (0.383%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84598.867 ms 0224: dt=31.104000, rms=0.543 (0.216%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101502.211 ms 0225: dt=36.288000, rms=0.541 (0.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93230.898 ms 0226: dt=36.288000, rms=0.541 (0.150%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93639.625 ms 0227: dt=36.288000, rms=0.540 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 95715.125 ms 0228: dt=36.288000, rms=0.539 (0.142%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 122857.219 ms 0229: dt=36.288000, rms=0.538 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94566.547 ms 0230: dt=36.288000, rms=0.537 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 105124.180 ms 0231: dt=36.288000, rms=0.536 (0.172%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 91908.812 ms 0232: dt=36.288000, rms=0.535 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84821.000 ms 0233: dt=62.208000, rms=0.534 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 90978.867 ms 0234: dt=25.920000, rms=0.534 (0.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94555.773 ms 0235: dt=82.944000, rms=0.533 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101917.055 ms 0236: dt=20.736000, rms=0.532 (0.153%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 113746.539 ms 0237: dt=580.608000, rms=0.527 (0.859%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96694.172 ms 0238: dt=31.104000, rms=0.523 (0.826%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 99502.422 ms 0239: dt=36.288000, rms=0.522 (0.149%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102908.781 ms 0240: dt=103.680000, rms=0.521 (0.165%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 83180.938 ms 0241: dt=25.920000, rms=0.521 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 89232.008 ms 0242: dt=62.208000, rms=0.520 (0.107%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 88714.898 ms 0243: dt=25.920000, rms=0.520 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96920.906 ms 0244: dt=82.944000, rms=0.519 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94155.664 ms 0245: dt=25.920000, rms=0.519 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 89652.922 ms 0246: dt=36.288000, rms=0.518 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 74017.812 ms 0247: dt=36.288000, rms=0.518 (0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 90829.195 ms 0248: dt=145.152000, rms=0.518 (0.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77436.867 ms 0249: dt=9.072000, rms=0.517 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84705.438 ms 0250: dt=9.072000, rms=0.517 (0.048%), neg=0, invalid=766 0251: dt=4.536000, rms=0.517 (0.014%), neg=0, invalid=766 0252: dt=0.567000, rms=0.517 (0.001%), neg=0, invalid=766 0253: dt=0.567000, rms=0.517 (0.002%), neg=0, invalid=766 0254: dt=0.017719, rms=0.517 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44502.973 ms 0255: dt=0.007594, rms=0.517 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46939.547 ms 0256: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81609.125 ms 0257: dt=44.800000, rms=0.507 (3.232%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 74522.125 ms 0258: dt=9.600000, rms=0.505 (0.465%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75305.656 ms 0259: dt=9.600000, rms=0.503 (0.450%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96106.805 ms 0260: dt=11.200000, rms=0.500 (0.464%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93935.000 ms 0261: dt=44.800000, rms=0.492 (1.542%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76218.523 ms 0262: dt=9.600000, rms=0.491 (0.282%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 92215.852 ms 0263: dt=11.200000, rms=0.490 (0.316%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 89398.641 ms 0264: dt=11.200000, rms=0.488 (0.265%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 95235.570 ms 0265: dt=11.200000, rms=0.487 (0.260%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 92562.445 ms 0266: dt=11.200000, rms=0.486 (0.235%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102771.367 ms 0267: dt=11.200000, rms=0.485 (0.226%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 88704.266 ms 0268: dt=11.200000, rms=0.484 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 114555.188 ms 0269: dt=11.200000, rms=0.483 (0.201%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 88609.812 ms 0270: dt=11.200000, rms=0.482 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 89916.008 ms 0271: dt=11.200000, rms=0.481 (0.177%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 108073.984 ms 0272: dt=11.200000, rms=0.480 (0.172%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85446.648 ms 0273: dt=11.200000, rms=0.479 (0.167%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101867.953 ms 0274: dt=38.400000, rms=0.477 (0.446%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75039.016 ms 0275: dt=2.800000, rms=0.477 (0.058%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 89878.281 ms 0276: dt=2.800000, rms=0.477 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102937.086 ms 0277: dt=8.000000, rms=0.476 (0.105%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96283.953 ms 0278: dt=44.800000, rms=0.474 (0.464%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85324.195 ms 0279: dt=2.800000, rms=0.474 (0.036%), neg=0, invalid=766 0280: dt=2.800000, rms=0.474 (0.037%), neg=0, invalid=766 0281: dt=2.800000, rms=0.473 (0.053%), neg=0, invalid=766 0282: dt=2.800000, rms=0.473 (0.064%), neg=0, invalid=766 0283: dt=2.800000, rms=0.473 (0.080%), neg=0, invalid=766 0284: dt=2.800000, rms=0.472 (0.104%), neg=0, invalid=766 0285: dt=2.800000, rms=0.472 (0.118%), neg=0, invalid=766 0286: dt=2.800000, rms=0.471 (0.133%), neg=0, invalid=766 0287: dt=2.800000, rms=0.470 (0.128%), neg=0, invalid=766 0288: dt=2.800000, rms=0.470 (0.139%), neg=0, invalid=766 0289: dt=2.800000, rms=0.469 (0.145%), neg=0, invalid=766 0290: dt=2.800000, rms=0.468 (0.144%), neg=0, invalid=766 0291: dt=2.800000, rms=0.468 (0.143%), neg=0, invalid=766 0292: dt=2.800000, rms=0.467 (0.145%), neg=0, invalid=766 0293: dt=2.800000, rms=0.466 (0.143%), neg=0, invalid=766 0294: dt=2.800000, rms=0.466 (0.140%), neg=0, invalid=766 0295: dt=2.800000, rms=0.465 (0.137%), neg=0, invalid=766 0296: dt=2.800000, rms=0.464 (0.132%), neg=0, invalid=766 0297: dt=2.800000, rms=0.464 (0.131%), neg=0, invalid=766 0298: dt=2.800000, rms=0.463 (0.126%), neg=0, invalid=766 0299: dt=2.800000, rms=0.463 (0.122%), neg=0, invalid=766 0300: dt=2.800000, rms=0.462 (0.115%), neg=0, invalid=766 0301: dt=2.800000, rms=0.462 (0.107%), neg=0, invalid=766 0302: dt=2.800000, rms=0.461 (0.108%), neg=0, invalid=766 0303: dt=2.800000, rms=0.461 (0.100%), neg=0, invalid=766 0304: dt=2.800000, rms=0.460 (0.094%), neg=0, invalid=766 0305: dt=2.800000, rms=0.460 (0.088%), neg=0, invalid=766 0306: dt=2.800000, rms=0.459 (0.085%), neg=0, invalid=766 0307: dt=2.800000, rms=0.459 (0.080%), neg=0, invalid=766 0308: dt=2.800000, rms=0.459 (0.075%), neg=0, invalid=766 0309: dt=2.800000, rms=0.458 (0.074%), neg=0, invalid=766 0310: dt=2.800000, rms=0.458 (0.070%), neg=0, invalid=766 0311: dt=2.800000, rms=0.458 (0.067%), neg=0, invalid=766 0312: dt=2.800000, rms=0.457 (0.068%), neg=0, invalid=766 0313: dt=2.800000, rms=0.457 (0.059%), neg=0, invalid=766 0314: dt=2.800000, rms=0.457 (0.059%), neg=0, invalid=766 0315: dt=2.800000, rms=0.457 (0.056%), neg=0, invalid=766 0316: dt=2.800000, rms=0.456 (0.054%), neg=0, invalid=766 0317: dt=2.800000, rms=0.456 (0.047%), neg=0, invalid=766 0318: dt=2.800000, rms=0.456 (0.050%), neg=0, invalid=766 0319: dt=2.800000, rms=0.456 (0.047%), neg=0, invalid=766 0320: dt=2.800000, rms=0.456 (0.046%), neg=0, invalid=766 0321: dt=2.800000, rms=0.455 (0.047%), neg=0, invalid=766 0322: dt=2.800000, rms=0.455 (0.039%), neg=0, invalid=766 0323: dt=2.800000, rms=0.455 (0.041%), neg=0, invalid=766 0324: dt=2.800000, rms=0.455 (0.038%), neg=0, invalid=766 0325: dt=2.800000, rms=0.455 (0.038%), neg=0, invalid=766 New invocation of recon-all Thu Jul 14 18:31:19 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base /opt/share/freesurfer/bin/recon-all -base CA149base -tp CA149T1 -tp CA149T2 -all subjid CA149base setenv SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Actual FREESURFER_HOME /opt/share/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux magma 2.6.34.10-0.6-desktop #1 SMP PREEMPT 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 56191628 kbytes vmemoryuse 59593840 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 515842 total used free shared buffers cached Mem: 66107712 51291288 14816424 0 752696 20184724 -/+ buffers/cache: 30353868 35753844 Swap: 8384508 4483056 3901452 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:20-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 0326: dt=2.800000, rms=0.454 (0.039%), neg=0, invalid=766 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:30-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/share/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/share/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### New invocation of recon-all Thu Jul 14 18:31:58 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base /opt/share/freesurfer/bin/recon-all -base CA149base -tp CA149T1 -tp CA149T2 -all subjid CA149base setenv SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Actual FREESURFER_HOME /opt/share/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux magma 2.6.34.10-0.6-desktop #1 SMP PREEMPT 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 56191628 kbytes vmemoryuse 59593840 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 515842 total used free shared buffers cached Mem: 66107712 50913008 15194704 0 752728 20321432 -/+ buffers/cache: 29838848 36268864 Swap: 8384508 4483056 3901452 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:31:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 0327: dt=2.800000, rms=0.454 (0.034%), neg=0, invalid=766 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/14-22:32:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: ncorriveau Machine: magma Platform: Linux PlatformVersion: 2.6.34.10-0.6-desktop CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/share/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/share/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Thu Jul 14 18:32:21 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz --lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --template /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz --average 1 --sat 4.685 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz'... Will use TP 1 as random initial target (seed 7899 ). MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) to TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 256) Dst: (1, 1, 1)mm and dim (256, 256, 256) Asserting both images: 1mm isotropic and (256, 256, 256) voxels - no Source reslice necessary - no Target reslice necessary Registration::computeMultiresRegistration - Gaussian Pyramid - Gaussian Pyramid - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.2611422594622 0 1.0000000000000 0 -11.6287113640282 0 0 1.0000000000000 4.1228113649287 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 12.3901 Iteration(f): 2 -- diff. to prev. transform: 4.03977 Iteration(f): 3 -- diff. to prev. transform: 3.55419 Iteration(f): 4 -- diff. to prev. transform: 1.84896 Iteration(f): 5 -- diff. to prev. transform: 2.14165 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 6.96327 Iteration(f): 2 -- diff. to prev. transform: 5.74141 Iteration(f): 3 -- diff. to prev. transform: 5.55055 Iteration(f): 4 -- diff. to prev. transform: 5.6916 Iteration(f): 5 -- diff. to prev. transform: 1.14683 max it: 5 reached! Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 7.52911 Iteration(f): 2 -- diff. to prev. transform: 1.02864 Iteration(f): 30328: dt=2.800000, rms=0.454 (0.038%), neg=0, invalid=766 -- diff. to prev. transform: 0.303 Iteration(f): 4 -- diff. to prev. transform: 0.0716646 Iteration(f): 5 -- diff. to prev. transform: 0.0915364 max it: 5 reached! Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 9.18169 Iteration(f): 2 -- diff. to prev. transform: 2.6423 Iteration(f): 3 -- diff. to prev. transform: 0.211904 Iteration(f): 4 -- diff. to prev. transform: 0.0198634 Iteration(f): 5 -- diff. to prev. transform: 0.00149082 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 10329: dt=2.800000, rms=0.454 (0.035%), neg=0, invalid=766 -- diff. to prev. transform: 0.233751 Iteration(f): 20330: dt=2.800000, rms=0.454 (0.034%), neg=0, invalid=766 -- diff. to prev. transform: 0.0179814 Iteration(f): 30331: dt=2.800000, rms=0.454 (0.032%), neg=0, invalid=766 -- diff. to prev. transform: 0.0014246 < 0.01 :-) - final transform: Tf = [ ... 0.9993262848404 0.0082085076700 0.0357714527092 -4.9039929491302 -0.0117454481286 0.9949365083652 0.0998167759964 -18.9631218587834 -0.0347709774863 -0.1001696796635 0.9943626171577 19.6990204039638 0 0 0 1.0000000000000 ] - final iscale: If = 1 computing coord of TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) wrt to TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) computing mean coord of TP 1 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/norm.mgz ) mapping back to rot, err = 2.23594e-08 computing mean coord of TP 2 ( /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/norm.mgz ) mapping back to rot, err = 2.3132e-08 warping movs and creating initial template... 0332: dt=2.800000, rms=0.454 (0.028%), neg=0, invalid=766 using median Writing final template: /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 3 minutes and 8 seconds. mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz --average 1 --ixforms /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --noit --template /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --template: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz as template output volume. reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/orig.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/orig.mgz'... warping movs and creating initial template... using median Writing final template: /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 26 seconds. /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms mri_concatenate_lta -invert1 CA149T1_to_CA149base.lta identity.nofile CA149base_to_CA149T1.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file CA149base_to_CA149T1.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 CA149T2_to_CA149base.lta identity.nofile CA149base_to_CA149T2.lta invert the first LTA before applying it 0333: dt=2.800000, rms=0.453 (0.031%), neg=0, invalid=766 Read individual LTAs Writing LTA to file CA149base_to_CA149T2.lta... mri_concatenate_lta successful. #-------------------------------------------- #@# MotionCor Thu Jul 14 18:36:00 EDT 2016 Found 1 runs /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig/001.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms mri_convert /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz --conform mri_convert /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/rawavg.mgz... TR=1950.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, -1.86265e-08, -6.70552e-08) j_ras = (-7.45058e-09, 1.32713e-08, -1) k_ras = (-7.45058e-09, 1, 2.58442e-08) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz... mri_add_xform_to_header -c /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/talairach.xfm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Jul 14 18:36:48 EDT 2016 0334: dt=2.800000, rms=0.453 (0.030%), neg=0, invalid=766 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm 0335: dt=2.800000, rms=0.453 (0.032%), neg=0, invalid=766 0336: dt=2.800000, rms=0.453 (0.031%), neg=0, invalid=766 0337: dt=2.800000, rms=0.453 (0.027%), neg=0, invalid=766 0338: dt=2.800000, rms=0.453 (0.026%), neg=0, invalid=766 0339: dt=2.800000, rms=0.453 (0.026%), neg=0, invalid=766 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 14 18:40:12 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7007, pval=0.4932 >= threshold=0.0050) awk -f /opt/share/freesurfer/bin/extract_talairach_avi_QA.awk /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/talairach_avi.log TalAviQA: 0.98581 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 14 18:40:13 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri /opt/share/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 2011/03/02 20:16:39 nicks Exp $ Linux magma 2.6.34.10-0.6-desktop #1 SMP PREEMPT 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 14 18:40:14 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.31167 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31167/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31167/nu0.mnc -odt float 0340: dt=2.800000, rms=0.452 (0.027%), neg=0, invalid=766 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=1950.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, -1.77636e-15, 4.81386e-16) j_ras = (0, 1.32713e-08, -1) k_ras = (-1.77636e-15, 1, 2.58442e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.31167/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jul 14 18:40:28 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.31167/nu0.mnc ./tmp.mri_nu_correct.mni.31167/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31167/0/ [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 18:40:28] running: /opt/share/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.31167/0/ ./tmp.mri_nu_correct.mni.31167/nu0.mnc ./tmp.mri_nu_correct.mni.31167/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0341: dt=2.800000, rms=0.452 (0.025%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0342: dt=2.800000, rms=0.452 (0.028%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0343: dt=2.800000, rms=0.452 (0.026%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0344: dt=2.800000, rms=0.452 (0.025%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.00098552 [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 18:42:53] running: /opt/share/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.31167/nu0.mnc ./tmp.mri_nu_correct.mni.31167/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done 0345: dt=2.800000, rms=0.452 (0.027%), neg=0, invalid=766 -------------------------------------------------------- Iteration 2 Thu Jul 14 18:43:10 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.31167/nu1.mnc ./tmp.mri_nu_correct.mni.31167/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.31167/1/ [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 18:43:10] running: /opt/share/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.31167/1/ ./tmp.mri_nu_correct.mni.31167/nu1.mnc ./tmp.mri_nu_correct.mni.31167/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0346: dt=2.800000, rms=0.452 (0.024%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 0347: dt=2.800000, rms=0.452 (0.022%), neg=0, invalid=766 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000988571 [ncorriveau@magma:/data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/] [2016-07-14 18:44:45] running: /opt/share/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.31167/nu1.mnc ./tmp.mri_nu_correct.mni.31167/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.31167/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31167/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.31167/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31167/ones.mgz sysname Linux hostname magma machine x86_64 user ncorriveau input ./tmp.mri_nu_correct.mni.31167/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.31167/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.31167/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31167/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31167/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31167/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31167/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31167/input.mean.dat sysname Linux hostname magma machine x86_64 user ncorriveau Loading ./tmp.mri_nu_correct.mni.31167/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.31167/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31167/ones.mgz --i ./tmp.mri_nu_correct.mni.31167/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31167/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31167/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31167/ones.mgz --i ./tmp.mri_nu_correct.mni.31167/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31167/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31167/output.mean.dat sysname Linux hostname magma machine x86_64 user ncorriveau Loading ./tmp.mri_nu_correct.mni.31167/ones.mgz Loading ./tmp.mri_nu_correct.mni.31167/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.31167/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.31167/nu2.mnc ./tmp.mri_nu_correct.mni.31167/nu2.mnc mul 1.02532602449051766058 Saving result to './tmp.mri_nu_correct.mni.31167/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.31167/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.31167/nu2.mnc nu.mgz --like orig.mgz gcamFindOptimalTimeStep: Complete in 155539.531 ms 0348: dt=44.800000, rms=0.452 (0.015%), neg=0, invalid=766 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.31167/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, 4.81386e-16) j_ras = (0, 1.32713e-08, -1) k_ras = (-1.77636e-15, 1, 2.58442e-08) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz 0349: dt=44.800000, rms=0.452 (-0.068%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=766 type change took 0 minutes and 46 seconds. mapping (24, 142) to ( 3, 110) Thu Jul 14 18:48:41 EDT 2016 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Thu Jul 14 18:48:41 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_normalize -g 1 -W ctrl_vol.mgz bias_vol.mgz nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.119 0.048 -0.089 -4.130; -0.024 1.068 0.389 -26.198; 0.112 -0.339 1.157 6.346; 0.000 0.000 0.000 1.000; writing ctrl pts to ctrl_vol.mgz writing bias field to bias_vol.mgz INFO: Modifying talairach volume c_(r,a,s) based on average_305 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 gcamFindOptimalTimeStep: Complete in 134493.094 ms 0350: dt=38.400000, rms=0.450 (0.373%), neg=0, invalid=766 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 gcamFindOptimalTimeStep: Complete in 85992.648 ms 0351: dt=6.795699, rms=0.450 (0.087%), neg=0, invalid=766 writing control point volume to ctrl_vol.mgz... building Voronoi diagram... performing soap bubble smoothing... gcamFindOptimalTimeStep: Complete in 119955.578 ms 0352: dt=32.000000, rms=0.449 (0.109%), neg=0, invalid=766 writing output to T1.mgz 3D bias adjustment took 7 minutes and 49 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 109 gm peak at 69 (69), valley at 58 (58) csf peak at 39, setting threshold to 59 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 61 (61) csf peak at 38, setting threshold to 60 writing bias field to bias_vol.mgz.... #-------------------------------------------- #@# Skull Stripping Thu Jul 14 18:56:35 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_robust_template --mov /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz --average 0 --ixforms /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T1_to_CA149base.lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/CA149T2_to_CA149base.lta --noit --finalnearest --template brainmask_template.mgz $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz as movable/source volume. --mov: Using /data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz as movable/source volume. Total: 2 input volumes --average: Using method 0 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --finalnearest: Use nearest neighbor interpolation for final average! --template: Using brainmask_template.mgz as template output volume. reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T1/mri/brainmask.mgz'... reading source '/data/belleville/ncorriveau/freesurfer/subjects/CA149T2/mri/brainmask.mgz'... warping movs and creating initial template... using mean Writing final template: brainmask_template.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 39 seconds. mri_mask -keep_mask_deletion_edits T1.mgz brainmask_template.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_template.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Found 16777216 voxels in mask Writing masked volume to brainmask.auto.mgz...done. INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------- #@# EM Registration Thu Jul 14 18:57:46 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_em_register -mask brainmask.mgz norm_template.mgz /opt/share/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'norm_template.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 gcamFindOptimalTimeStep: Complete in 101349.820 ms 0353: dt=6.400000, rms=0.449 (0.020%), neg=0, invalid=766 0354: dt=6.400000, rms=0.449 (0.029%), neg=0, invalid=766 0355: dt=6.400000, rms=0.449 (0.031%), neg=0, invalid=766 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.1 skull bounding box = (67, 75, 59) --> (190, 203, 209) using (108, 118, 134) as brain centroid... mean wm in atlas = 107, using box (93,102,116) --> (123, 133,152) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -6181.3 ************************************************ First Search limited to translation only. ************************************************ 0356: dt=6.400000, rms=0.449 (0.033%), neg=0, invalid=766 Found translation: (-0.3, -13.4, -24.1): log p = -5970.789 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** 0357: dt=6.400000, rms=0.448 (0.036%), neg=0, invalid=766 0358: dt=6.400000, rms=0.448 (0.040%), neg=0, invalid=766 0359: dt=6.400000, rms=0.448 (0.037%), neg=0, invalid=766 0360: dt=6.400000, rms=0.448 (0.035%), neg=0, invalid=766 0361: dt=6.400000, rms=0.448 (0.027%), neg=0, invalid=766 0362: dt=6.400000, rms=0.448 (0.024%), neg=0, invalid=766 0363: dt=6.400000, rms=0.448 (0.023%), neg=0, invalid=766 Result so far: scale 1.000: max_log_p=-5501.1, old_max_log_p =-5970.8 (thresh=-5964.8) 1.226 -0.156 -0.042 -2.951; 0.161 1.184 0.317 -91.749; 0.000 -0.298 1.111 0.858; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** gcamFindOptimalTimeStep: Complete in 202877.984 ms 0364: dt=44.800000, rms=0.447 (0.046%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 167411.234 ms 0365: dt=2.800000, rms=0.447 (0.000%), neg=0, invalid=766 0366: dt=2.800000, rms=0.447 (0.012%), neg=0, invalid=766 0367: dt=2.800000, rms=0.447 (0.001%), neg=0, invalid=766 0368: dt=2.800000, rms=0.447 (0.006%), neg=0, invalid=766 0369: dt=2.800000, rms=0.447 (0.012%), neg=0, invalid=766 Result so far: scale 1.000: max_log_p=-5501.1, old_max_log_p =-5501.1 (thresh=-5495.6) 1.226 -0.156 -0.042 -2.951; 0.161 1.184 0.317 -91.749; 0.000 -0.298 1.111 0.858; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** 0370: dt=2.800000, rms=0.447 (0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 181757.422 ms 0371: dt=0.000000, rms=0.468 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 Result so far: scale 0.250: max_log_p=-5351.5, old_max_log_p =-5501.1 (thresh=-5495.6) 1.162 -0.100 -0.061 -3.095; 0.131 1.222 0.367 -100.878; 0.035 -0.336 1.077 5.749; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** gcamFindOptimalTimeStep: Complete in 169206.828 ms 0372: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 145218.078 ms 0373: dt=1.536000, rms=0.504 (0.959%), neg=0, invalid=766 Result so far: scale 0.250: max_log_p=-5351.5, old_max_log_p =-5351.5 (thresh=-5346.2) 1.162 -0.100 -0.061 -3.095; 0.131 1.222 0.367 -100.878; 0.035 -0.336 1.077 5.749; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** gcamFindOptimalTimeStep: Complete in 120329.031 ms 0374: dt=0.448000, rms=0.504 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 130123.711 ms 0375: dt=0.250000, rms=0.504 (0.008%), neg=0, invalid=766 0376: dt=0.250000, rms=0.504 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=766 Result so far: scale 0.062: max_log_p=-5321.0, old_max_log_p =-5351.5 (thresh=-5346.2) 1.159 -0.125 -0.087 4.789; 0.160 1.222 0.356 -102.686; 0.055 -0.327 1.075 1.752; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** gcamFindOptimalTimeStep: Complete in 189140.391 ms 0377: dt=0.807692, rms=0.504 (0.079%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 173631.953 ms 0378: dt=0.112000, rms=0.504 (0.002%), neg=0, invalid=766 0379: dt=0.112000, rms=0.504 (0.002%), neg=0, invalid=766 0380: dt=0.112000, rms=0.504 (-0.004%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 Result so far: scale 0.062: max_log_p=-5320.0, old_max_log_p =-5321.0 (thresh=-5315.6) 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 5315.8 after pass:transform: ( 1.16, -0.13, -0.08, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.33, 1.08, 3.10) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 5315.8 tol 0.000010 Resulting transform: 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -5320.0 (old=-6181.3) transform before final EM align: 1.158 -0.128 -0.079 4.089; 0.160 1.222 0.356 -102.686; 0.046 -0.326 1.077 3.103; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.15781 -0.12793 -0.07856 4.08935; 0.15961 1.22160 0.35647 -102.68574; 0.04570 -0.32612 1.07676 3.10253; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 664615.6 after pass:transform: ( 1.16, -0.13, -0.08, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.33, 1.08, 3.10) dfp_em_step_func: 011: -log(p) = 663240.2 after pass:transform: ( 1.17, -0.12, -0.07, 4.09) ( 0.16, 1.22, 0.36, -102.69) ( 0.05, -0.32, 1.08, 3.10) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 663240.2 tol 0.000000 final transform: 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 48 minutes and 0 seconds. #-------------------------------------- #@# CA Normalize Thu Jul 14 19:45:47 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz norm_template.mgz /opt/share/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 volumes reading atlas from '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... gcamFindOptimalTimeStep: Complete in 136456.594 ms 0381: dt=0.112000, rms=0.456 (0.683%), neg=0, invalid=766 reading input volume from norm_template.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=22.1 skull bounding box = (67, 75, 59) --> (190, 203, 209) using (108, 118, 134) as brain centroid... mean wm in atlas = 107, using box (93,102,116) --> (123, 133,152) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 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 (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 125.0 0 of 1687 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 0 of 2067 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 125.0 0 of 29 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 125.0 0 of 40 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) Brain_Stem: limiting intensities to 85.0 --> 125.0 9 of 39 (23.1%) samples deleted using 3862 total control points for intensity normalization... bias field = 1.001 +- 0.023 2 of 3853 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 1 of 1690 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 125.0 0 of 2043 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 125.0 0 of 58 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 125.0 0 of 76 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) gcamFindOptimalTimeStep: Complete in 99802.078 ms 0382: dt=0.028000, rms=0.455 (0.137%), neg=0, invalid=766 Brain_Stem: limiting intensities to 84.0 --> 125.0 29 of 92 (31.5%) samples deleted using 3959 total control points for intensity normalization... bias field = 0.998 +- 0.022 2 of 3929 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (122, 75, 60) --> (182, 169, 204) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 2 of 1739 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 77, 62) --> (128, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 125.0 7 of 2085 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 147, 86) --> (171, 180, 133) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 125.0 0 of 95 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 147, 86) --> (128, 185, 136) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 125.0 0 of 82 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 137, 116) --> (143, 192, 143) Brain_Stem: limiting intensities to 69.0 --> 125.0 0 of 210 (0.0%) samples deleted using 4211 total control points for intensity normalization... bias field = 0.997 +- 0.024 5 of 4202 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 5 minutes and 31 seconds. #-------------------------------------- #@# CA Reg Thu Jul 14 19:51:19 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/share/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcamFindOptimalTimeStep: Complete in 123040.914 ms 0383: dt=0.080000, rms=0.454 (0.368%), neg=0, invalid=766 gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.70 (predicted orig area = 4.7) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 142478.703 ms 0384: dt=0.028000, rms=0.453 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 127759.727 ms 0001: dt=129.472000, rms=0.678 (7.650%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 146012.125 ms 0385: dt=0.080000, rms=0.452 (0.302%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 127484.188 ms 0002: dt=129.472000, rms=0.664 (1.997%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 145655.062 ms 0386: dt=0.028000, rms=0.451 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 169076.984 ms 0003: dt=129.472000, rms=0.652 (1.829%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 154823.781 ms 0387: dt=0.080000, rms=0.450 (0.250%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126134.719 ms 0004: dt=110.976000, rms=0.649 (0.475%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 152634.219 ms 0388: dt=0.112000, rms=0.449 (0.304%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 152704.312 ms 0389: dt=0.080000, rms=0.448 (0.181%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 223507.344 ms 0005: dt=221.952000, rms=0.641 (1.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 117704.906 ms 0390: dt=0.028000, rms=0.448 (0.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 143147.641 ms 0006: dt=55.488000, rms=0.639 (0.293%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 145563.000 ms 0391: dt=0.112000, rms=0.447 (0.215%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 113072.555 ms 0392: dt=0.112000, rms=0.446 (0.183%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 193499.812 ms 0007: dt=369.920000, rms=0.636 (0.446%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101075.352 ms 0393: dt=0.096341, rms=0.445 (0.134%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80970.055 ms 0394: dt=0.112000, rms=0.445 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 132050.484 ms 0008: dt=110.976000, rms=0.632 (0.729%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96386.125 ms 0395: dt=0.080000, rms=0.444 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94385.508 ms 0396: dt=0.028000, rms=0.444 (0.027%), neg=0, invalid=766 0397: dt=0.028000, rms=0.444 (0.027%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 133139.828 ms 0009: dt=55.488000, rms=0.631 (0.111%), neg=0, invalid=766 0398: dt=0.028000, rms=0.444 (0.051%), neg=0, invalid=766 0399: dt=0.028000, rms=0.444 (0.069%), neg=0, invalid=766 0400: dt=0.028000, rms=0.443 (0.085%), neg=0, invalid=766 0010: dt=55.488000, rms=0.631 (0.056%), neg=0, invalid=766 0401: dt=0.028000, rms=0.443 (0.096%), neg=0, invalid=766 0402: dt=0.028000, rms=0.442 (0.104%), neg=0, invalid=766 0011: dt=55.488000, rms=0.630 (0.120%), neg=0, invalid=766 0403: dt=0.014000, rms=0.442 (0.010%), neg=0, invalid=766 0404: dt=0.014000, rms=0.442 (0.007%), neg=0, invalid=766 0012: dt=55.488000, rms=0.629 (0.205%), neg=0, invalid=766 0013: dt=55.488000, rms=0.627 (0.293%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 99535.195 ms 0405: dt=0.112000, rms=0.442 (0.061%), neg=0, invalid=766 0014: dt=55.488000, rms=0.625 (0.307%), neg=0, invalid=766 0015: dt=55.488000, rms=0.623 (0.288%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 116932.492 ms 0406: dt=0.112000, rms=0.442 (0.052%), neg=0, invalid=766 0016: dt=55.488000, rms=0.622 (0.264%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101957.156 ms 0407: dt=0.112000, rms=0.442 (0.053%), neg=0, invalid=766 0017: dt=55.488000, rms=0.620 (0.229%), neg=0, invalid=766 0018: dt=55.488000, rms=0.619 (0.226%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77451.234 ms 0408: dt=0.028000, rms=0.442 (0.013%), neg=0, invalid=766 0409: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0019: dt=55.488000, rms=0.617 (0.233%), neg=0, invalid=766 0410: dt=0.028000, rms=0.441 (0.021%), neg=0, invalid=766 0411: dt=0.028000, rms=0.441 (0.029%), neg=0, invalid=766 0412: dt=0.028000, rms=0.441 (0.010%), neg=0, invalid=766 0020: dt=55.488000, rms=0.616 (0.229%), neg=0, invalid=766 0413: dt=0.028000, rms=0.441 (0.021%), neg=0, invalid=766 0414: dt=0.028000, rms=0.441 (0.030%), neg=0, invalid=766 0415: dt=0.028000, rms=0.441 (0.034%), neg=0, invalid=766 0021: dt=55.488000, rms=0.615 (0.208%), neg=0, invalid=766 0416: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0417: dt=0.028000, rms=0.440 (0.045%), neg=0, invalid=766 0418: dt=0.028000, rms=0.440 (0.044%), neg=0, invalid=766 0419: dt=0.028000, rms=0.440 (0.051%), neg=0, invalid=766 0022: dt=55.488000, rms=0.613 (0.200%), neg=0, invalid=766 0420: dt=0.028000, rms=0.440 (0.051%), neg=0, invalid=766 0421: dt=0.028000, rms=0.440 (0.053%), neg=0, invalid=766 0023: dt=55.488000, rms=0.612 (0.189%), neg=0, invalid=766 0422: dt=0.028000, rms=0.439 (0.051%), neg=0, invalid=766 0423: dt=0.028000, rms=0.439 (0.049%), neg=0, invalid=766 0424: dt=0.028000, rms=0.439 (0.047%), neg=0, invalid=766 0024: dt=55.488000, rms=0.611 (0.185%), neg=0, invalid=766 0425: dt=0.028000, rms=0.439 (0.046%), neg=0, invalid=766 0426: dt=0.028000, rms=0.439 (0.043%), neg=0, invalid=766 0025: dt=55.488000, rms=0.610 (0.187%), neg=0, invalid=766 0427: dt=0.028000, rms=0.438 (0.041%), neg=0, invalid=766 0428: dt=0.028000, rms=0.438 (0.041%), neg=0, invalid=766 0026: dt=55.488000, rms=0.609 (0.196%), neg=0, invalid=766 0429: dt=0.028000, rms=0.438 (0.032%), neg=0, invalid=766 0430: dt=0.028000, rms=0.438 (0.033%), neg=0, invalid=766 0431: dt=0.028000, rms=0.438 (0.031%), neg=0, invalid=766 0027: dt=55.488000, rms=0.608 (0.189%), neg=0, invalid=766 0432: dt=0.028000, rms=0.438 (0.028%), neg=0, invalid=766 0028: dt=55.488000, rms=0.607 (0.161%), neg=0, invalid=766 0433: dt=0.028000, rms=0.438 (0.026%), neg=0, invalid=766 0434: dt=0.028000, rms=0.437 (0.023%), neg=0, invalid=766 0029: dt=55.488000, rms=0.606 (0.148%), neg=0, invalid=766 0435: dt=0.028000, rms=0.437 (0.018%), neg=0, invalid=766 0030: dt=55.488000, rms=0.605 (0.132%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 129544.969 ms 0436: dt=0.112000, rms=0.437 (0.001%), neg=0, invalid=766 0031: dt=55.488000, rms=0.604 (0.133%), neg=0, invalid=766 0437: dt=0.056000, rms=0.437 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.437, neg=0, invalid=766 0032: dt=55.488000, rms=0.603 (0.147%), neg=0, invalid=766 0033: dt=55.488000, rms=0.602 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 133963.125 ms 0438: dt=0.028000, rms=0.437 (0.038%), neg=0, invalid=766 0034: dt=55.488000, rms=0.602 (0.118%), neg=0, invalid=766 0035: dt=55.488000, rms=0.601 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 192842.969 ms 0439: dt=0.080000, rms=0.437 (0.100%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 206989.438 ms 0036: dt=1479.680000, rms=0.600 (0.124%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 190017.578 ms 0440: dt=0.112000, rms=0.436 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 161162.266 ms 0441: dt=0.028000, rms=0.436 (0.021%), neg=0, invalid=766 0442: dt=0.028000, rms=0.436 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 243218.281 ms 0037: dt=129.472000, rms=0.599 (0.165%), neg=0, invalid=766 0443: dt=0.028000, rms=0.436 (0.040%), neg=0, invalid=766 0444: dt=0.028000, rms=0.436 (0.048%), neg=0, invalid=766 0445: dt=0.028000, rms=0.436 (0.013%), neg=0, invalid=766 0446: dt=0.028000, rms=0.436 (0.025%), neg=0, invalid=766 0447: dt=0.028000, rms=0.435 (0.031%), neg=0, invalid=766 0448: dt=0.028000, rms=0.435 (0.037%), neg=0, invalid=766 0449: dt=0.028000, rms=0.435 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 186139.516 ms 0038: dt=8.092000, rms=0.599 (-0.007%), neg=0, invalid=766 0450: dt=0.028000, rms=0.435 (0.012%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.599, neg=0, invalid=766 0451: dt=0.028000, rms=0.435 (0.017%), neg=0, invalid=766 0452: dt=0.028000, rms=0.435 (0.021%), neg=0, invalid=766 0453: dt=0.028000, rms=0.435 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102276.344 ms 0454: dt=0.112000, rms=0.435 (0.012%), neg=0, invalid=766 0455: dt=0.056000, rms=0.435 (-0.001%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 246521.531 ms 0039: dt=73.984000, rms=0.599 (0.032%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 124959.445 ms iter 0, gcam->neg = 140 after 42 iterations, nbhd size=4, neg = 0 0456: dt=44.800000, rms=0.424 (2.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177829.984 ms 0040: dt=517.888000, rms=0.598 (0.267%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 110914.945 ms iter 0, gcam->neg = 12 after 36 iterations, nbhd size=4, neg = 0 0457: dt=25.600000, rms=0.422 (0.408%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 130535.672 ms 0041: dt=32.368000, rms=0.597 (0.016%), neg=0, invalid=766 0042: dt=32.368000, rms=0.597 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 123892.266 ms 0458: dt=19.200000, rms=0.421 (0.308%), neg=0, invalid=766 0043: dt=32.368000, rms=0.597 (-0.006%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 145046.609 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0459: dt=9.600000, rms=0.420 (0.187%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 125229.727 ms 0044: dt=145.152000, rms=0.594 (1.238%), neg=0, invalid=766 0460: dt=9.600000, rms=0.419 (0.165%), neg=0, invalid=766 0461: dt=9.600000, rms=0.418 (0.206%), neg=0, invalid=766 0462: dt=9.600000, rms=0.417 (0.262%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 23 iterations, nbhd size=3, neg = 0 0463: dt=9.600000, rms=0.416 (0.243%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 190682.969 ms 0045: dt=103.680000, rms=0.585 (1.489%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 36 iterations, nbhd size=4, neg = 0 0464: dt=9.600000, rms=0.415 (0.233%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159119.688 ms 0046: dt=25.920000, rms=0.583 (0.375%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 30 iterations, nbhd size=3, neg = 0 0465: dt=9.600000, rms=0.414 (0.199%), neg=0, invalid=766 0466: dt=9.600000, rms=0.414 (0.181%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0467: dt=9.600000, rms=0.413 (0.125%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 173060.656 ms 0047: dt=124.416000, rms=0.579 (0.587%), neg=0, invalid=766 0468: dt=9.600000, rms=0.412 (0.174%), neg=0, invalid=766 0469: dt=9.600000, rms=0.412 (0.158%), neg=0, invalid=766 0470: dt=9.600000, rms=0.411 (0.155%), neg=0, invalid=766 0471: dt=9.600000, rms=0.411 (0.116%), neg=0, invalid=766 0472: dt=9.600000, rms=0.410 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 180180.859 ms 0048: dt=31.104000, rms=0.577 (0.430%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 134978.219 ms 0473: dt=19.200000, rms=0.410 (0.066%), neg=0, invalid=766 0474: dt=19.200000, rms=0.410 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 183883.047 ms 0049: dt=62.208000, rms=0.575 (0.387%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 152278.297 ms 0475: dt=11.200000, rms=0.409 (0.225%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171833.000 ms 0050: dt=31.104000, rms=0.573 (0.215%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 121477.406 ms 0476: dt=11.200000, rms=0.408 (0.158%), neg=0, invalid=766 0051: dt=31.104000, rms=0.572 (0.203%), neg=0, invalid=766 0477: dt=11.200000, rms=0.408 (0.138%), neg=0, invalid=766 0478: dt=11.200000, rms=0.407 (0.194%), neg=0, invalid=766 0052: dt=31.104000, rms=0.571 (0.261%), neg=0, invalid=766 0479: dt=11.200000, rms=0.406 (0.195%), neg=0, invalid=766 0480: dt=11.200000, rms=0.406 (0.168%), neg=0, invalid=766 0053: dt=31.104000, rms=0.568 (0.424%), neg=0, invalid=766 0481: dt=11.200000, rms=0.405 (0.096%), neg=0, invalid=766 0054: dt=31.104000, rms=0.566 (0.448%), neg=0, invalid=766 0055: dt=31.104000, rms=0.563 (0.509%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0482: dt=11.200000, rms=0.405 (0.053%), neg=0, invalid=766 0056: dt=31.104000, rms=0.560 (0.495%), neg=0, invalid=766 0057: dt=31.104000, rms=0.557 (0.497%), neg=0, invalid=766 0058: dt=31.104000, rms=0.555 (0.476%), neg=0, invalid=766 0059: dt=31.104000, rms=0.552 (0.417%), neg=0, invalid=766 0060: dt=31.104000, rms=0.550 (0.396%), neg=0, invalid=766 0061: dt=31.104000, rms=0.548 (0.329%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 155213.375 ms iter 0, gcam->neg = 1 after 47 iterations, nbhd size=4, neg = 0 0483: dt=9.600000, rms=0.405 (0.016%), neg=0, invalid=766 0062: dt=31.104000, rms=0.547 (0.352%), neg=0, invalid=766 0484: dt=9.600000, rms=0.405 (0.016%), neg=0, invalid=766 0063: dt=31.104000, rms=0.545 (0.293%), neg=0, invalid=766 0485: dt=9.600000, rms=0.405 (0.015%), neg=0, invalid=766 0064: dt=31.104000, rms=0.544 (0.243%), neg=0, invalid=766 0486: dt=9.600000, rms=0.405 (0.025%), neg=0, invalid=766 0065: dt=31.104000, rms=0.542 (0.248%), neg=0, invalid=766 0487: dt=9.600000, rms=0.405 (0.020%), neg=0, invalid=766 0066: dt=31.104000, rms=0.541 (0.237%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=766 0067: dt=31.104000, rms=0.540 (0.235%), neg=0, invalid=766 0068: dt=31.104000, rms=0.539 (0.199%), neg=0, invalid=766 0069: dt=31.104000, rms=0.538 (0.172%), neg=0, invalid=766 0070: dt=31.104000, rms=0.537 (0.150%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171541.297 ms 0488: dt=1.008000, rms=0.409 (0.009%), neg=0, invalid=766 0071: dt=31.104000, rms=0.536 (0.154%), neg=0, invalid=766 0072: dt=31.104000, rms=0.535 (0.147%), neg=0, invalid=766 0073: dt=31.104000, rms=0.535 (0.118%), neg=0, invalid=766 0074: dt=31.104000, rms=0.534 (0.123%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 178632.078 ms 0489: dt=1.728000, rms=0.409 (0.016%), neg=0, invalid=766 0075: dt=31.104000, rms=0.533 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159278.422 ms 0490: dt=0.252000, rms=0.409 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 219376.875 ms 0076: dt=25.920000, rms=0.533 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79950.062 ms iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0491: dt=3.456000, rms=0.409 (0.047%), neg=0, invalid=766 0077: dt=25.920000, rms=0.533 (0.015%), neg=0, invalid=766 0078: dt=25.920000, rms=0.533 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 157202.531 ms 0492: dt=4.032000, rms=0.409 (0.048%), neg=0, invalid=766 0079: dt=25.920000, rms=0.533 (0.006%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 125208.852 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=2.304000, rms=0.409 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 11 iterations, nbhd size=1, neg = 0 0494: dt=2.304000, rms=0.409 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 15 iterations, nbhd size=1, neg = 0 0495: dt=2.304000, rms=0.409 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 259506.125 ms 0080: dt=103.680000, rms=0.532 (0.279%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0496: dt=2.304000, rms=0.409 (-0.039%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177265.734 ms 0497: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 242276.859 ms 0081: dt=36.288000, rms=0.531 (0.128%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 0082: dt=36.288000, rms=0.531 (0.059%), neg=0, invalid=766 0083: dt=36.288000, rms=0.530 (0.076%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 195729.328 ms 0498: dt=0.000375, rms=0.415 (0.000%), neg=0, invalid=766 0084: dt=36.288000, rms=0.530 (0.100%), neg=0, invalid=766 0499: dt=0.000375, rms=0.415 (-0.000%), neg=0, invalid=766 0085: dt=36.288000, rms=0.529 (0.095%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 0086: dt=36.288000, rms=0.529 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212173.406 ms 0087: dt=82.944000, rms=0.529 (0.020%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.550, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 209372.562 ms 0088: dt=1.600000, rms=0.550 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 188848.688 ms 0089: dt=0.125000, rms=0.550 (0.001%), neg=0, invalid=766 0090: dt=0.125000, rms=0.550 (0.000%), neg=0, invalid=766 0091: dt=0.125000, rms=0.550 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.550, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 168879.578 ms 0092: dt=1.600000, rms=0.550 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 231239.953 ms iter 0, gcam->neg = 502 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 66730.641 ms iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.003 (22.301%) 0500: dt=1.346939, rms=0.384 (5.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 199198.891 ms 0093: dt=0.001953, rms=0.550 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.610, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 227744.406 ms 0501: dt=0.000094, rms=0.384 (-0.010%), neg=0, invalid=766 0502: dt=0.000094, rms=0.384 (0.000%), neg=0, invalid=766 0503: dt=0.000094, rms=0.384 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171454.625 ms 0094: dt=4.794872, rms=0.592 (2.840%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 179011.312 ms 0504: dt=0.000078, rms=0.384 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 165393.062 ms 0095: dt=1.872340, rms=0.592 (0.071%), neg=0, invalid=766 0096: dt=1.872340, rms=0.592 (-0.022%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 179367.297 ms 0505: dt=0.000000, rms=0.384 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.379, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159190.109 ms 0097: dt=0.252000, rms=0.592 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 193264.828 ms iter 0, gcam->neg = 157 after 17 iterations, nbhd size=2, neg = 0 0506: dt=0.306667, rms=0.374 (1.174%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 190181.641 ms 0098: dt=0.144000, rms=0.592 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 220444.812 ms 0507: dt=0.001750, rms=0.374 (-0.008%), neg=0, invalid=766 0508: dt=0.001750, rms=0.374 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 190236.891 ms 0099: dt=0.015750, rms=0.592 (-0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0509: dt=0.001750, rms=0.374 (0.005%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.648, neg=0, invalid=766 0510: dt=0.001750, rms=0.374 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0511: dt=0.001750, rms=0.374 (0.008%), neg=0, invalid=766 0512: dt=0.001750, rms=0.374 (0.010%), neg=0, invalid=766 0513: dt=0.001750, rms=0.374 (0.014%), neg=0, invalid=766 0514: dt=0.001750, rms=0.374 (0.011%), neg=0, invalid=766 0515: dt=0.001750, rms=0.374 (0.014%), neg=0, invalid=766 0516: dt=0.001750, rms=0.374 (0.016%), neg=0, invalid=766 0517: dt=0.001750, rms=0.374 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176419.391 ms 0100: dt=1.189904, rms=0.643 (0.712%), neg=0, invalid=766 0518: dt=0.001750, rms=0.374 (0.017%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212131.625 ms 0101: dt=1.876543, rms=0.639 (0.685%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 194136.047 ms iter 0, gcam->neg = 24 after 16 iterations, nbhd size=2, neg = 0 0519: dt=0.112000, rms=0.373 (0.264%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 167300.984 ms 0102: dt=0.448000, rms=0.639 (0.047%), neg=0, invalid=766 0103: dt=0.448000, rms=0.639 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 164683.469 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.003000, rms=0.373 (0.007%), neg=0, invalid=766 0104: dt=0.448000, rms=0.639 (0.008%), neg=0, invalid=766 0521: dt=0.003000, rms=0.373 (0.006%), neg=0, invalid=766 0522: dt=0.003000, rms=0.373 (0.010%), neg=0, invalid=766 0105: dt=0.448000, rms=0.639 (-0.046%), neg=0, invalid=766 0523: dt=0.003000, rms=0.373 (0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 0524: dt=0.003000, rms=0.373 (0.018%), neg=0, invalid=766 0525: dt=0.003000, rms=0.373 (0.023%), neg=0, invalid=766 0526: dt=0.003000, rms=0.372 (0.024%), neg=0, invalid=766 0527: dt=0.003000, rms=0.372 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0528: dt=0.003000, rms=0.372 (0.031%), neg=0, invalid=766 0529: dt=0.003000, rms=0.372 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 144897.188 ms 0106: dt=1.536000, rms=0.637 (0.178%), neg=0, invalid=766 0530: dt=0.003000, rms=0.372 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0531: dt=0.003000, rms=0.372 (0.033%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 200942.250 ms 0107: dt=0.000000, rms=0.637 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 120611.547 ms iter 0, gcam->neg = 26 after 17 iterations, nbhd size=2, neg = 0 0532: dt=0.064000, rms=0.372 (0.075%), neg=0, invalid=766 0108: dt=0.100000, rms=0.637 (-0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 125091.359 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0533: dt=0.006000, rms=0.372 (0.008%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.371, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 188103.422 ms 0109: dt=0.143037, rms=0.596 (0.882%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 204429.547 ms iter 0, gcam->neg = 57 after 8 iterations, nbhd size=1, neg = 0 0534: dt=0.112000, rms=0.370 (0.422%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 201618.109 ms 0110: dt=0.239726, rms=0.596 (0.080%), neg=0, invalid=766 0111: dt=0.239726, rms=0.592 (0.598%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 207200.781 ms 0535: dt=0.001750, rms=0.370 (0.000%), neg=0, invalid=766 0536: dt=0.001750, rms=0.370 (0.004%), neg=0, invalid=766 0537: dt=0.001750, rms=0.369 (0.010%), neg=0, invalid=766 0112: dt=0.119863, rms=0.592 (-0.258%), neg=0, invalid=766 0538: dt=0.001750, rms=0.369 (0.015%), neg=0, invalid=766 0539: dt=0.001750, rms=0.369 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0540: dt=0.001750, rms=0.369 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0541: dt=0.001750, rms=0.369 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0542: dt=0.001750, rms=0.369 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 160282.969 ms 0113: dt=0.000000, rms=0.592 (0.000%), neg=0, invalid=766 0543: dt=0.001750, rms=0.369 (0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=766 0544: dt=0.001750, rms=0.369 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0545: dt=0.001750, rms=0.369 (0.029%), neg=0, invalid=766 0546: dt=0.001750, rms=0.369 (0.034%), neg=0, invalid=766 0547: dt=0.001750, rms=0.369 (0.031%), neg=0, invalid=766 0548: dt=0.001750, rms=0.368 (0.034%), neg=0, invalid=766 0549: dt=0.001750, rms=0.368 (0.036%), neg=0, invalid=766 0550: dt=0.001750, rms=0.368 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177408.469 ms 0114: dt=0.028000, rms=0.592 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 106640.719 ms iter 0, gcam->neg = 32 after 19 iterations, nbhd size=2, neg = 0 0551: dt=0.064000, rms=0.368 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 189775.438 ms 0115: dt=0.019975, rms=0.592 (0.002%), neg=0, invalid=766 0116: dt=0.019975, rms=0.592 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126967.922 ms 0552: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.368, neg=0, invalid=766 0117: dt=0.019975, rms=0.592 (-0.007%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12067 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (985 voxels, overlap=0.355) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (985 voxels, peak = 20), gca=19.8 gca peak = 0.14022 (22) mri peak = 0.13083 (23) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (940 voxels, overlap=0.584) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (940 voxels, peak = 20), gca=19.8 gca peak = 0.24234 (100) mri peak = 0.18069 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (317 voxels, overlap=0.255) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (317 voxels, peak = 108), gca=107.5 gca peak = 0.19192 (97) mri peak = 0.15241 (106) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (287 voxels, overlap=0.244) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (287 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.08374 (73) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (619 voxels, overlap=0.070) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (619 voxels, peak = 72), gca=72.4 gcamFindOptimalTimeStep: Complete in 129273.016 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0553: dt=0.003000, rms=0.368 (0.008%), neg=0, invalid=766 gca peak = 0.29892 (64) mri peak = 0.07620 (72) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (435 voxels, overlap=0.177) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (435 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.09928 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (51455 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (51455 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.09567 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (51365 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (51365 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03437 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (20819 voxels, overlap=0.389) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (20819 voxels, peak = 72), gca=72.4 gca peak = 0.13270 (63) mri peak = 0.03158 (68) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22252 voxels, overlap=0.596) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22252 voxels, peak = 69), gca=69.3 gca peak = 0.15182 (70) mri peak = 0.08373 (83) Right_Caudate (50): linear fit = 1.20 x + 0.0 (418 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.20 x + 0.0 (418 voxels, peak = 84), gca=84.0 gcamFindOptimalTimeStep: Complete in 125098.656 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0554: dt=0.004000, rms=0.368 (0.008%), neg=0, invalid=766 gca peak = 0.14251 (76) mri peak = 0.10560 (85) Left_Caudate (11): linear fit = 1.08 x + 0.0 (469 voxels, overlap=0.488) Left_Caudate (11): linear fit = 1.08 x + 0.0 (469 voxels, peak = 82), gca=81.7 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0555: dt=0.004000, rms=0.368 (0.012%), neg=0, invalid=766 gca peak = 0.12116 (60) mri peak = 0.04738 (65) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22074 voxels, overlap=0.712) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (22074 voxels, peak = 68), gca=67.5 0556: dt=0.004000, rms=0.368 (0.019%), neg=0, invalid=766 gca peak = 0.12723 (61) mri peak = 0.04579 (63) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25814 voxels, overlap=0.907) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25814 voxels, peak = 66), gca=65.6 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0557: dt=0.004000, rms=0.367 (0.027%), neg=0, invalid=766 0558: dt=0.004000, rms=0.367 (0.038%), neg=0, invalid=766 gca peak = 0.22684 (88) mri peak = 0.10267 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7052 voxels, overlap=0.687) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7052 voxels, peak = 92), gca=92.4 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0559: dt=0.004000, rms=0.367 (0.042%), neg=0, invalid=766 gca peak = 0.21067 (87) mri peak = 0.11077 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6085 voxels, overlap=0.806) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6085 voxels, peak = 91), gca=91.3 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0560: dt=0.004000, rms=0.367 (0.048%), neg=0, invalid=766 gca peak = 0.25455 (62) mri peak = 0.14050 (71) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (233 voxels, overlap=0.141) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (233 voxels, peak = 70), gca=69.8 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0561: dt=0.004000, rms=0.367 (0.051%), neg=0, invalid=766 gca peak = 0.39668 (62) mri peak = 0.14410 (71) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (229 voxels, overlap=0.242) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (229 voxels, peak = 68), gca=68.2 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0562: dt=0.004000, rms=0.367 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0563: dt=0.004000, rms=0.366 (0.061%), neg=0, invalid=766 gca peak = 0.10129 (93) mri peak = 0.07422 (98) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3372 voxels, overlap=0.904) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3372 voxels, peak = 95), gca=95.3 gca peak = 0.12071 (89) mri peak = 0.07394 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3339 voxels, overlap=0.476) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3339 voxels, peak = 96), gca=95.7 iter 0, gcam->neg = 5 after 17 iterations, nbhd size=2, neg = 0 0564: dt=0.004000, rms=0.366 (0.062%), neg=0, invalid=766 gca peak = 0.13716 (82) mri peak = 0.06836 (97) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1813 voxels, overlap=0.176) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1813 voxels, peak = 94), gca=94.3 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0565: dt=0.004000, rms=0.366 (0.065%), neg=0, invalid=766 gca peak = 0.15214 (84) mri peak = 0.06240 (89) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1793 voxels, overlap=0.852) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1793 voxels, peak = 92), gca=92.4 gca peak = 0.08983 (85) mri peak = 0.06529 (93) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9393 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9393 voxels, peak = 91), gca=91.4 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0566: dt=0.004000, rms=0.366 (0.061%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gca peak = 0.11809 (92) mri peak = 0.09786 (104) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (772 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (772 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.07683 (101) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (908 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (908 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.09568 (24) gca peak = 0.13542 (27) mri peak = 0.08153 (24) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (264 voxels, overlap=0.468) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (264 voxels, peak = 23), gca=23.0 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) gcamFindOptimalTimeStep: Complete in 99418.461 ms iter 0, gcam->neg = 17 after 43 iterations, nbhd size=4, neg = 0 0567: dt=4.800000, rms=0.366 (-0.133%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.366, neg=0, invalid=766 not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Right_Pallidum too bright - rescaling by 0.985 (from 1.075) to 105.9 (was 107.5) saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.620, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 162971.906 ms iter 0, gcam->neg = 51 after 52 iterations, nbhd size=1, neg = 0 0568: dt=9.600000, rms=0.366 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 140942.094 ms 0118: dt=92.480000, rms=0.615 (0.789%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 187580.250 ms 0119: dt=129.472000, rms=0.613 (0.288%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 136952.672 ms 0120: dt=129.472000, rms=0.610 (0.428%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 146470.172 ms 0121: dt=129.472000, rms=0.609 (0.173%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 124825.914 ms 0122: dt=110.976000, rms=0.608 (0.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 185864.375 ms iter 0, gcam->neg = 39 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 77544.883 ms iter 1, dt=0.000000: new neg 5, old_neg 5, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0569: dt=6.400000, rms=0.366 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 135480.906 ms 0123: dt=92.480000, rms=0.607 (0.139%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.366, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176831.078 ms 0124: dt=129.472000, rms=0.605 (0.224%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 193144.609 ms 0125: dt=73.984000, rms=0.605 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171191.688 ms iter 0, gcam->neg = 43 after 64 iterations, nbhd size=2, neg = 0 0570: dt=0.720000, rms=0.365 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 214750.594 ms 0126: dt=295.936000, rms=0.603 (0.268%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 186273.109 ms 0127: dt=55.488000, rms=0.602 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 187828.656 ms 0128: dt=2071.552000, rms=0.595 (1.126%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 166156.891 ms 0129: dt=55.488000, rms=0.592 (0.458%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 213352.172 ms iter 0, gcam->neg = 35 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 68552.812 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0571: dt=0.720000, rms=0.365 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176876.812 ms 0130: dt=887.808000, rms=0.589 (0.479%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 124316.211 ms 0131: dt=73.984000, rms=0.589 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 157379.781 ms 0132: dt=129.472000, rms=0.588 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 140474.625 ms 0133: dt=129.472000, rms=0.588 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 162549.547 ms iter 0, gcam->neg = 37 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 67647.539 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0572: dt=1.008000, rms=0.365 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 242735.562 ms 0134: dt=110.976000, rms=0.588 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177633.766 ms 0135: dt=92.480000, rms=0.587 (0.040%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176201.625 ms iter 0, gcam->neg = 34 after 61 iterations, nbhd size=3, neg = 0 0573: dt=0.246575, rms=0.365 (0.116%), neg=0, invalid=766 0136: dt=92.480000, rms=0.587 (0.051%), neg=0, invalid=766 0137: dt=92.480000, rms=0.587 (0.067%), neg=0, invalid=766 0138: dt=92.480000, rms=0.586 (0.102%), neg=0, invalid=766 0139: dt=92.480000, rms=0.585 (0.110%), neg=0, invalid=766 0140: dt=92.480000, rms=0.585 (0.144%), neg=0, invalid=766 0141: dt=92.480000, rms=0.584 (0.134%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 148710.281 ms iter 0, gcam->neg = 10 after 41 iterations, nbhd size=2, neg = 0 0574: dt=0.079880, rms=0.365 (0.024%), neg=0, invalid=766 0142: dt=92.480000, rms=0.583 (0.145%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 23 iterations, nbhd size=3, neg = 0 0575: dt=0.079880, rms=0.365 (0.037%), neg=0, invalid=766 0143: dt=92.480000, rms=0.582 (0.136%), neg=0, invalid=766 0144: dt=92.480000, rms=0.581 (0.151%), neg=0, invalid=766 0145: dt=92.480000, rms=0.580 (0.139%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 37 iterations, nbhd size=4, neg = 0 0576: dt=0.079880, rms=0.365 (0.064%), neg=0, invalid=766 0146: dt=92.480000, rms=0.580 (0.139%), neg=0, invalid=766 0147: dt=92.480000, rms=0.579 (0.130%), neg=0, invalid=766 0148: dt=92.480000, rms=0.578 (0.134%), neg=0, invalid=766 0149: dt=92.480000, rms=0.577 (0.129%), neg=0, invalid=766 0150: dt=92.480000, rms=0.577 (0.117%), neg=0, invalid=766 0151: dt=92.480000, rms=0.576 (0.116%), neg=0, invalid=766 0152: dt=92.480000, rms=0.575 (0.114%), neg=0, invalid=766 0153: dt=92.480000, rms=0.575 (0.118%), neg=0, invalid=766 0154: dt=92.480000, rms=0.574 (0.108%), neg=0, invalid=766 0155: dt=92.480000, rms=0.573 (0.103%), neg=0, invalid=766 0156: dt=92.480000, rms=0.573 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 77053.914 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0577: dt=0.079880, rms=0.365 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 0157: dt=92.480000, rms=0.572 (0.090%), neg=0, invalid=766 0158: dt=92.480000, rms=0.572 (0.087%), neg=0, invalid=766 0159: dt=92.480000, rms=0.571 (0.087%), neg=0, invalid=766 0160: dt=92.480000, rms=0.571 (0.086%), neg=0, invalid=766 0161: dt=92.480000, rms=0.570 (0.081%), neg=0, invalid=766 0162: dt=92.480000, rms=0.570 (0.080%), neg=0, invalid=766 0163: dt=92.480000, rms=0.570 (0.077%), neg=0, invalid=766 0164: dt=92.480000, rms=0.569 (0.072%), neg=0, invalid=766 0165: dt=92.480000, rms=0.569 (0.071%), neg=0, invalid=766 0166: dt=92.480000, rms=0.568 (0.068%), neg=0, invalid=766 0167: dt=92.480000, rms=0.568 (0.064%), neg=0, invalid=766 0168: dt=92.480000, rms=0.568 (0.064%), neg=0, invalid=766 0169: dt=92.480000, rms=0.567 (0.061%), neg=0, invalid=766 0170: dt=92.480000, rms=0.567 (0.057%), neg=0, invalid=766 0171: dt=92.480000, rms=0.567 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 209263.156 ms iter 0, gcam->neg = 23 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 70711.961 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0578: dt=0.230769, rms=0.365 (0.000%), neg=0, invalid=766 0172: dt=92.480000, rms=0.566 (0.050%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.364, neg=0, invalid=766 0173: dt=92.480000, rms=0.566 (0.046%), neg=0, invalid=766 0174: dt=92.480000, rms=0.566 (0.048%), neg=0, invalid=766 0175: dt=92.480000, rms=0.566 (0.046%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 149635.188 ms 0579: dt=0.000109, rms=0.364 (0.000%), neg=0, invalid=766 0176: dt=92.480000, rms=0.565 (0.047%), neg=0, invalid=766 0177: dt=92.480000, rms=0.565 (0.046%), neg=0, invalid=766 0178: dt=92.480000, rms=0.565 (0.045%), neg=0, invalid=766 0179: dt=92.480000, rms=0.565 (0.038%), neg=0, invalid=766 0180: dt=92.480000, rms=0.564 (0.037%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 161330.562 ms iter 0, gcam->neg = 73 after 30 iterations, nbhd size=3, neg = 0 0580: dt=0.075252, rms=0.363 (0.260%), neg=0, invalid=766 0181: dt=92.480000, rms=0.564 (0.038%), neg=0, invalid=766 0182: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 0183: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 131916.047 ms iter 0, gcam->neg = 2 after 15 iterations, nbhd size=2, neg = 0 0581: dt=0.005001, rms=0.363 (0.015%), neg=0, invalid=766 0184: dt=92.480000, rms=0.564 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0582: dt=0.005001, rms=0.363 (0.015%), neg=0, invalid=766 0185: dt=92.480000, rms=0.563 (0.034%), neg=0, invalid=766 0186: dt=92.480000, rms=0.563 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0583: dt=0.005001, rms=0.363 (0.028%), neg=0, invalid=766 0187: dt=92.480000, rms=0.563 (0.033%), neg=0, invalid=766 0188: dt=92.480000, rms=0.563 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=2, neg = 0 0584: dt=0.005001, rms=0.363 (0.039%), neg=0, invalid=766 0189: dt=92.480000, rms=0.563 (0.031%), neg=0, invalid=766 0190: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 35 iterations, nbhd size=1, neg = 0 0585: dt=0.005001, rms=0.363 (0.046%), neg=0, invalid=766 0191: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 0192: dt=92.480000, rms=0.562 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 20 iterations, nbhd size=3, neg = 0 0586: dt=0.005001, rms=0.363 (0.055%), neg=0, invalid=766 0193: dt=92.480000, rms=0.562 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 16 iterations, nbhd size=2, neg = 0 0587: dt=0.005001, rms=0.362 (0.062%), neg=0, invalid=766 0194: dt=92.480000, rms=0.562 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0588: dt=0.005001, rms=0.362 (0.068%), neg=0, invalid=766 0195: dt=92.480000, rms=0.562 (0.031%), neg=0, invalid=766 0196: dt=92.480000, rms=0.561 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 26 iterations, nbhd size=3, neg = 0 0589: dt=0.005001, rms=0.362 (0.069%), neg=0, invalid=766 0197: dt=92.480000, rms=0.561 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0590: dt=0.005001, rms=0.362 (0.074%), neg=0, invalid=766 0198: dt=92.480000, rms=0.561 (0.028%), neg=0, invalid=766 0199: dt=92.480000, rms=0.561 (0.024%), neg=0, invalid=766 0200: dt=92.480000, rms=0.561 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 60 iterations, nbhd size=1, neg = 0 0591: dt=0.005001, rms=0.361 (0.069%), neg=0, invalid=766 0201: dt=92.480000, rms=0.561 (0.026%), neg=0, invalid=766 0202: dt=92.480000, rms=0.561 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 36 iterations, nbhd size=4, neg = 0 0592: dt=0.005001, rms=0.361 (0.057%), neg=0, invalid=766 0203: dt=92.480000, rms=0.560 (0.024%), neg=0, invalid=766 0204: dt=92.480000, rms=0.560 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 161573.188 ms 0593: dt=0.001750, rms=0.361 (0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.361, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176393.859 ms 0205: dt=129.472000, rms=0.560 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 167676.031 ms 0594: dt=0.001500, rms=0.361 (0.004%), neg=0, invalid=766 0206: dt=129.472000, rms=0.560 (0.003%), neg=0, invalid=766 0207: dt=129.472000, rms=0.560 (0.006%), neg=0, invalid=766 0208: dt=129.472000, rms=0.560 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 183110.469 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0595: dt=0.001000, rms=0.361 (0.003%), neg=0, invalid=766 0209: dt=129.472000, rms=0.560 (0.012%), neg=0, invalid=766 0596: dt=0.001000, rms=0.361 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0597: dt=0.001000, rms=0.361 (0.005%), neg=0, invalid=766 0210: dt=129.472000, rms=0.560 (0.011%), neg=0, invalid=766 0211: dt=129.472000, rms=0.560 (0.016%), neg=0, invalid=766 0212: dt=129.472000, rms=0.560 (0.016%), neg=0, invalid=766 0213: dt=129.472000, rms=0.560 (0.015%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 152024.484 ms 0214: dt=129.472000, rms=0.559 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 181017.703 ms 0215: dt=369.920000, rms=0.558 (0.110%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 44074.410 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0598: dt=0.001000, rms=0.361 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.361, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177551.297 ms 0216: dt=32.368000, rms=0.558 (0.034%), neg=0, invalid=766 0217: dt=32.368000, rms=0.558 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 138090.859 ms iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0599: dt=0.007000, rms=0.361 (0.024%), neg=0, invalid=766 0218: dt=32.368000, rms=0.558 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.560, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 172829.312 ms iter 0, gcam->neg = 13 after 6 iterations, nbhd size=1, neg = 0 0600: dt=0.020000, rms=0.361 (0.067%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 184725.438 ms 0219: dt=145.152000, rms=0.556 (0.757%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 163149.531 ms iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0601: dt=0.012000, rms=0.361 (0.039%), neg=0, invalid=766 0602: dt=0.012000, rms=0.360 (0.037%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 175721.969 ms 0220: dt=82.944000, rms=0.551 (0.776%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 28 iterations, nbhd size=4, neg = 0 0603: dt=0.012000, rms=0.360 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 8 iterations, nbhd size=1, neg = 0 0604: dt=0.012000, rms=0.360 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 146044.891 ms 0221: dt=20.736000, rms=0.549 (0.392%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 26 iterations, nbhd size=3, neg = 0 0605: dt=0.012000, rms=0.359 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 49 iterations, nbhd size=3, neg = 0 0606: dt=0.012000, rms=0.359 (0.124%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 194848.875 ms 0222: dt=145.152000, rms=0.546 (0.594%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 17 iterations, nbhd size=2, neg = 0 0607: dt=0.012000, rms=0.358 (0.137%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 162018.156 ms 0223: dt=31.104000, rms=0.544 (0.383%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 172986.312 ms 0224: dt=31.104000, rms=0.543 (0.216%), neg=0, invalid=766 iter 0, gcam->neg = 62 after 101 iterations, nbhd size=3, neg = 0 0608: dt=0.012000, rms=0.358 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 53 after 19 iterations, nbhd size=2, neg = 0 0609: dt=0.012000, rms=0.357 (0.144%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 193472.891 ms 0225: dt=36.288000, rms=0.541 (0.220%), neg=0, invalid=766 iter 0, gcam->neg = 60 after 21 iterations, nbhd size=2, neg = 0 0610: dt=0.012000, rms=0.357 (0.139%), neg=0, invalid=766 iter 0, gcam->neg = 65 after 30 iterations, nbhd size=3, neg = 0 0611: dt=0.012000, rms=0.357 (0.127%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 168465.719 ms 0226: dt=36.288000, rms=0.541 (0.150%), neg=0, invalid=766 iter 0, gcam->neg = 77 after 46 iterations, nbhd size=4, neg = 0 0612: dt=0.012000, rms=0.356 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 155450.266 ms 0227: dt=36.288000, rms=0.540 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 128414.680 ms 0228: dt=36.288000, rms=0.539 (0.142%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 158882.391 ms 0229: dt=36.288000, rms=0.538 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 166375.328 ms 0230: dt=36.288000, rms=0.537 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 78 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 69804.109 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0613: dt=0.012000, rms=0.356 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 157253.578 ms 0231: dt=36.288000, rms=0.536 (0.172%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 123024.391 ms 0232: dt=36.288000, rms=0.535 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 175753.531 ms 0614: dt=0.001750, rms=0.356 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 133058.750 ms 0233: dt=62.208000, rms=0.534 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 182772.328 ms 0615: dt=0.001750, rms=0.356 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.356, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 142751.047 ms 0234: dt=25.920000, rms=0.534 (0.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 164799.094 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0616: dt=0.004000, rms=0.356 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 139850.594 ms 0235: dt=82.944000, rms=0.533 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159686.172 ms iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0617: dt=0.020036, rms=0.356 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212221.141 ms 0236: dt=20.736000, rms=0.532 (0.153%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 186407.266 ms 0618: dt=0.001750, rms=0.356 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 185856.734 ms 0237: dt=580.608000, rms=0.527 (0.859%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159642.969 ms 0238: dt=31.104000, rms=0.523 (0.826%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 154727.406 ms 0239: dt=36.288000, rms=0.522 (0.149%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 168320.125 ms 0240: dt=103.680000, rms=0.521 (0.165%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 41938.496 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0619: dt=0.001750, rms=0.356 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.356, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 111238.266 ms 0241: dt=25.920000, rms=0.521 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 106599.352 ms iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0620: dt=0.007000, rms=0.356 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 153737.078 ms 0242: dt=62.208000, rms=0.520 (0.107%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 197568.375 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0621: dt=0.003000, rms=0.355 (0.010%), neg=0, invalid=766 0622: dt=0.003000, rms=0.355 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0623: dt=0.003000, rms=0.355 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 153334.469 ms 0243: dt=25.920000, rms=0.520 (0.066%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0624: dt=0.003000, rms=0.355 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0625: dt=0.003000, rms=0.355 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 167507.328 ms 0244: dt=82.944000, rms=0.519 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0626: dt=0.003000, rms=0.355 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 21 iterations, nbhd size=3, neg = 0 0627: dt=0.003000, rms=0.355 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 21 iterations, nbhd size=3, neg = 0 0628: dt=0.003000, rms=0.355 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 145680.156 ms 0245: dt=25.920000, rms=0.519 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 23 iterations, nbhd size=3, neg = 0 0629: dt=0.003000, rms=0.355 (0.048%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0630: dt=0.003000, rms=0.354 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 16 iterations, nbhd size=2, neg = 0 0631: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159583.516 ms 0246: dt=36.288000, rms=0.518 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 16 iterations, nbhd size=2, neg = 0 0632: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 20 iterations, nbhd size=3, neg = 0 0633: dt=0.003000, rms=0.354 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 15 iterations, nbhd size=2, neg = 0 0634: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 144609.547 ms 0247: dt=36.288000, rms=0.518 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 6 iterations, nbhd size=1, neg = 0 0635: dt=0.003000, rms=0.353 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 161674.891 ms 0248: dt=145.152000, rms=0.518 (0.108%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 51 iterations, nbhd size=3, neg = 0 0636: dt=0.003000, rms=0.353 (0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.353, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 125552.711 ms 0249: dt=9.072000, rms=0.517 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 172759.719 ms 0637: dt=0.001750, rms=0.353 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171341.281 ms 0250: dt=9.072000, rms=0.517 (0.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 158051.578 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0638: dt=0.004000, rms=0.353 (0.011%), neg=0, invalid=766 0251: dt=4.536000, rms=0.517 (0.014%), neg=0, invalid=766 0252: dt=0.567000, rms=0.517 (0.001%), neg=0, invalid=766 0253: dt=0.567000, rms=0.517 (0.002%), neg=0, invalid=766 0254: dt=0.017719, rms=0.517 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 146692.375 ms iter 0, gcam->neg = 2 after 21 iterations, nbhd size=3, neg = 0 0639: dt=0.005001, rms=0.353 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 97164.938 ms 0255: dt=0.007594, rms=0.517 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177510.625 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0640: dt=0.006000, rms=0.353 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 83443.539 ms 0256: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 176991.812 ms iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0641: dt=0.007000, rms=0.353 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 204725.891 ms 0257: dt=44.800000, rms=0.507 (3.232%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 140048.156 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0642: dt=0.006000, rms=0.353 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0643: dt=0.006000, rms=0.353 (0.015%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 132297.656 ms 0258: dt=9.600000, rms=0.505 (0.465%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 31 iterations, nbhd size=4, neg = 0 0644: dt=0.006000, rms=0.353 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 22 iterations, nbhd size=3, neg = 0 0645: dt=0.006000, rms=0.353 (0.039%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 143180.547 ms 0259: dt=9.600000, rms=0.503 (0.450%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 35 iterations, nbhd size=3, neg = 0 0646: dt=0.006000, rms=0.353 (0.041%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 184359.953 ms 0260: dt=11.200000, rms=0.500 (0.464%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 18 iterations, nbhd size=2, neg = 0 0647: dt=0.006000, rms=0.352 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212304.922 ms 0261: dt=44.800000, rms=0.492 (1.542%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 31 iterations, nbhd size=4, neg = 0 0648: dt=0.006000, rms=0.352 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 21 iterations, nbhd size=2, neg = 0 0649: dt=0.006000, rms=0.352 (0.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212237.656 ms 0262: dt=9.600000, rms=0.491 (0.282%), neg=0, invalid=766 iter 0, gcam->neg = 31 after 17 iterations, nbhd size=2, neg = 0 0650: dt=0.006000, rms=0.352 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 19 iterations, nbhd size=2, neg = 0 0651: dt=0.006000, rms=0.351 (0.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 158498.547 ms 0263: dt=11.200000, rms=0.490 (0.316%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 38 iterations, nbhd size=4, neg = 0 0652: dt=0.006000, rms=0.351 (0.064%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 18 hours, 52 minutes and 48 seconds. #-------------------------------------- #@# CA Reg Inv Fri Jul 15 06:29:55 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_register -invert-and-save transforms/talairach.m3z gcamFindOptimalTimeStep: Complete in 145220.672 ms 0264: dt=11.200000, rms=0.488 (0.265%), neg=0, invalid=766 Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Jul 15 06:33:30 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/share/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcamFindOptimalTimeStep: Complete in 152963.406 ms 0265: dt=11.200000, rms=0.487 (0.260%), neg=0, invalid=766 zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 12119142 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 4 minutes and 4 seconds. #-------------------------------------- #@# SkullLTA Fri Jul 15 06:37:35 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/share/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/share/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcamFindOptimalTimeStep: Complete in 149000.812 ms 0266: dt=11.200000, rms=0.486 (0.235%), neg=0, invalid=766 gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=12.0 skull bounding box = (52, 51, 45) --> (204, 226, 230) using (103, 109, 138) as brain centroid... mean wm in atlas = 126, using box (84,87,115) --> (121, 130,160) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** gcamFindOptimalTimeStep: Complete in 146575.484 ms 0267: dt=11.200000, rms=0.485 (0.226%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159445.156 ms 0268: dt=11.200000, rms=0.484 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 130564.891 ms 0269: dt=11.200000, rms=0.483 (0.201%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 116254.562 ms 0270: dt=11.200000, rms=0.482 (0.188%), neg=0, invalid=766 Result so far: scale 1.000: max_log_p=-10306.9, old_max_log_p =-10351.7 (thresh=-10341.3) 1.177 0.042 -0.022 -24.081; 0.006 1.319 0.389 -100.340; 0.045 -0.298 0.999 10.823; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** gcamFindOptimalTimeStep: Complete in 107086.844 ms 0271: dt=11.200000, rms=0.481 (0.177%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 110058.156 ms 0272: dt=11.200000, rms=0.480 (0.172%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 107409.094 ms 0273: dt=11.200000, rms=0.479 (0.167%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177103.812 ms 0274: dt=38.400000, rms=0.477 (0.446%), neg=0, invalid=766 Result so far: scale 1.000: max_log_p=-10306.9, old_max_log_p =-10306.9 (thresh=-10296.6) 1.177 0.042 -0.022 -24.081; 0.006 1.319 0.389 -100.340; 0.045 -0.298 0.999 10.823; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** gcamFindOptimalTimeStep: Complete in 152168.312 ms 0275: dt=2.800000, rms=0.477 (0.058%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 171498.141 ms 0276: dt=2.800000, rms=0.477 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 185457.406 ms 0277: dt=8.000000, rms=0.476 (0.105%), neg=0, invalid=766 Result so far: scale 0.250: max_log_p=-10292.4, old_max_log_p =-10306.9 (thresh=-10296.6) 1.149 -0.086 -0.053 -3.635; 0.120 1.363 0.293 -106.249; 0.048 -0.155 0.976 -1.265; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** gcamFindOptimalTimeStep: Complete in 150894.781 ms 0278: dt=44.800000, rms=0.474 (0.464%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159614.594 ms 0279: dt=2.800000, rms=0.474 (0.036%), neg=0, invalid=766 0280: dt=2.800000, rms=0.474 (0.037%), neg=0, invalid=766 0281: dt=2.800000, rms=0.473 (0.053%), neg=0, invalid=766 0282: dt=2.800000, rms=0.473 (0.064%), neg=0, invalid=766 0283: dt=2.800000, rms=0.473 (0.080%), neg=0, invalid=766 0284: dt=2.800000, rms=0.472 (0.104%), neg=0, invalid=766 0285: dt=2.800000, rms=0.472 (0.118%), neg=0, invalid=766 0286: dt=2.800000, rms=0.471 (0.133%), neg=0, invalid=766 0287: dt=2.800000, rms=0.470 (0.128%), neg=0, invalid=766 0288: dt=2.800000, rms=0.470 (0.139%), neg=0, invalid=766 0289: dt=2.800000, rms=0.469 (0.145%), neg=0, invalid=766 Result so far: scale 0.250: max_log_p=-10292.2, old_max_log_p =-10292.4 (thresh=-10282.1) 1.172 -0.091 -0.021 -9.814; 0.119 1.367 0.261 -100.742; 0.014 -0.106 0.968 -2.282; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** 0290: dt=2.800000, rms=0.468 (0.144%), neg=0, invalid=766 0291: dt=2.800000, rms=0.468 (0.143%), neg=0, invalid=766 0292: dt=2.800000, rms=0.467 (0.145%), neg=0, invalid=766 0293: dt=2.800000, rms=0.466 (0.143%), neg=0, invalid=766 0294: dt=2.800000, rms=0.466 (0.140%), neg=0, invalid=766 0295: dt=2.800000, rms=0.465 (0.137%), neg=0, invalid=766 0296: dt=2.800000, rms=0.464 (0.132%), neg=0, invalid=766 0297: dt=2.800000, rms=0.464 (0.131%), neg=0, invalid=766 0298: dt=2.800000, rms=0.463 (0.126%), neg=0, invalid=766 0299: dt=2.800000, rms=0.463 (0.122%), neg=0, invalid=766 0300: dt=2.800000, rms=0.462 (0.115%), neg=0, invalid=766 0301: dt=2.800000, rms=0.462 (0.107%), neg=0, invalid=766 0302: dt=2.800000, rms=0.461 (0.108%), neg=0, invalid=766 0303: dt=2.800000, rms=0.461 (0.100%), neg=0, invalid=766 0304: dt=2.800000, rms=0.460 (0.094%), neg=0, invalid=766 0305: dt=2.800000, rms=0.460 (0.088%), neg=0, invalid=766 0306: dt=2.800000, rms=0.459 (0.085%), neg=0, invalid=766 0307: dt=2.800000, rms=0.459 (0.080%), neg=0, invalid=766 Result so far: scale 0.062: max_log_p=-10288.0, old_max_log_p =-10292.2 (thresh=-10281.9) 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 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 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 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: 006: -log(p) = 10288.0 tol 0.000010 Resulting transform: 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 0.000 0.000 0.000 1.000; 0308: dt=2.800000, rms=0.459 (0.075%), neg=0, invalid=766 0309: dt=2.800000, rms=0.458 (0.074%), neg=0, invalid=766 pass 1, spacing 8: log(p) = -10288.0 (old=-10351.7) transform before final EM align: 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 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 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; 0310: dt=2.800000, rms=0.458 (0.070%), neg=0, invalid=766 dfp_em_step_func: 007: -log(p) = 1144886.8 after pass:transform: ( 1.17, -0.09, -0.01, -12.23) ( 0.12, 1.37, 0.25, -100.11) ( -0.00, -0.09, 0.97, -2.11) dfp_em_step_func: 008: -log(p) = 1144886.6 after pass:transform: ( 1.17, -0.09, -0.01, -12.23) ( 0.12, 1.37, 0.25, -100.11) ( -0.00, -0.09, 0.97, -2.11) dfp_em_step_func: 009: -log(p) = 1144879.6 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... 0311: dt=2.800000, rms=0.458 (0.067%), neg=0, invalid=766 dfp_em_step_func: 010: -log(p) = 1144874.8 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... 0312: dt=2.800000, rms=0.457 (0.068%), neg=0, invalid=766 dfp_em_step_func: 011: -log(p) = 1144874.5 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) 0313: dt=2.800000, rms=0.457 (0.059%), neg=0, invalid=766 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... dfp_em_step_func: 012: -log(p) = 1144874.2 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) 0314: dt=2.800000, rms=0.457 (0.059%), neg=0, invalid=766 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... 0315: dt=2.800000, rms=0.457 (0.056%), neg=0, invalid=766 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: 014: -log(p) = 1144874.2 tol 0.000000 final transform: 1.178 -0.088 -0.003 -12.227; 0.114 1.366 0.248 -100.105; -0.012 -0.103 0.971 -2.109; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 64 minutes and 35 seconds. #-------------------------------------- #@# SubCort Seg Fri Jul 15 07:42:10 EDT 2016 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /opt/share/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 0316: dt=2.800000, rms=0.456 (0.054%), neg=0, invalid=766 0317: dt=2.800000, rms=0.456 (0.047%), neg=0, invalid=766 0318: dt=2.800000, rms=0.456 (0.050%), neg=0, invalid=766 0319: dt=2.800000, rms=0.456 (0.047%), neg=0, invalid=766 0320: dt=2.800000, rms=0.456 (0.046%), neg=0, invalid=766 0321: dt=2.800000, rms=0.455 (0.047%), neg=0, invalid=766 0322: dt=2.800000, rms=0.455 (0.039%), neg=0, invalid=766 0323: dt=2.800000, rms=0.455 (0.041%), neg=0, invalid=766 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /opt/share/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /opt/share/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 = 0.14205 (23) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1063 voxels, overlap=0.375) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1063 voxels, peak = 22), gca=22.3 0324: dt=2.800000, rms=0.455 (0.038%), neg=0, invalid=766 gca peak = 0.14982 (20) mri peak = 0.14912 (22) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (1301 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (1301 voxels, peak = 19), gca=19.0 0325: dt=2.800000, rms=0.455 (0.038%), neg=0, invalid=766 gca peak = 0.28003 (97) mri peak = 0.15045 (108) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (394 voxels, overlap=0.041) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (394 voxels, peak = 104), gca=104.3 0326: dt=2.800000, rms=0.454 (0.039%), neg=0, invalid=766 gca peak = 0.18160 (96) mri peak = 0.16043 (107) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (374 voxels, overlap=0.074) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (374 voxels, peak = 106), gca=105.6 0327: dt=2.800000, rms=0.454 (0.034%), neg=0, invalid=766 0328: dt=2.800000, rms=0.454 (0.038%), neg=0, invalid=766 gca peak = 0.27536 (62) mri peak = 0.09225 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1005 voxels, overlap=0.240) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1005 voxels, peak = 71), gca=71.3 0329: dt=2.800000, rms=0.454 (0.035%), neg=0, invalid=766 gca peak = 0.32745 (63) mri peak = 0.11376 (72) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (979 voxels, overlap=0.413) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (979 voxels, peak = 71), gca=70.9 0330: dt=2.800000, rms=0.454 (0.034%), neg=0, invalid=766 gca peak = 0.08597 (105) mri peak = 0.11210 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (28895 voxels, overlap=0.499) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (28895 voxels, peak = 110), gca=110.2 0331: dt=2.800000, rms=0.454 (0.032%), neg=0, invalid=766 gca peak = 0.09209 (106) mri peak = 0.10834 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26012 voxels, overlap=0.504) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26012 voxels, peak = 109), gca=108.6 0332: dt=2.800000, rms=0.454 (0.028%), neg=0, invalid=766 gca peak = 0.07826 (63) mri peak = 0.04324 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (34745 voxels, overlap=0.626) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (34745 voxels, peak = 72), gca=72.4 0333: dt=2.800000, rms=0.453 (0.031%), neg=0, invalid=766 gca peak = 0.08598 (64) mri peak = 0.04422 (71) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (32986 voxels, overlap=0.573) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (32986 voxels, peak = 72), gca=72.0 0334: dt=2.800000, rms=0.453 (0.030%), neg=0, invalid=766 gca peak = 0.24164 (71) mri peak = 0.12121 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (756 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.17 x + 0.0 (756 voxels, peak = 83), gca=83.4 0335: dt=2.800000, rms=0.453 (0.032%), neg=0, invalid=766 gca peak = 0.18227 (75) mri peak = 0.12791 (83) Left_Caudate (11): linear fit = 1.10 x + 0.0 (749 voxels, overlap=0.516) Left_Caudate (11): linear fit = 1.10 x + 0.0 (749 voxels, peak = 82), gca=82.5 0336: dt=2.800000, rms=0.453 (0.031%), neg=0, invalid=766 gca peak = 0.10629 (62) mri peak = 0.05837 (67) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23363 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23363 voxels, peak = 70), gca=69.8 gca peak = 0.11668 (59) mri peak = 0.05601 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24936 voxels, overlap=0.872) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24936 voxels, peak = 63), gca=63.4 0337: dt=2.800000, rms=0.453 (0.027%), neg=0, invalid=766 gca peak = 0.17849 (88) mri peak = 0.12519 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5454 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5454 voxels, peak = 92), gca=92.4 0338: dt=2.800000, rms=0.453 (0.026%), neg=0, invalid=766 gca peak = 0.16819 (86) mri peak = 0.12860 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5324 voxels, overlap=0.826) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5324 voxels, peak = 90), gca=90.3 0339: dt=2.800000, rms=0.453 (0.026%), neg=0, invalid=766 gca peak = 0.41688 (64) mri peak = 0.12667 (69) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (407 voxels, overlap=0.001) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (407 voxels, peak = 70), gca=70.4 gca peak = 0.42394 (62) mri peak = 0.14970 (70) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (499 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (499 voxels, peak = 68), gca=68.2 0340: dt=2.800000, rms=0.452 (0.027%), neg=0, invalid=766 gca peak = 0.10041 (96) mri peak = 0.09064 (98) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3079 voxels, overlap=0.872) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3079 voxels, peak = 98), gca=98.4 0341: dt=2.800000, rms=0.452 (0.025%), neg=0, invalid=766 gca peak = 0.13978 (88) mri peak = 0.08243 (98) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3312 voxels, overlap=0.516) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3312 voxels, peak = 97), gca=96.8 0342: dt=2.800000, rms=0.452 (0.028%), neg=0, invalid=766 gca peak = 0.08514 (81) mri peak = 0.06803 (95) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1804 voxels, overlap=0.630) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1804 voxels, peak = 89), gca=89.1 0343: dt=2.800000, rms=0.452 (0.026%), neg=0, invalid=766 gca peak = 0.09624 (82) mri peak = 0.07530 (92) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1607 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1607 voxels, peak = 88), gca=88.2 gca peak = 0.07543 (88) mri peak = 0.06208 (88) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10410 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10410 voxels, peak = 92), gca=92.4 0344: dt=2.800000, rms=0.452 (0.025%), neg=0, invalid=766 gca peak = 0.12757 (95) mri peak = 0.10407 (104) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1256 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1256 voxels, peak = 104), gca=104.5 0345: dt=2.800000, rms=0.452 (0.027%), neg=0, invalid=766 gca peak = 0.17004 (92) mri peak = 0.08530 (103) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1362 voxels, overlap=0.410) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1362 voxels, peak = 101), gca=101.2 0346: dt=2.800000, rms=0.452 (0.024%), neg=0, invalid=766 gca peak = 0.21361 (36) mri peak = 0.17246 (24) 0347: dt=2.800000, rms=0.452 (0.022%), neg=0, invalid=766 gca peak = 0.26069 (23) mri peak = 0.18750 (25) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (96 voxels, overlap=0.696) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (96 voxels, peak = 21), gca=21.3 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) gcamFindOptimalTimeStep: Complete in 135921.016 ms 0348: dt=44.800000, rms=0.452 (0.015%), neg=0, invalid=766 0349: dt=44.800000, rms=0.452 (-0.068%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 124839.648 ms 0350: dt=38.400000, rms=0.450 (0.373%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 169968.906 ms 0351: dt=6.795699, rms=0.450 (0.087%), neg=0, invalid=766 not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.90 x + 0.0 Left_Pallidum too bright - rescaling by 1.005 (from 1.100) to 106.2 (was 105.6) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14514 (23) mri peak = 0.14205 (23) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=0.864) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 23), gca=23.0 gca peak = 0.15050 (19) mri peak = 0.14912 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1301 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1301 voxels, peak = 19), gca=19.5 gca peak = 0.24146 (105) mri peak = 0.15045 (108) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, peak = 105), gca=105.0 gca peak = 0.17034 (107) mri peak = 0.16043 (107) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (374 voxels, overlap=0.818) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (374 voxels, peak = 104), gca=104.3 gca peak = 0.25238 (71) mri peak = 0.09225 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1005 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1005 voxels, peak = 71), gca=71.0 gca peak = 0.31227 (71) mri peak = 0.11376 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (979 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (979 voxels, peak = 71), gca=71.0 gcamFindOptimalTimeStep: Complete in 149768.531 ms 0352: dt=32.000000, rms=0.449 (0.109%), neg=0, invalid=766 gca peak = 0.08006 (112) mri peak = 0.11210 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28895 voxels, overlap=0.671) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28895 voxels, peak = 112), gca=112.0 gca peak = 0.08505 (108) mri peak = 0.10834 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26012 voxels, overlap=0.639) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26012 voxels, peak = 108), gca=108.0 gca peak = 0.06954 (72) mri peak = 0.04324 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34745 voxels, overlap=0.901) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34745 voxels, peak = 70), gca=70.2 gca peak = 0.07883 (72) mri peak = 0.04422 (71) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (32986 voxels, overlap=0.899) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (32986 voxels, peak = 70), gca=70.2 gcamFindOptimalTimeStep: Complete in 112473.820 ms 0353: dt=6.400000, rms=0.449 (0.020%), neg=0, invalid=766 gca peak = 0.21717 (83) mri peak = 0.12121 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (756 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (756 voxels, peak = 83), gca=83.0 gca peak = 0.13780 (82) mri peak = 0.12791 (83) Left_Caudate (11): linear fit = 0.98 x + 0.0 (749 voxels, overlap=0.741) Left_Caudate (11): linear fit = 0.98 x + 0.0 (749 voxels, peak = 80), gca=80.0 0354: dt=6.400000, rms=0.449 (0.029%), neg=0, invalid=766 0355: dt=6.400000, rms=0.449 (0.031%), neg=0, invalid=766 gca peak = 0.09301 (70) mri peak = 0.05837 (67) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23363 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23363 voxels, peak = 70), gca=70.0 0356: dt=6.400000, rms=0.449 (0.033%), neg=0, invalid=766 gca peak = 0.12039 (64) mri peak = 0.05601 (65) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (24936 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (24936 voxels, peak = 66), gca=65.6 0357: dt=6.400000, rms=0.448 (0.036%), neg=0, invalid=766 gca peak = 0.16848 (92) mri peak = 0.12519 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5454 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5454 voxels, peak = 92), gca=92.0 0358: dt=6.400000, rms=0.448 (0.040%), neg=0, invalid=766 gca peak = 0.15998 (91) mri peak = 0.12860 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5324 voxels, overlap=0.970) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5324 voxels, peak = 91), gca=91.0 0359: dt=6.400000, rms=0.448 (0.037%), neg=0, invalid=766 gca peak = 0.30566 (70) mri peak = 0.12667 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (407 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (407 voxels, peak = 70), gca=70.0 gca peak = 0.35282 (69) mri peak = 0.14970 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (499 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (499 voxels, peak = 69), gca=69.0 0360: dt=6.400000, rms=0.448 (0.035%), neg=0, invalid=766 gca peak = 0.09784 (97) mri peak = 0.09064 (98) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3079 voxels, overlap=0.930) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3079 voxels, peak = 97), gca=97.0 0361: dt=6.400000, rms=0.448 (0.027%), neg=0, invalid=766 gca peak = 0.09781 (97) mri peak = 0.08243 (98) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3312 voxels, overlap=0.899) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3312 voxels, peak = 97), gca=97.0 0362: dt=6.400000, rms=0.448 (0.024%), neg=0, invalid=766 gca peak = 0.08109 (91) mri peak = 0.06803 (95) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1804 voxels, overlap=0.973) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1804 voxels, peak = 91), gca=91.0 gca peak = 0.09427 (88) mri peak = 0.07530 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1607 voxels, overlap=0.984) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1607 voxels, peak = 88), gca=88.0 0363: dt=6.400000, rms=0.448 (0.023%), neg=0, invalid=766 gca peak = 0.07247 (90) mri peak = 0.06208 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10410 voxels, overlap=0.853) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10410 voxels, peak = 90), gca=90.0 gca peak = 0.13771 (104) mri peak = 0.10407 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1256 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1256 voxels, peak = 104), gca=104.0 gca peak = 0.12455 (102) mri peak = 0.08530 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1362 voxels, overlap=0.868) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1362 voxels, peak = 102), gca=102.0 gca peak = 0.22647 (34) mri peak = 0.17246 (24) gcamFindOptimalTimeStep: Complete in 129278.570 ms 0364: dt=44.800000, rms=0.447 (0.046%), neg=0, invalid=766 gca peak = 0.23444 (21) mri peak = 0.18750 (25) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (96 voxels, overlap=0.808) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (96 voxels, peak = 21), gca=21.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.23325 (40) gca peak Third_Ventricle = 0.22647 (34) gca peak CSF = 0.25620 (35) gca peak Left_Accumbens_area = 0.51667 (77) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.27366 (84) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (38) gca peak WM_hypointensities = 0.14892 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34481 (76) gcamFindOptimalTimeStep: Complete in 111434.578 ms 0365: dt=2.800000, rms=0.447 (0.000%), neg=0, invalid=766 0366: dt=2.800000, rms=0.447 (0.012%), neg=0, invalid=766 0367: dt=2.800000, rms=0.447 (0.001%), neg=0, invalid=766 0368: dt=2.800000, rms=0.447 (0.006%), neg=0, invalid=766 0369: dt=2.800000, rms=0.447 (0.012%), neg=0, invalid=766 0370: dt=2.800000, rms=0.447 (0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 187898.484 ms 0371: dt=0.000000, rms=0.468 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 136781.500 ms 0372: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177103.516 ms 0373: dt=1.536000, rms=0.504 (0.959%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 169299.203 ms 0374: dt=0.448000, rms=0.504 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 122974.586 ms 0375: dt=0.250000, rms=0.504 (0.008%), neg=0, invalid=766 not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Right_Pallidum too bright - rescaling by 1.016 (from 1.000) to 106.7 (was 105.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 18188 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 285 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 52314 changed. image ll: -2.052, PF=1.000 pass 2: 7485 changed. pass 3: 2577 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 71 minutes and 18 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/cc_up.lta CA149base will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/cc_up.lta 0376: dt=0.250000, rms=0.504 (-0.007%), neg=0, invalid=766 reading aseg from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.auto_noCCseg.mgz reading norm from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm.mgz 27429 voxels in left wm, 27563 in right wm, xrange [122, 131] searching rotation angles z=[-3 11], y=[-9 5] searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 global minimum found at slice 126.2, rotations (-2.43, 3.67) final transformation (x=126.2, yr=-2.433, zr=3.666): 0.997 -0.064 -0.042 15.026; 0.064 0.998 -0.003 0.516; 0.042 -0.000 0.999 -0.248; 0.000 0.000 0.000 1.000; blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=766 updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 139 119 eigenvectors: -0.001 0.010 1.000; -0.131 -0.991 0.010; 0.991 -0.131 0.002; error in mid anterior detected - correcting... writing aseg with callosum to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.3 minutes #-------------------------------------- #@# Merge ASeg Fri Jul 15 08:55:51 EDT 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Jul 15 08:55:52 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 985 control points removed building Voronoi diagram... gcamFindOptimalTimeStep: Complete in 236222.859 ms 0377: dt=0.807692, rms=0.504 (0.079%), neg=0, invalid=766 performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 gcamFindOptimalTimeStep: Complete in 229744.219 ms 0378: dt=0.112000, rms=0.504 (0.002%), neg=0, invalid=766 building Voronoi diagram... 0379: dt=0.112000, rms=0.504 (0.002%), neg=0, invalid=766 performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 10 minutes and 12 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 76 (76), valley at 35 (35) csf peak at 20, setting threshold to 57 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 36 (36) csf peak at 20, setting threshold to 58 #-------------------------------------------- #@# Mask BFS Fri Jul 15 09:06:25 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1234975 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Jul 15 09:06:35 EDT 2016 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... 0380: dt=0.112000, rms=0.504 (-0.004%), neg=0, invalid=766 computing class statistics for intensity windows... WM (102.0): 101.2 +- 6.6 [80.0 --> 125.0] GM (76.0) : 74.5 +- 9.4 [30.0 --> 96.0] setting bottom of white matter range to 83.9 setting top of gray matter range to 93.3 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 1463 sparsely connected voxels removed... thickening thin strands.... gcamFindOptimalTimeStep: Complete in 150346.422 ms 0381: dt=0.112000, rms=0.456 (0.683%), neg=0, invalid=766 20 segments, 1897 filled 0 bright non-wm voxels segmented. 1096 diagonally connected voxels added... white matter segmentation took 4.6 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 1.94 minutes reading wm segmentation from wm.seg.mgz... 18 voxels added to wm to prevent paths from MTL structures to cortex 1501 additional wm voxels added 0 additional wm voxels added SEG EDIT: 28854 voxels turned on, 34266 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 99 new 99 115,126,128 old 99 new 99 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 15 found - 15 modified | TOTAL: 25 pass 2 (xy-): 0 found - 15 modified | TOTAL: 25 pass 1 (yz+): 15 found - 15 modified | TOTAL: 40 pass 2 (yz+): 0 found - 15 modified | TOTAL: 40 pass 1 (yz-): 12 found - 12 modified | TOTAL: 52 pass 2 (yz-): 0 found - 12 modified | TOTAL: 52 pass 1 (xz+): 14 found - 14 modified | TOTAL: 66 pass 2 (xz+): 0 found - 14 modified | TOTAL: 66 pass 1 (xz-): 11 found - 11 modified | TOTAL: 77 pass 2 (xz-): 0 found - 11 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 11 found - 11 modified | TOTAL: 23 pass 2 (+++): 0 found - 11 modified | TOTAL: 23 pass 1 (+++): 4 found - 4 modified | TOTAL: 27 pass 2 (+++): 0 found - 4 modified | TOTAL: 27 pass 1 (+++): 0 found - 0 modified | TOTAL: 27 Iteration Number : 1 pass 1 (++): 19 found - 19 modified | TOTAL: 19 pass 2 (++): 0 found - 19 modified | TOTAL: 19 pass 1 (+-): 29 found - 29 modified | TOTAL: 48 pass 2 (+-): 0 found - 29 modified | TOTAL: 48 pass 1 (--): 26 found - 26 modified | TOTAL: 74 pass 2 (--): 0 found - 26 modified | TOTAL: 74 pass 1 (-+): 20 found - 20 modified | TOTAL: 94 pass 2 (-+): 0 found - 20 modified | TOTAL: 94 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 207 (out of 457998: 0.045197) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Jul 15 09:13:31 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; gcamFindOptimalTimeStep: Complete in 146911.688 ms 0382: dt=0.028000, rms=0.455 (0.137%), neg=0, invalid=766 voxel to talairach voxel transform 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1264 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (129, 105, 97), TAL = (-1.0, -31.0, 23.0) talairach voxel to voxel transform 0.845 0.089 0.025 5.581; -0.091 0.743 -0.251 77.491; -0.065 0.218 0.850 20.011; 0.000 0.000 0.000 1.000; segmentation indicates cc at (129, 105, 97) --> (-1.0, -31.0, 23.0) done. gcamFindOptimalTimeStep: Complete in 156186.953 ms 0383: dt=0.080000, rms=0.454 (0.368%), neg=0, invalid=766 writing output to filled.mgz... filling took 3.5 minutes talairach cc position changed to (-1.00, -31.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(17.00, -31.00, 23.00) SRC: (111.03, 121.13, 118.07) search lh wm seed point around talairach space (-19.00, -31.00, 23.00), SRC: (141.44, 117.86, 115.72) 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 Fri Jul 15 09:17:00 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 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+): 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 220752: 0.003171) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 70: 3334 vertices, 3530 faces slice 80: 11801 vertices, 12122 faces slice 90: 21827 vertices, 22137 faces slice 100: 31521 vertices, 31850 faces slice 110: 40701 vertices, 41022 faces slice 120: 50310 vertices, 50637 faces slice 130: 60027 vertices, 60359 faces slice 140: 69024 vertices, 69347 faces slice 150: 78151 vertices, 78452 faces slice 160: 86634 vertices, 86895 faces slice 170: 93508 vertices, 93788 faces slice 180: 99436 vertices, 99649 faces slice 190: 104402 vertices, 104567 faces slice 200: 107461 vertices, 107559 faces slice 210: 108302 vertices, 108324 faces slice 220: 108302 vertices, 108324 faces slice 230: 108302 vertices, 108324 faces slice 240: 108302 vertices, 108324 faces slice 250: 108302 vertices, 108324 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... 108302 voxel in cpt #1: X=-22 [v=108302,e=324972,f=216648] located at (-24.370428, -3.206571, 8.361665) For the whole surface: X=-22 [v=108302,e=324972,f=216648] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Jul 15 09:17:42 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Fri Jul 15 09:17:54 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts avg radius = 43.3 mm, total surface area = 58061 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.4 minutes Not saving sulc step 000: RMS=0.095 (target=0.015) step 005: RMS=0.069 (target=0.015) step 010: RMS=0.051 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (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=0.024 (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 Fri Jul 15 09:19:19 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... gcamFindOptimalTimeStep: Complete in 146340.938 ms 0384: dt=0.028000, rms=0.453 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 156510.375 ms 0385: dt=0.080000, rms=0.452 (0.302%), neg=0, invalid=766 surface projected - minimizing metric distortion... vertex spacing 1.12 +- 0.60 (0.00-->7.42) (max @ vno 80562 --> 80581) face area 0.03 +- 0.04 (-0.14-->0.65) gcamFindOptimalTimeStep: Complete in 158771.031 ms 0386: dt=0.028000, rms=0.451 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 137785.484 ms 0387: dt=0.080000, rms=0.450 (0.250%), neg=0, invalid=766 scaling brain by 0.361... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.781, avgs=0 005/300: dt: 0.9000, rms radial error=175.524, avgs=0 010/300: dt: 0.9000, rms radial error=174.972, avgs=0 015/300: dt: 0.9000, rms radial error=174.246, avgs=0 020/300: dt: 0.9000, rms radial error=173.418, avgs=0 025/300: dt: 0.9000, rms radial error=172.532, avgs=0 030/300: dt: 0.9000, rms radial error=171.613, avgs=0 035/300: dt: 0.9000, rms radial error=170.680, avgs=0 040/300: dt: 0.9000, rms radial error=169.741, avgs=0 045/300: dt: 0.9000, rms radial error=168.798, avgs=0 050/300: dt: 0.9000, rms radial error=167.856, avgs=0 055/300: dt: 0.9000, rms radial error=166.916, avgs=0 060/300: dt: 0.9000, rms radial error=165.979, avgs=0 065/300: dt: 0.9000, rms radial error=165.047, avgs=0 070/300: dt: 0.9000, rms radial error=164.119, avgs=0 075/300: dt: 0.9000, rms radial error=163.196, avgs=0 080/300: dt: 0.9000, rms radial error=162.278, avgs=0 085/300: dt: 0.9000, rms radial error=161.365, avgs=0 090/300: dt: 0.9000, rms radial error=160.456, avgs=0 095/300: dt: 0.9000, rms radial error=159.552, avgs=0 100/300: dt: 0.9000, rms radial error=158.653, avgs=0 105/300: dt: 0.9000, rms radial error=157.759, avgs=0 110/300: dt: 0.9000, rms radial error=156.870, avgs=0 115/300: dt: 0.9000, rms radial error=155.988, avgs=0 120/300: dt: 0.9000, rms radial error=155.112, avgs=0 125/300: dt: 0.9000, rms radial error=154.241, avgs=0 130/300: dt: 0.9000, rms radial error=153.375, avgs=0 135/300: dt: 0.9000, rms radial error=152.513, avgs=0 140/300: dt: 0.9000, rms radial error=151.656, avgs=0 145/300: dt: 0.9000, rms radial error=150.804, avgs=0 150/300: dt: 0.9000, rms radial error=149.956, avgs=0 155/300: dt: 0.9000, rms radial error=149.113, avgs=0 160/300: dt: 0.9000, rms radial error=148.275, avgs=0 165/300: dt: 0.9000, rms radial error=147.441, avgs=0 170/300: dt: 0.9000, rms radial error=146.611, avgs=0 175/300: dt: 0.9000, rms radial error=145.786, avgs=0 180/300: dt: 0.9000, rms radial error=144.965, avgs=0 185/300: dt: 0.9000, rms radial error=144.149, avgs=0 190/300: dt: 0.9000, rms radial error=143.338, avgs=0 195/300: dt: 0.9000, rms radial error=142.531, avgs=0 200/300: dt: 0.9000, rms radial error=141.728, avgs=0 205/300: dt: 0.9000, rms radial error=140.930, avgs=0 210/300: dt: 0.9000, rms radial error=140.136, avgs=0 215/300: dt: 0.9000, rms radial error=139.347, avgs=0 220/300: dt: 0.9000, rms radial error=138.562, avgs=0 225/300: dt: 0.9000, rms radial error=137.781, avgs=0 230/300: dt: 0.9000, rms radial error=137.005, avgs=0 235/300: dt: 0.9000, rms radial error=136.233, avgs=0 240/300: dt: 0.9000, rms radial error=135.465, avgs=0 245/300: dt: 0.9000, rms radial error=134.702, avgs=0 250/300: dt: 0.9000, rms radial error=133.943, avgs=0 255/300: dt: 0.9000, rms radial error=133.188, avgs=0 260/300: dt: 0.9000, rms radial error=132.437, avgs=0 265/300: dt: 0.9000, rms radial error=131.690, avgs=0 270/300: dt: 0.9000, rms radial error=130.948, avgs=0 275/300: dt: 0.9000, rms radial error=130.210, avgs=0 280/300: dt: 0.9000, rms radial error=129.476, avgs=0 285/300: dt: 0.9000, rms radial error=128.746, avgs=0 290/300: dt: 0.9000, rms radial error=128.020, avgs=0 295/300: dt: 0.9000, rms radial error=127.299, avgs=0 300/300: dt: 0.9000, rms radial error=126.581, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11933.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 1761.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00025 epoch 3 (K=160.0), pass 1, starting sse = 138.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00645 epoch 4 (K=640.0), pass 1, starting sse = 6.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00621 final dwriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.18 hours istance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Jul 15 09:29:59 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 CA149base 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-22 (nv=108302, nf=216648, ne=324972, g=12) 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... 1245 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7081 (-4.3541) -vertex loglikelihood: -5.7394 (-2.8697) -normal dot loglikelihood: -3.6279 (-3.6279) -quad curv loglikelihood: -6.4271 (-3.2135) Total Loglikelihood : -24.5025 CORRECTING DEFECT 0 (vertices=21, convex hull=25) After retessellation of defect 0, euler #=-9 (107518,322201,214674) : difference with theory (-12) = -3 CORRECTING DEFECT 1 (vertices=37, convex hull=76) gcamFindOptimalTimeStep: Complete in 102320.820 ms 0388: dt=0.112000, rms=0.449 (0.304%), neg=0, invalid=766 After retessellation of defect 1, euler #=-8 (107527,322259,214724) : difference with theory (-11) = -3 CORRECTING DEFECT 2 (vertices=8, convex hull=15) gcamFindOptimalTimeStep: Complete in 122429.398 ms 0389: dt=0.080000, rms=0.448 (0.181%), neg=0, invalid=766 After retessellation of defect 2, euler #=-7 (107528,322266,214731) : difference with theory (-10) = -3 CORRECTING DEFECT 3 (vertices=31, convex hull=51) After retessellation of defect 3, euler #=-6 (107547,322345,214792) : difference with theory (-9) = -3 CORRECTING DEFECT 4 (vertices=26, convex hull=21) After retessellation of defect 4, euler #=-5 (107551,322360,214804) : difference with theory (-8) = -3 CORRECTING DEFECT 5 (vertices=195, convex hull=61) gcamFindOptimalTimeStep: Complete in 143828.891 ms 0390: dt=0.028000, rms=0.448 (0.056%), neg=0, invalid=766 After retessellation of defect 5, euler #=-4 (107562,322421,214855) : difference with theory (-7) = -3 CORRECTING DEFECT 6 (vertices=37, convex hull=70) After retessellation of defect 6, euler #=-3 (107582,322505,214920) : difference with theory (-6) = -3 CORRECTING DEFECT 7 (vertices=75, convex hull=81) After retessellation of defect 7, euler #=-3 (107615,322649,215031) : difference with theory (-5) = -2 CORRECTING DEFECT 8 (vertices=127, convex hull=148) gcamFindOptimalTimeStep: Complete in 200880.344 ms 0391: dt=0.112000, rms=0.447 (0.215%), neg=0, invalid=766 After retessellation of defect 8, euler #=-3 (107661,322855,215191) : difference with theory (-4) = -1 CORRECTING DEFECT 9 (vertices=28, convex hull=47) gcamFindOptimalTimeStep: Complete in 122785.180 ms 0392: dt=0.112000, rms=0.446 (0.183%), neg=0, invalid=766 After retessellation of defect 9, euler #=-2 (107675,322911,215234) : difference with theory (-3) = -1 CORRECTING DEFECT 10 (vertices=28, convex hull=23) gcamFindOptimalTimeStep: Complete in 138003.953 ms 0393: dt=0.096341, rms=0.445 (0.134%), neg=0, invalid=766 After retessellation of defect 10, euler #=-2 (107681,322940,215257) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=63, convex hull=40) After retessellation of defect 11, euler #=-1 (107687,322973,215285) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=66) After retessellation of defect 12, euler #=0 (107697,323028,215331) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=31, convex hull=56) After retessellation of defect 13, euler #=1 (107711,323093,215383) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=48, convex hull=82) gcamFindOptimalTimeStep: Complete in 186624.219 ms 0394: dt=0.112000, rms=0.445 (0.139%), neg=0, invalid=766 After retessellation of defect 14, euler #=2 (107738,323208,215472) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.05-->5.54) (max @ vno 75908 --> 75920) 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 (0.05-->5.54) (max @ vno 75908 --> 75920) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 55 mutations (33.5%), 109 crossovers (66.5%), 52 vertices were eliminated building final representation... 564 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=107738, nf=215472, ne=323208, g=0) writing corrected surface to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.3 minutes 0 defective edges removing intersecting faces 000: 58 intersecting 001: 6 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 107738 - 323208 + 215472 = 2 --> 0 holes F =2V-4: 215472 = 215476-4 (0) 2E=3F: 646416 = 646416 (0) total defect index = 0 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 13 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Jul 15 09:52:34 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7462 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 83.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.7 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.81) (max @ vno 81921 --> 107629) face area 0.28 +- 0.12 (0.00-->1.13) gcamFindOptimalTimeStep: Complete in 209191.109 ms 0395: dt=0.080000, rms=0.444 (0.087%), neg=0, invalid=766 mean absolute distance = 0.86 +- 1.06 2979 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=75 using class modes intead of means.... mean inside = 95.0, mean outside = 81.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.5, 9 (9) missing vertices, mean dist 0.3 [0.8 (%35.4)->0.9 (%64.6))] %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 gcamFindOptimalTimeStep: Complete in 181987.000 ms 0396: dt=0.028000, rms=0.444 (0.027%), neg=0, invalid=766 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->3.85) (max @ vno 81921 --> 107629) face area 0.28 +- 0.13 (0.00-->1.66) 0397: dt=0.028000, rms=0.444 (0.027%), neg=0, invalid=766 mean absolute distance = 0.45 +- 0.85 2929 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3291322.8, rms=8.56 001: dt: 0.5000, sse=3703650.5, rms=6.06 002: dt: 0.5000, sse=3847908.5, rms=4.39 003: dt: 0.5000, sse=4049931.2, rms=3.31 004: dt: 0.5000, sse=4129320.2, rms=2.68 005: dt: 0.5000, sse=4214587.5, rms=2.35 006: dt: 0.5000, sse=4212396.5, rms=2.21 007: dt: 0.5000, sse=4252234.5, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4245008.0, rms=2.11 009: dt: 0.2500, sse=2622303.2, rms=1.48 010: dt: 0.2500, sse=2473091.0, rms=1.40 rms = 1.38, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2429420.2, rms=1.38 rms = 1.37, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2401884.0, rms=1.37 positioning took 3.1 minutes 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=86.4, 24 (1) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %56 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 0398: dt=0.028000, rms=0.444 (0.051%), neg=0, invalid=766 0399: dt=0.028000, rms=0.444 (0.069%), neg=0, invalid=766 0400: dt=0.028000, rms=0.443 (0.085%), neg=0, invalid=766 0401: dt=0.028000, rms=0.443 (0.096%), neg=0, invalid=766 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->4.07) (max @ vno 70431 --> 69542) face area 0.35 +- 0.16 (0.00-->2.45) mean absolute distance = 0.38 +- 0.53 3452 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2744818.2, rms=3.78 013: dt: 0.5000, sse=2963821.5, rms=2.38 014: dt: 0.5000, sse=3192575.5, rms=1.88 015: dt: 0.5000, sse=3234785.8, rms=1.67 rms = 1.65, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=3480803.5, rms=1.65 017: dt: 0.2500, sse=2708241.5, rms=1.24 018: dt: 0.2500, sse=2605611.8, rms=1.19 rms = 1.18, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2577163.5, rms=1.18 rms = 1.18, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2555069.5, rms=1.18 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 12 (1) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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 0402: dt=0.028000, rms=0.442 (0.104%), neg=0, invalid=766 0403: dt=0.014000, rms=0.442 (0.010%), neg=0, invalid=766 0404: dt=0.014000, rms=0.442 (0.007%), neg=0, invalid=766 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->4.50) (max @ vno 70431 --> 69542) face area 0.34 +- 0.16 (0.00-->2.55) mean absolute distance = 0.28 +- 0.37 2898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2808080.8, rms=3.79 021: dt: 0.5000, sse=2953509.5, rms=2.07 022: dt: 0.5000, sse=3108183.2, rms=1.65 023: dt: 0.5000, sse=3214451.8, rms=1.49 rms = 1.60, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=2867498.8, rms=1.22 025: dt: 0.2500, sse=2744902.5, rms=1.11 rms = 1.10, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2708585.8, rms=1.10 rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2690677.2, rms=1.10 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=90.3, 11 (0) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.2 (%39.2))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=2722549.5, rms=1.85 028: dt: 0.5000, sse=3230767.2, rms=1.15 rms = 1.30, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3020761.5, rms=0.97 030: dt: 0.2500, sse=2913785.8, rms=0.91 rms = 0.90, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2932323.0, rms=0.90 rms = 0.91, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=2932323.0, rms=0.90 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 2088 vertices erasing segment 1 (vno[0] = 65137) erasing segment 2 (vno[0] = 77469) erasing segment 3 (vno[0] = 78212) erasing segment 4 (vno[0] = 79130) erasing segment 5 (vno[0] = 79140) erasing segment 6 (vno[0] = 79962) erasing segment 7 (vno[0] = 81767) erasing segment 8 (vno[0] = 82568) erasing segment 9 (vno[0] = 83391) erasing segment 10 (vno[0] = 85016) erasing segment 11 (vno[0] = 85048) erasing segment 12 (vno[0] = 107676) writing cortex label to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.cortex.label... LabelWrite: saving to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.cortex.label writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->4.54) (max @ vno 70431 --> 69542) face area 0.33 +- 0.16 (0.00-->2.54) refinement took 13.5 minutes #-------------------------------------------- #@# Smooth2 lh Fri Jul 15 10:06:08 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Fri Jul 15 10:06:17 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 43.5 mm, total surface area = 65234 mm^2 gcamFindOptimalTimeStep: Complete in 173193.203 ms 0405: dt=0.112000, rms=0.442 (0.061%), neg=0, invalid=766 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.110 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (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=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 1.7 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 gcamFindOptimalTimeStep: Complete in 156700.234 ms 0406: dt=0.112000, rms=0.442 (0.052%), neg=0, invalid=766 262 vertices thresholded to be in k1 ~ [-0.21 0.43], k2 ~ [-0.11 0.07] total integrated curvature = 0.613*4pi (7.708) --> 0 handles ICI = 1.5, FI = 7.4, variation=133.919 151 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 = 0.001 136 vertices thresholded to be in [-0.14 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Fri Jul 15 10:10:39 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm CA149base 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 [ CA149base/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 [ 174 ] Gb_filter = 0 WARN: S lookup min: -0.068964 WARN: S explicit min: 0.000000 vertex = 1430 #-------------------------------------------- #@# Sphere lh Fri Jul 15 10:10:55 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... gcamFindOptimalTimeStep: Complete in 170737.938 ms 0407: dt=0.112000, rms=0.442 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 146428.500 ms 0408: dt=0.028000, rms=0.442 (0.013%), neg=0, invalid=766 0409: dt=0.028000, rms=0.441 (0.012%), neg=0, invalid=766 0410: dt=0.028000, rms=0.441 (0.021%), neg=0, invalid=766 0411: dt=0.028000, rms=0.441 (0.029%), neg=0, invalid=766 0412: dt=0.028000, rms=0.441 (0.010%), neg=0, invalid=766 0413: dt=0.028000, rms=0.441 (0.021%), neg=0, invalid=766 0414: dt=0.028000, rms=0.441 (0.030%), neg=0, invalid=766 0415: dt=0.028000, rms=0.441 (0.034%), neg=0, invalid=766 0416: dt=0.028000, rms=0.441 (0.042%), neg=0, invalid=766 0417: dt=0.028000, rms=0.440 (0.045%), neg=0, invalid=766 0418: dt=0.028000, rms=0.440 (0.044%), neg=0, invalid=766 0419: dt=0.028000, rms=0.440 (0.051%), neg=0, invalid=766 0420: dt=0.028000, rms=0.440 (0.051%), neg=0, invalid=766 0421: dt=0.028000, rms=0.440 (0.053%), neg=0, invalid=766 0422: dt=0.028000, rms=0.439 (0.051%), neg=0, invalid=766 0423: dt=0.028000, rms=0.439 (0.049%), neg=0, invalid=766 0424: dt=0.028000, rms=0.439 (0.047%), neg=0, invalid=766 0425: dt=0.028000, rms=0.439 (0.046%), neg=0, invalid=766 0426: dt=0.028000, rms=0.439 (0.043%), neg=0, invalid=766 0427: dt=0.028000, rms=0.438 (0.041%), neg=0, invalid=766 0428: dt=0.028000, rms=0.438 (0.041%), neg=0, invalid=766 0429: dt=0.028000, rms=0.438 (0.032%), neg=0, invalid=766 0430: dt=0.028000, rms=0.438 (0.033%), neg=0, invalid=766 0431: dt=0.028000, rms=0.438 (0.031%), neg=0, invalid=766 0432: dt=0.028000, rms=0.438 (0.028%), neg=0, invalid=766 0433: dt=0.028000, rms=0.438 (0.026%), neg=0, invalid=766 0434: dt=0.028000, rms=0.437 (0.023%), neg=0, invalid=766 0435: dt=0.028000, rms=0.437 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 211405.469 ms 0436: dt=0.112000, rms=0.437 (0.001%), neg=0, invalid=766 0437: dt=0.056000, rms=0.437 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.437, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 120620.250 ms 0438: dt=0.028000, rms=0.437 (0.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 133779.047 ms 0439: dt=0.080000, rms=0.437 (0.100%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 163194.516 ms 0440: dt=0.112000, rms=0.436 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 117764.172 ms 0441: dt=0.028000, rms=0.436 (0.021%), neg=0, invalid=766 0442: dt=0.028000, rms=0.436 (0.018%), neg=0, invalid=766 0443: dt=0.028000, rms=0.436 (0.040%), neg=0, invalid=766 0444: dt=0.028000, rms=0.436 (0.048%), neg=0, invalid=766 0445: dt=0.028000, rms=0.436 (0.013%), neg=0, invalid=766 0446: dt=0.028000, rms=0.436 (0.025%), neg=0, invalid=766 0447: dt=0.028000, rms=0.435 (0.031%), neg=0, invalid=766 0448: dt=0.028000, rms=0.435 (0.037%), neg=0, invalid=766 0449: dt=0.028000, rms=0.435 (0.008%), neg=0, invalid=766 0450: dt=0.028000, rms=0.435 (0.012%), neg=0, invalid=766 0451: dt=0.028000, rms=0.435 (0.017%), neg=0, invalid=766 0452: dt=0.028000, rms=0.435 (0.021%), neg=0, invalid=766 0453: dt=0.028000, rms=0.435 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 159758.234 ms 0454: dt=0.112000, rms=0.435 (0.012%), neg=0, invalid=766 0455: dt=0.056000, rms=0.435 (-0.001%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 242434.109 ms iter 0, gcam->neg = 140 after 42 iterations, nbhd size=4, neg = 0 0456: dt=44.800000, rms=0.424 (2.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 225539.766 ms iter 0, gcam->neg = 12 after 36 iterations, nbhd size=4, neg = 0 0457: dt=25.600000, rms=0.422 (0.408%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 160248.750 ms 0458: dt=19.200000, rms=0.421 (0.308%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 214687.625 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0459: dt=9.600000, rms=0.420 (0.187%), neg=0, invalid=766 0460: dt=9.600000, rms=0.419 (0.165%), neg=0, invalid=766 0461: dt=9.600000, rms=0.418 (0.206%), neg=0, invalid=766 0462: dt=9.600000, rms=0.417 (0.262%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 23 iterations, nbhd size=3, neg = 0 0463: dt=9.600000, rms=0.416 (0.243%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 36 iterations, nbhd size=4, neg = 0 0464: dt=9.600000, rms=0.415 (0.233%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 30 iterations, nbhd size=3, neg = 0 0465: dt=9.600000, rms=0.414 (0.199%), neg=0, invalid=766 0466: dt=9.600000, rms=0.414 (0.181%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0467: dt=9.600000, rms=0.413 (0.125%), neg=0, invalid=766 0468: dt=9.600000, rms=0.412 (0.174%), neg=0, invalid=766 0469: dt=9.600000, rms=0.412 (0.158%), neg=0, invalid=766 0470: dt=9.600000, rms=0.411 (0.155%), neg=0, invalid=766 0471: dt=9.600000, rms=0.411 (0.116%), neg=0, invalid=766 0472: dt=9.600000, rms=0.410 (0.111%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 110756.516 ms 0473: dt=19.200000, rms=0.410 (0.066%), neg=0, invalid=766 0474: dt=19.200000, rms=0.410 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 143014.812 ms 0475: dt=11.200000, rms=0.409 (0.225%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 181851.719 ms 0476: dt=11.200000, rms=0.408 (0.158%), neg=0, invalid=766 0477: dt=11.200000, rms=0.408 (0.138%), neg=0, invalid=766 0478: dt=11.200000, rms=0.407 (0.194%), neg=0, invalid=766 0479: dt=11.200000, rms=0.406 (0.195%), neg=0, invalid=766 0480: dt=11.200000, rms=0.406 (0.168%), neg=0, invalid=766 0481: dt=11.200000, rms=0.405 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0482: dt=11.200000, rms=0.405 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 213364.000 ms iter 0, gcam->neg = 1 after 47 iterations, nbhd size=4, neg = 0 0483: dt=9.600000, rms=0.405 (0.016%), neg=0, invalid=766 0484: dt=9.600000, rms=0.405 (0.016%), neg=0, invalid=766 0485: dt=9.600000, rms=0.405 (0.015%), neg=0, invalid=766 0486: dt=9.600000, rms=0.405 (0.025%), neg=0, invalid=766 0487: dt=9.600000, rms=0.405 (0.020%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 170034.156 ms 0488: dt=1.008000, rms=0.409 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 221473.047 ms 0489: dt=1.728000, rms=0.409 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 208277.891 ms 0490: dt=0.252000, rms=0.409 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177847.875 ms iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0491: dt=3.456000, rms=0.409 (0.047%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 174318.531 ms 0492: dt=4.032000, rms=0.409 (0.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 228521.469 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=2.304000, rms=0.409 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 11 iterations, nbhd size=1, neg = 0 0494: dt=2.304000, rms=0.409 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 15 iterations, nbhd size=1, neg = 0 0495: dt=2.304000, rms=0.409 (0.006%), neg=0, invalid=766 writing spherical brain to ../surf/lh.sphere spherical transformation took 2.66 hours scaling brain by 0.339... pass 1: epoch 1 of 3 starting distance error %18.65 pass 1: epoch 2 of 3 starting distance error %18.64 unfolding complete - removing small folds... starting distance error %18.59 removing remaining folds... final distance error %18.61 expanding nbhd size to 1 #-------------------------------------------- #@# Surf Reg lh Fri Jul 15 12:50:28 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_register -curv ../surf/lh.sphere /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif... iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0496: dt=2.304000, rms=0.409 (-0.039%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 202073.703 ms 0497: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 173342.812 ms 0498: dt=0.000375, rms=0.415 (0.000%), neg=0, invalid=766 0499: dt=0.000375, rms=0.415 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 154876.766 ms iter 0, gcam->neg = 502 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 97839.422 ms iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.003 (22.301%) 0500: dt=1.346939, rms=0.384 (5.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 217319.109 ms 0501: dt=0.000094, rms=0.384 (-0.010%), neg=0, invalid=766 0502: dt=0.000094, rms=0.384 (0.000%), neg=0, invalid=766 0503: dt=0.000094, rms=0.384 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 221448.594 ms 0504: dt=0.000078, rms=0.384 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 180884.000 ms 0505: dt=0.000000, rms=0.384 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.379, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212524.484 ms iter 0, gcam->neg = 157 after 17 iterations, nbhd size=2, neg = 0 0506: dt=0.306667, rms=0.374 (1.174%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 147916.781 ms 0507: dt=0.001750, rms=0.374 (-0.008%), neg=0, invalid=766 0508: dt=0.001750, rms=0.374 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0509: dt=0.001750, rms=0.374 (0.005%), neg=0, invalid=766 0510: dt=0.001750, rms=0.374 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0511: dt=0.001750, rms=0.374 (0.008%), neg=0, invalid=766 0512: dt=0.001750, rms=0.374 (0.010%), neg=0, invalid=766 0513: dt=0.001750, rms=0.374 (0.014%), neg=0, invalid=766 0514: dt=0.001750, rms=0.374 (0.011%), neg=0, invalid=766 0515: dt=0.001750, rms=0.374 (0.014%), neg=0, invalid=766 0516: dt=0.001750, rms=0.374 (0.016%), neg=0, invalid=766 0517: dt=0.001750, rms=0.374 (0.017%), neg=0, invalid=766 0518: dt=0.001750, rms=0.374 (0.017%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 192838.578 ms iter 0, gcam->neg = 24 after 16 iterations, nbhd size=2, neg = 0 0519: dt=0.112000, rms=0.373 (0.264%), neg=0, invalid=766 writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.615 curvature mean = 0.030, std = 0.936 curvature mean = 0.018, std = 0.890 curvature mean = 0.015, std = 0.972 curvature mean = 0.006, std = 0.958 curvature mean = 0.014, std = 0.986 curvature mean = 0.003, std = 0.983 curvature mean = 0.013, std = 0.990 curvature mean = 0.000, std = 0.993 curvature mean = -0.025, std = 0.272 curvature mean = 0.003, std = 0.068 curvature mean = 0.046, std = 0.404 curvature mean = 0.003, std = 0.082 curvature mean = 0.016, std = 0.598 curvature mean = 0.003, std = 0.088 curvature mean = 0.009, std = 0.725 curvature mean = 0.003, std = 0.092 curvature mean = 0.003, std = 0.812 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Jul 15 14:05:37 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Jul 15 14:05:43 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mrisp_paint -a 5 /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Jul 15 14:05:47 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base lh ../surf/lh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ gcamFindOptimalTimeStep: Complete in 170895.969 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.003000, rms=0.373 (0.007%), neg=0, invalid=766 0521: dt=0.003000, rms=0.373 (0.006%), neg=0, invalid=766 reading atlas from /opt/share/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... 844 labels changed using aseg relabeling using gibbs priors... 000: 2442 changed, 107738 examined... 001: 568 changed, 10616 examined... 002: 127 changed, 3190 examined... 003: 47 changed, 763 examined... 004: 24 changed, 296 examined... 005: 7 changed, 146 examined... 006: 3 changed, 45 examined... 007: 0 changed, 21 examined... 170 labels changed using aseg 000: 105 total segments, 65 labels (175 vertices) changed 001: 41 total segments, 2 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1419 vertices marked for relabeling... 1419 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 2 minutes and 0 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Jul 15 14:07:47 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... 0522: dt=0.003000, rms=0.373 (0.010%), neg=0, invalid=766 reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7462 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... computing class statistics... 0523: dt=0.003000, rms=0.373 (0.013%), neg=0, invalid=766 border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 83.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.7 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=75 using class modes intead of means.... mean inside = 95.0, mean outside = 81.1 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.81) (max @ vno 81921 --> 107629) face area 0.28 +- 0.12 (0.00-->1.13) 0524: dt=0.003000, rms=0.373 (0.018%), neg=0, invalid=766 mean absolute distance = 0.86 +- 1.06 3018 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 206 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=84.5, 9 (9) missing vertices, mean dist 0.3 [0.9 (%35.4)->0.9 (%64.6))] %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 0525: dt=0.003000, rms=0.373 (0.023%), neg=0, invalid=766 0526: dt=0.003000, rms=0.372 (0.024%), neg=0, invalid=766 0527: dt=0.003000, rms=0.372 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0528: dt=0.003000, rms=0.372 (0.031%), neg=0, invalid=766 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->3.85) (max @ vno 81921 --> 107629) face area 0.28 +- 0.13 (0.00-->1.66) 0529: dt=0.003000, rms=0.372 (0.029%), neg=0, invalid=766 mean absolute distance = 0.45 +- 0.86 2978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3295717.5, rms=8.55 001: dt: 0.5000, sse=3713652.5, rms=6.06 002: dt: 0.5000, sse=3857956.2, rms=4.38 003: dt: 0.5000, sse=4058731.0, rms=3.31 004: dt: 0.5000, sse=4139295.8, rms=2.67 005: dt: 0.5000, sse=4224950.0, rms=2.35 006: dt: 0.5000, sse=4223366.0, rms=2.21 007: dt: 0.5000, sse=4263232.0, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4255626.5, rms=2.11 009: dt: 0.2500, sse=2632026.5, rms=1.48 010: dt: 0.2500, sse=2482888.8, rms=1.40 rms = 1.39, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2439602.2, rms=1.39 rms = 1.37, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2412031.5, rms=1.37 positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 150 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown deleting segment 10 with 103 points - only 20.39% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=86.4, 26 (1) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %57 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 0530: dt=0.003000, rms=0.372 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0531: dt=0.003000, rms=0.372 (0.033%), neg=0, invalid=766 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->4.07) (max @ vno 70431 --> 69542) face area 0.35 +- 0.16 (0.00-->2.17) mean absolute distance = 0.38 +- 0.53 3520 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2763453.0, rms=3.78 013: dt: 0.5000, sse=2982197.5, rms=2.38 014: dt: 0.5000, sse=3214474.8, rms=1.88 015: dt: 0.5000, sse=3257349.0, rms=1.67 rms = 1.65, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=3504993.5, rms=1.65 017: dt: 0.2500, sse=2730598.2, rms=1.25 018: dt: 0.2500, sse=2627259.0, rms=1.19 rms = 1.19, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2599168.2, rms=1.19 rms = 1.18, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2577158.8, rms=1.18 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 181 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 81 points - only 25.93% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown mean border=89.2, 21 (1) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->4.50) (max @ vno 70431 --> 69542) face area 0.34 +- 0.16 (0.00-->2.33) mean absolute distance = 0.28 +- 0.37 2965 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2830717.8, rms=3.78 021: dt: 0.5000, sse=2976108.8, rms=2.07 022: dt: 0.5000, sse=3132238.5, rms=1.65 023: dt: 0.5000, sse=3236581.5, rms=1.49 rms = 1.60, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=2889254.2, rms=1.23 025: dt: 0.2500, sse=2766427.2, rms=1.12 rms = 1.11, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2730579.0, rms=1.11 rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2713168.8, rms=1.10 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 190 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 78 points - only 26.92% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown mean border=90.3, 34 (0) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.2 (%39.2))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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=2745304.8, rms=1.86 028: dt: 0.5000, sse=3258741.2, rms=1.16 rms = 1.31, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3048059.2, rms=0.98 030: dt: 0.2500, sse=2941546.5, rms=0.92 rms = 0.91, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2960732.0, rms=0.91 rms = 0.91, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=2960732.0, rms=0.91 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=63.9, 23 (23) missing vertices, mean dist 1.9 [3.7 (%0.0)->2.5 (%100.0))] %33 local maxima, %41 large gradients and %22 min vals, 757 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 gcamFindOptimalTimeStep: Complete in 203260.156 ms iter 0, gcam->neg = 26 after 17 iterations, nbhd size=2, neg = 0 0532: dt=0.064000, rms=0.372 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 220806.297 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0533: dt=0.006000, rms=0.372 (0.008%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.371, neg=0, invalid=766 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=17218796.0, rms=27.26 001: dt: 0.5000, sse=14020590.0, rms=24.26 002: dt: 0.5000, sse=11444568.0, rms=21.58 003: dt: 0.5000, sse=9468405.0, rms=19.19 004: dt: 0.5000, sse=8044845.0, rms=17.06 005: dt: 0.5000, sse=6992998.0, rms=15.12 006: dt: 0.5000, sse=6196389.0, rms=13.35 007: dt: 0.5000, sse=5553184.5, rms=11.60 008: dt: 0.5000, sse=5032635.0, rms=9.87 009: dt: 0.5000, sse=4679310.0, rms=8.18 010: dt: 0.5000, sse=4470950.0, rms=6.70 011: dt: 0.5000, sse=4413658.0, rms=5.52 012: dt: 0.5000, sse=4461597.0, rms=4.76 013: dt: 0.5000, sse=4539051.0, rms=4.31 014: dt: 0.5000, sse=4582165.5, rms=4.04 015: dt: 0.5000, sse=4604929.5, rms=3.88 016: dt: 0.5000, sse=4648533.0, rms=3.77 017: dt: 0.5000, sse=4622838.5, rms=3.68 018: dt: 0.5000, sse=4645615.0, rms=3.63 019: dt: 0.5000, sse=4633281.5, rms=3.58 rms = 3.55, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=4672408.0, rms=3.55 021: dt: 0.2500, sse=2927254.8, rms=2.55 022: dt: 0.2500, sse=2725787.2, rms=2.27 023: dt: 0.2500, sse=2632736.0, rms=2.20 rms = 2.17, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=2596539.8, rms=2.17 025: dt: 0.1250, sse=2482972.2, rms=2.06 rms = 2.04, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2474079.8, rms=2.04 positioning took 5.6 minutes mean border=61.0, 562 (3) missing vertices, mean dist 0.2 [0.2 (%35.6)->0.4 (%64.4))] %51 local maxima, %29 large gradients and %15 min vals, 353 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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=3026981.0, rms=4.88 027: dt: 0.5000, sse=3132055.5, rms=3.37 rms = 3.48, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=2876624.2, rms=2.63 029: dt: 0.2500, sse=2858784.5, rms=2.24 030: dt: 0.2500, sse=2829848.8, rms=2.09 031: dt: 0.2500, sse=2818531.5, rms=2.03 rms = 2.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=2827632.5, rms=2.00 033: dt: 0.1250, sse=2750646.5, rms=1.91 rms = 1.90, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=2744104.0, rms=1.90 positioning took 1.9 minutes mean border=59.4, 658 (3) missing vertices, mean dist 0.1 [0.2 (%35.4)->0.3 (%64.6))] %64 local maxima, %16 large gradients and %15 min vals, 342 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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 gcamFindOptimalTimeStep: Complete in 147181.812 ms iter 0, gcam->neg = 57 after 8 iterations, nbhd size=1, neg = 0 0534: dt=0.112000, rms=0.370 (0.422%), neg=0, invalid=766 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2849652.2, rms=2.87 rms = 3.14, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=2747334.0, rms=2.27 036: dt: 0.2500, sse=2766987.2, rms=1.96 037: dt: 0.2500, sse=2821522.5, rms=1.88 rms = 1.86, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=2836499.5, rms=1.86 039: dt: 0.1250, sse=2785453.0, rms=1.80 rms = 1.79, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=2778287.0, rms=1.79 positioning took 1.5 minutes mean border=58.6, 1399 (3) missing vertices, mean dist 0.0 [0.2 (%43.6)->0.2 (%56.4))] %69 local maxima, %11 large gradients and %14 min vals, 310 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=2798088.5, rms=2.07 rms = 2.55, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=2749086.2, rms=1.85 042: dt: 0.2500, sse=2817024.0, rms=1.78 rms = 1.75, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=2836532.5, rms=1.75 rms = 1.71, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=2796414.2, rms=1.71 positioning took 1.1 minutes writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.area.pial vertex spacing 0.98 +- 0.39 (0.02-->6.53) (max @ vno 50951 --> 50950) face area 0.38 +- 0.27 (0.00-->6.72) measuring cortical thickness... gcamFindOptimalTimeStep: Complete in 168056.688 ms 0535: dt=0.001750, rms=0.370 (0.000%), neg=0, invalid=766 writing cortical thickness estimate to 'thickness' file. 0 of 107738 vertices processed 25000 of 107738 vertices processed 50000 of 107738 vertices processed 75000 of 107738 vertices processed 100000 of 107738 vertices processed 0 of 107738 vertices processed 25000 of 107738 vertices processed 50000 of 107738 vertices processed 75000 of 107738 vertices processed 100000 of 107738 vertices processed thickness calculation complete, 821:637 truncations. 51847 vertices at 0 distance 69833 vertices at 1 distance 50889 vertices at 2 distance 20084 vertices at 3 distance 7714 vertices at 4 distance 3038 vertices at 5 distance 1190 vertices at 6 distance 472 vertices at 7 distance 244 vertices at 8 distance 148 vertices at 9 distance 76 vertices at 10 distance 59 vertices at 11 distance 39 vertices at 12 distance 48 vertices at 13 distance 40 vertices at 14 distance 40 vertices at 15 distance 25 vertices at 16 distance 28 vertices at 17 distance 16 vertices at 18 distance 20 vertices at 19 distance 16 vertices at 20 distance writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.thickness positioning took 24.1 minutes #-------------------------------------------- #@# Surf Volume lh Fri Jul 15 14:31:53 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 ] #----------------------------------------- #@# Parcellation Stats lh Fri Jul 15 14:31:55 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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) 0536: dt=0.001750, rms=0.370 (0.004%), neg=0, invalid=766 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 1325 906 2253 2.499 0.520 0.101 0.023 7 1.3 bankssts 1006 649 2109 3.494 0.541 0.154 0.044 19 1.7 caudalanteriorcingulate 2729 1797 5100 2.584 0.494 0.124 0.038 26 4.2 caudalmiddlefrontal 1882 1168 2037 1.732 0.465 0.165 0.055 34 4.4 cuneus 567 381 1693 3.327 0.729 0.126 0.034 5 0.8 entorhinal 3580 2459 7213 2.653 0.759 0.149 0.048 47 6.7 fusiform 5401 3554 9186 2.345 0.558 0.133 0.060 84 15.6 inferiorparietal 3971 2702 8853 2.938 0.755 0.147 0.045 59 7.1 inferiortemporal 1210 768 2044 2.647 0.677 0.139 0.052 17 2.0 isthmuscingulate 5674 3618 8942 2.270 0.568 0.149 0.051 83 11.2 lateraloccipital 2960 1958 5624 2.694 0.500 0.137 0.046 37 5.6 lateralorbitofrontal 3808 2573 4500 1.689 0.533 0.150 0.049 49 7.9 lingual 2432 1636 4486 2.523 0.712 0.147 0.124 58 7.3 medialorbitofrontal 3041 2099 7571 2.939 0.693 0.143 0.046 45 5.7 middletemporal 860 580 2122 3.082 0.814 0.103 0.026 6 0.8 parahippocampal 1924 1146 2579 2.104 0.525 0.106 0.029 14 2.4 paracentral 2148 1438 3907 2.496 0.526 0.120 0.031 22 2.7 parsopercularis 862 539 2032 2.935 0.544 0.153 0.062 16 1.9 parsorbitalis 1687 1130 2894 2.260 0.593 0.122 0.029 16 2.0 parstriangularis 1438 947 1250 1.445 0.411 0.158 0.068 42 4.7 pericalcarine 5675 3584 7931 1.994 0.597 0.119 0.035 61 8.7 postcentral 1596 1037 2844 2.593 0.583 0.148 0.076 31 5.4 posteriorcingulate 6086 3750 10193 2.529 0.540 0.116 0.042 77 9.6 precentral 4297 2844 6672 2.207 0.558 0.137 0.039 53 6.8 precuneus 1245 825 2626 2.820 0.824 0.145 0.052 22 2.4 rostralanteriorcingulate 5590 3822 10119 2.423 0.581 0.158 0.055 91 12.1 rostralmiddlefrontal 8119 5437 16189 2.641 0.550 0.137 0.046 106 16.4 superiorfrontal 6268 4062 9446 2.129 0.517 0.115 0.031 59 7.7 superiorparietal 4305 2858 9371 2.880 0.735 0.116 0.032 41 5.8 superiortemporal 4412 2954 8443 2.653 0.504 0.139 0.043 56 7.2 supramarginal 175 131 471 2.632 0.406 0.179 0.058 3 0.3 frontalpole 607 426 2562 4.026 0.474 0.164 0.074 12 1.6 temporalpole 636 386 992 2.372 0.424 0.124 0.038 6 1.0 transversetemporal 3136 2032 6572 3.228 0.887 0.140 0.072 54 8.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Jul 15 14:32:48 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base lh ../surf/lh.sphere.reg /opt/share/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 0537: dt=0.001750, rms=0.369 (0.010%), neg=0, invalid=766 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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 0538: dt=0.001750, rms=0.369 (0.015%), neg=0, invalid=766 0539: dt=0.001750, rms=0.369 (0.016%), neg=0, invalid=766 input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 31 labels changed using aseg relabeling using gibbs priors... 000: 7462 changed, 107738 examined... 001: 1761 changed, 28734 examined... 002: 515 changed, 9052 examined... 003: 215 changed, 2858 examined... 004: 92 changed, 1212 examined... 005: 38 changed, 509 examined... 006: 18 changed, 209 examined... 007: 7 changed, 97 examined... 008: 8 changed, 50 examined... 009: 5 changed, 35 examined... 010: 1 changed, 24 examined... 011: 0 changed, 5 examined... 22 labels changed using aseg 000: 224 total segments, 141 labels (1199 vertices) changed 001: 89 total segments, 7 labels (33 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 95 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 951 vertices marked for relabeling... 951 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 2 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Jul 15 14:35:19 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0540: dt=0.001750, rms=0.369 (0.021%), neg=0, invalid=766 reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 771 581 1492 2.443 0.694 0.176 0.053 13 1.7 G_and_S_frontomargin 1303 860 2150 2.281 0.614 0.147 0.048 17 2.5 G_and_S_occipital_inf 1320 719 1801 2.055 0.552 0.106 0.028 15 1.6 G_and_S_paracentral 1195 814 2364 2.571 0.359 0.155 0.046 17 2.3 G_and_S_subcentral 557 390 1251 2.486 0.484 0.181 0.055 11 1.2 G_and_S_transv_frontopol 2232 1532 4304 2.658 0.693 0.142 0.044 32 3.9 G_and_S_cingul-Ant 1315 881 2451 2.964 0.587 0.145 0.042 20 2.3 G_and_S_cingul-Mid-Ant 1309 898 2184 2.431 0.490 0.138 0.038 15 2.0 G_and_S_cingul-Mid-Post 472 293 1057 3.011 0.329 0.178 0.072 10 1.6 G_cingul-Post-dorsal 317 181 479 2.490 0.770 0.117 0.037 3 0.4 G_cingul-Post-ventral 1578 951 1874 1.810 0.508 0.172 0.064 32 4.3 G_cuneus 1113 737 2505 2.709 0.404 0.143 0.041 16 1.9 G_front_inf-Opercular 263 151 667 3.029 0.493 0.144 0.083 6 0.7 G_front_inf-Orbital 1031 676 2159 2.501 0.500 0.136 0.036 13 1.5 G_front_inf-Triangul 3165 2080 6901 2.628 0.502 0.159 0.063 56 7.6 G_front_middle 5490 3493 12031 2.733 0.538 0.139 0.054 83 13.2 G_front_sup 510 290 1035 3.111 0.622 0.174 0.123 20 2.5 G_Ins_lg_and_S_cent_ins 637 391 1929 3.935 0.775 0.163 0.097 14 2.3 G_insular_short 1675 1035 3278 2.577 0.438 0.148 0.068 33 4.2 G_occipital_middle 1325 848 2148 2.205 0.525 0.128 0.036 15 2.0 G_occipital_sup 1333 901 2789 2.647 0.641 0.152 0.052 19 2.7 G_oc-temp_lat-fusifor 2989 1961 3635 1.708 0.555 0.160 0.055 44 7.0 G_oc-temp_med-Lingual 1120 757 3540 3.444 0.748 0.124 0.036 11 1.5 G_oc-temp_med-Parahip 2253 1433 5120 2.860 0.534 0.152 0.059 38 5.3 G_orbital 2047 1318 4448 2.705 0.524 0.161 0.097 56 10.2 G_pariet_inf-Angular 2354 1546 5325 2.807 0.435 0.149 0.051 38 4.7 G_pariet_inf-Supramar 2063 1327 3771 2.271 0.507 0.115 0.037 23 2.8 G_parietal_sup 2246 1318 3455 2.147 0.523 0.119 0.040 28 4.0 G_postcentral 2337 1236 4563 2.775 0.456 0.113 0.061 44 4.7 G_precentral 1984 1286 3897 2.445 0.459 0.147 0.043 31 3.4 G_precuneus 897 605 2118 2.637 0.607 0.164 0.071 19 2.8 G_rectus 355 220 520 2.411 0.837 0.181 0.491 26 2.7 G_subcallosal 527 300 898 2.412 0.394 0.125 0.044 6 1.0 G_temp_sup-G_T_transv 1592 1021 4519 3.188 0.594 0.139 0.040 21 2.7 G_temp_sup-Lateral 513 357 1476 3.821 0.506 0.115 0.030 4 0.6 G_temp_sup-Plan_polar 684 481 1359 2.481 0.557 0.111 0.037 6 1.0 G_temp_sup-Plan_tempo 2162 1453 5903 3.201 0.667 0.167 0.056 44 4.6 G_temporal_inf 1952 1330 5449 3.055 0.536 0.157 0.057 36 4.4 G_temporal_middle 336 226 374 1.785 0.515 0.099 0.017 2 0.2 Lat_Fis-ant-Horizont 301 218 394 1.978 0.460 0.099 0.020 1 0.3 Lat_Fis-ant-Vertical 936 638 1128 2.132 0.486 0.121 0.038 7 1.2 Lat_Fis-post 1928 1202 2815 2.071 0.573 0.162 0.059 30 4.7 Pole_occipital 1497 1041 5465 3.792 0.721 0.159 0.062 25 3.6 Pole_temporal 1849 1259 1812 1.573 0.556 0.146 0.056 45 5.0 S_calcarine 2852 1916 3171 1.843 0.663 0.111 0.029 20 3.6 S_central 1035 684 1290 1.987 0.492 0.115 0.028 9 1.2 S_cingul-Marginalis 406 287 710 3.007 0.564 0.114 0.036 2 0.6 S_circular_insula_ant 1388 955 2400 2.937 0.893 0.085 0.019 5 1.0 S_circular_insula_inf 1645 1139 2533 2.545 0.622 0.119 0.031 12 2.2 S_circular_insula_sup 962 672 1554 2.526 0.671 0.121 0.027 9 1.1 S_collat_transv_ant 245 164 245 1.884 0.406 0.152 0.048 3 0.5 S_collat_transv_post 1652 1124 2310 2.211 0.431 0.119 0.032 15 2.0 S_front_inf 990 672 1370 2.154 0.587 0.134 0.040 12 1.6 S_front_middle 2110 1452 3247 2.475 0.475 0.115 0.027 14 2.5 S_front_sup 325 243 439 2.410 0.546 0.134 0.026 2 0.5 S_interm_prim-Jensen 2347 1537 2883 1.997 0.479 0.113 0.026 18 2.4 S_intrapariet_and_P_trans 894 581 1263 2.420 0.460 0.149 0.051 12 1.7 S_oc_middle_and_Lunatus 1037 696 1176 1.861 0.420 0.102 0.022 5 1.0 S_oc_sup_and_transversal 406 295 635 2.214 0.304 0.116 0.025 3 0.4 S_occipital_ant 626 422 867 2.447 0.411 0.155 0.043 9 1.0 S_oc-temp_lat 1417 984 1966 2.179 0.623 0.120 0.031 11 1.7 S_oc-temp_med_and_Lingual 292 210 487 2.414 0.541 0.153 0.042 3 0.6 S_orbital_lateral 769 534 1270 2.600 0.760 0.143 0.078 13 1.8 S_orbital_med-olfact 874 604 1365 2.428 0.443 0.126 0.032 7 1.2 S_orbital-H_Shaped 1691 1133 1821 1.818 0.544 0.129 0.036 16 2.6 S_parieto_occipital 983 614 1400 3.001 0.987 0.155 0.092 24 3.6 S_pericallosal 2502 1659 3438 2.196 0.574 0.114 0.027 20 2.9 S_postcentral 1357 898 2100 2.529 0.473 0.116 0.028 10 1.7 S_precentral-inf-part 982 694 1422 2.334 0.475 0.103 0.020 5 0.9 S_precentral-sup-part 482 328 823 2.859 0.819 0.117 0.039 5 0.5 S_suborbital 856 574 1271 2.356 0.494 0.135 0.049 8 1.3 S_subparietal 1155 814 1805 2.557 0.532 0.124 0.027 8 1.5 S_temporal_inf 4229 2851 6288 2.304 0.556 0.107 0.027 29 4.7 S_temporal_sup 310 223 444 2.661 0.539 0.122 0.026 3 0.3 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Fri Jul 15 14:36:09 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0541: dt=0.001750, rms=0.369 (0.022%), neg=0, invalid=766 Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 = 2 (out of 220413: 0.000907) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 70: 1871 vertices, 2014 faces slice 80: 8130 vertices, 8403 faces slice 90: 17828 vertices, 18160 faces slice 100: 27899 vertices, 28237 faces slice 110: 37324 vertices, 37608 faces slice 120: 47308 vertices, 47645 faces slice 130: 56924 vertices, 57274 faces slice 140: 66296 vertices, 66633 faces slice 150: 75298 vertices, 75636 faces slice 160: 83910 vertices, 84223 faces slice 170: 90966 vertices, 91210 faces slice 180: 97108 vertices, 97315 faces slice 190: 102267 vertices, 102467 faces slice 200: 106187 vertices, 106301 faces slice 210: 107700 vertices, 107718 faces slice 220: 107700 vertices, 107718 faces slice 230: 107700 vertices, 107718 faces slice 240: 107700 vertices, 107718 faces slice 250: 107700 vertices, 107718 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... 107700 voxel in cpt #1: X=-18 [v=107700,e=323154,f=215436] located at (27.432730, -0.096760, 4.756945) For the whole surface: X=-18 [v=107700,e=323154,f=215436] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Jul 15 14:36:42 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Fri Jul 15 14:36:50 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts avg radius = 42.8 mm, total surface area = 57540 mm^2 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0542: dt=0.001750, rms=0.369 (0.022%), neg=0, invalid=766 0543: dt=0.001750, rms=0.369 (0.027%), neg=0, invalid=766 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.7 minutes Not saving sulc step 000: RMS=0.096 (target=0.015) step 005: RMS=0.070 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (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 rh Fri Jul 15 14:38:35 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... 0544: dt=0.001750, rms=0.369 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0545: dt=0.001750, rms=0.369 (0.029%), neg=0, invalid=766 0546: dt=0.001750, rms=0.369 (0.034%), neg=0, invalid=766 0547: dt=0.001750, rms=0.369 (0.031%), neg=0, invalid=766 0548: dt=0.001750, rms=0.368 (0.034%), neg=0, invalid=766 surface projected - minimizing metric distortion... vertex spacing 1.12 +- 0.60 (0.00-->6.52) (max @ vno 49973 --> 50874) face area 0.03 +- 0.04 (-0.33-->0.80) 0549: dt=0.001750, rms=0.368 (0.036%), neg=0, invalid=766 0550: dt=0.001750, rms=0.368 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 206569.938 ms iter 0, gcam->neg = 32 after 19 iterations, nbhd size=2, neg = 0 0551: dt=0.064000, rms=0.368 (0.128%), neg=0, invalid=766 scaling brain by 0.361... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.839, avgs=0 005/300: dt: 0.9000, rms radial error=175.580, avgs=0 010/300: dt: 0.9000, rms radial error=175.025, avgs=0 015/300: dt: 0.9000, rms radial error=174.295, avgs=0 020/300: dt: 0.9000, rms radial error=173.464, avgs=0 025/300: dt: 0.9000, rms radial error=172.577, avgs=0 030/300: dt: 0.9000, rms radial error=171.663, avgs=0 035/300: dt: 0.9000, rms radial error=170.732, avgs=0 040/300: dt: 0.9000, rms radial error=169.794, avgs=0 045/300: dt: 0.9000, rms radial error=168.853, avgs=0 050/300: dt: 0.9000, rms radial error=167.914, avgs=0 055/300: dt: 0.9000, rms radial error=166.977, avgs=0 060/300: dt: 0.9000, rms radial error=166.043, avgs=0 065/300: dt: 0.9000, rms radial error=165.114, avgs=0 070/300: dt: 0.9000, rms radial error=164.189, avgs=0 075/300: dt: 0.9000, rms radial error=163.269, avgs=0 080/300: dt: 0.9000, rms radial error=162.353, avgs=0 085/300: dt: 0.9000, rms radial error=161.442, avgs=0 090/300: dt: 0.9000, rms radial error=160.536, avgs=0 095/300: dt: 0.9000, rms radial error=159.635, avgs=0 100/300: dt: 0.9000, rms radial error=158.739, avgs=0 105/300: dt: 0.9000, rms radial error=157.848, avgs=0 110/300: dt: 0.9000, rms radial error=156.962, avgs=0 115/300: dt: 0.9000, rms radial error=156.081, avgs=0 120/300: dt: 0.9000, rms radial error=155.204, avgs=0 125/300: dt: 0.9000, rms radial error=154.333, avgs=0 130/300: dt: 0.9000, rms radial error=153.466, avgs=0 135/300: dt: 0.9000, rms radial error=152.604, avgs=0 140/300: dt: 0.9000, rms radial error=151.747, avgs=0 145/300: dt: 0.9000, rms radial error=150.895, avgs=0 150/300: dt: 0.9000, rms radial error=150.048, avgs=0 155/300: dt: 0.9000, rms radial error=149.204, avgs=0 160/300: dt: 0.9000, rms radial error=148.366, avgs=0 165/300: dt: 0.9000, rms radial error=147.532, avgs=0 170/300: dt: 0.9000, rms radial error=146.703, avgs=0 175/300: dt: 0.9000, rms radial error=145.878, avgs=0 180/300: dt: 0.9000, rms radial error=145.058, avgs=0 185/300: dt: 0.9000, rms radial error=144.242, avgs=0 190/300: dt: 0.9000, rms radial error=143.431, avgs=0 195/300: dt: 0.9000, rms radial error=142.624, avgs=0 200/300: dt: 0.9000, rms radial error=141.821, avgs=0 205/300: dt: 0.9000, rms radial error=141.023, avgs=0 210/300: dt: 0.9000, rms radial error=140.230, avgs=0 215/300: dt: 0.9000, rms radial error=139.440, avgs=0 220/300: dt: 0.9000, rms radial error=138.655, avgs=0 225/300: dt: 0.9000, rms radial error=137.875, avgs=0 230/300: dt: 0.9000, rms radial error=137.098, avgs=0 235/300: dt: 0.9000, rms radial error=136.326, avgs=0 240/300: dt: 0.9000, rms radial error=135.558, avgs=0 245/300: dt: 0.9000, rms radial error=134.795, avgs=0 250/300: dt: 0.9000, rms radial error=134.035, avgs=0 255/300: dt: 0.9000, rms radial error=133.280, avgs=0 260/300: dt: 0.9000, rms radial error=132.530, avgs=0 265/300: dt: 0.9000, rms radial error=131.783, avgs=0 270/300: dt: 0.9000, rms radial error=131.040, avgs=0 275/300: dt: 0.9000, rms radial error=130.302, avgs=0 280/300: dt: 0.9000, rms radial error=129.568, avgs=0 285/300: dt: 0.9000, rms radial error=128.838, avgs=0 290/300: dt: 0.9000, rms radial error=128.112, avgs=0 295/300: dt: 0.9000, rms radial error=127.390, avgs=0 300/300: dt: 0.9000, rms radial error=126.672, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11866.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 1750.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 142.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/12 = 0.01110 epoch 4 (K=640.0), pass 1, starting sse = 6.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/15 = 0.01283 final dwriting spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.22 hours istance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Jul 15 14:52:01 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 CA149base 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-18 (nv=107700, nf=215436, ne=323154, g=10) 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 5 iterations marking ambiguous vertices... 1589 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 5 -merging segment 17 into 5 19 defects to be corrected 0 vertices coincident reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7448 (-4.3724) -vertex loglikelihood: -5.7542 (-2.8771) -normal dot loglikelihood: -3.6713 (-3.6713) -quad curv loglikelihood: -6.4561 (-3.2281) Total Loglikelihood : -24.6264 CORRECTING DEFECT 0 (vertices=200, convex hull=217) gcamFindOptimalTimeStep: Complete in 232095.828 ms 0552: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.368, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 242358.125 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0553: dt=0.003000, rms=0.368 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 263451.688 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0554: dt=0.004000, rms=0.368 (0.008%), neg=0, invalid=766 After retessellation of defect 0, euler #=-18 (106686,319664,212960) : difference with theory (-16) = 2 CORRECTING DEFECT 1 (vertices=14, convex hull=29) iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0555: dt=0.004000, rms=0.368 (0.012%), neg=0, invalid=766 0556: dt=0.004000, rms=0.368 (0.019%), neg=0, invalid=766 After retessellation of defect 1, euler #=-17 (106691,319688,212980) : difference with theory (-15) = 2 CORRECTING DEFECT 2 (vertices=55, convex hull=46) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0557: dt=0.004000, rms=0.367 (0.027%), neg=0, invalid=766 0558: dt=0.004000, rms=0.367 (0.038%), neg=0, invalid=766 After retessellation of defect 2, euler #=-16 (106701,319735,213018) : difference with theory (-14) = 2 CORRECTING DEFECT 3 (vertices=67, convex hull=100) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0559: dt=0.004000, rms=0.367 (0.042%), neg=0, invalid=766 After retessellation of defect 3, euler #=-15 (106742,319903,213146) : difference with theory (-13) = 2 CORRECTING DEFECT 4 (vertices=8, convex hull=19) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0560: dt=0.004000, rms=0.367 (0.048%), neg=0, invalid=766 After retessellation of defect 4, euler #=-14 (106746,319920,213160) : difference with theory (-12) = 2 CORRECTING DEFECT 5 (vertices=291, convex hull=221) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0561: dt=0.004000, rms=0.367 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0562: dt=0.004000, rms=0.367 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0563: dt=0.004000, rms=0.366 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 17 iterations, nbhd size=2, neg = 0 0564: dt=0.004000, rms=0.366 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0565: dt=0.004000, rms=0.366 (0.065%), neg=0, invalid=766 After retessellation of defect 5, euler #=-11 (106835,320299,213453) : difference with theory (-11) = 0 CORRECTING DEFECT 6 (vertices=9, convex hull=29) iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0566: dt=0.004000, rms=0.366 (0.061%), neg=0, invalid=766 Warning - incorrect dp selected!!!!(-84.030656 >= -84.030663 ) After retessellation of defect 6, euler #=-10 (106837,320313,213466) : difference with theory (-10) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=76) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 After retessellation of defect 7, euler #=-9 (106850,320378,213519) : difference with theory (-9) = 0 CORRECTING DEFECT 8 (vertices=30, convex hull=54) After retessellation of defect 8, euler #=-8 (106867,320448,213573) : difference with theory (-8) = 0 CORRECTING DEFECT 9 (vertices=14, convex hull=21) After retessellation of defect 9, euler #=-7 (106869,320461,213585) : difference with theory (-7) = 0 CORRECTING DEFECT 10 (vertices=42, convex hull=76) After retessellation of defect 10, euler #=-6 (106878,320516,213632) : difference with theory (-6) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=23) After retessellation of defect 11, euler #=-5 (106880,320528,213643) : difference with theory (-5) = 0 CORRECTING DEFECT 12 (vertices=26, convex hull=22) gcamFindOptimalTimeStep: Complete in 202143.156 ms iter 0, gcam->neg = 17 after 43 iterations, nbhd size=4, neg = 0 0567: dt=4.800000, rms=0.366 (-0.133%), neg=0, invalid=766 After retessellation of defect 12, euler #=-4 (106884,320546,213658) : difference with theory (-4) = 0 CORRECTING DEFECT 13 (vertices=34, convex hull=54) blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.366, neg=0, invalid=766 After retessellation of defect 13, euler #=-3 (106895,320599,213701) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=11, convex hull=23) After retessellation of defect 14, euler #=-2 (106896,320608,213710) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=114, convex hull=63) After retessellation of defect 15, euler #=-1 (106906,320664,213757) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=10, convex hull=25) After retessellation of defect 16, euler #=0 (106908,320677,213769) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=32, convex hull=65) After retessellation of defect 17, euler #=1 (106928,320763,213836) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=28, convex hull=40) After retessellation of defect 18, euler #=2 (106934,320796,213864) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.07-->8.34) (max @ vno 39919 --> 46904) 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 (0.07-->8.34) (max @ vno 39919 --> 46904) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 90 mutations (35.9%), 161 crossovers (64.1%), 102 vertices were eliminated building final representation... 766 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=106934, nf=213864, ne=320796, g=0) writing corrected surface to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 41.7 minutes 0 defective edges removing intersecting faces 000: 140 intersecting 001: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 106934 - 320796 + 213864 = 2 --> 0 holes F =2V-4: 213864 = 213868-4 (0) 2E=3F: 641592 = 641592 (0) total defect index = 0 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Jul 15 15:33:58 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... gcamFindOptimalTimeStep: Complete in 175183.781 ms iter 0, gcam->neg = 51 after 52 iterations, nbhd size=1, neg = 0 0568: dt=9.600000, rms=0.366 (0.106%), neg=0, invalid=766 reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7076 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.2 +- 6.4 [70.0 --> 110.0] GM (86.0) : 83.9 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 108.4 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.4 (was 40) setting MAX_GRAY to 95.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->4.63) (max @ vno 39919 --> 46904) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.82 +- 1.04 2997 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=76 using class modes intead of means.... mean inside = 94.8, mean outside = 81.0 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 3 vertex label from ripped group mean border=85.1, 49 (49) missing vertices, mean dist 0.2 [0.8 (%38.1)->0.8 (%61.9))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.24) (max @ vno 50644 --> 106680) face area 0.28 +- 0.13 (0.00-->3.20) mean absolute distance = 0.44 +- 0.83 2892 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3107924.5, rms=8.09 001: dt: 0.5000, sse=3630637.8, rms=5.65 002: dt: 0.5000, sse=3785014.8, rms=4.09 003: dt: 0.5000, sse=3954610.8, rms=3.14 004: dt: 0.5000, sse=4050235.0, rms=2.60 005: dt: 0.5000, sse=4133877.8, rms=2.32 006: dt: 0.5000, sse=4147756.8, rms=2.20 007: dt: 0.5000, sse=4173903.2, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4171583.5, rms=2.11 009: dt: 0.2500, sse=2615376.5, rms=1.48 010: dt: 0.2500, sse=2460308.8, rms=1.39 rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2415770.5, rms=1.37 rms = 1.35, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2391620.2, rms=1.35 positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.9, 26 (6) missing vertices, mean dist -0.2 [0.5 (%62.3)->0.3 (%37.7))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.10-->4.51) (max @ vno 50644 --> 106680) face area 0.35 +- 0.16 (0.00-->4.20) mean absolute distance = 0.37 +- 0.52 3119 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2687874.8, rms=3.58 013: dt: 0.5000, sse=2909154.8, rms=2.21 014: dt: 0.5000, sse=3126316.5, rms=1.79 015: dt: 0.5000, sse=3189664.5, rms=1.62 rms = 1.63, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=2785005.8, rms=1.38 017: dt: 0.2500, sse=2623047.8, rms=1.23 rms = 1.20, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=2577220.5, rms=1.20 rms = 1.18, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=2554407.2, rms=1.18 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.3, 23 (3) missing vertices, mean dist -0.2 [0.4 (%69.5)->0.2 (%30.5))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->4.69) (max @ vno 50644 --> 106680) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.28 +- 0.37 2959 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2756407.2, rms=3.44 020: dt: 0.5000, sse=2932529.0, rms=1.92 021: dt: 0.5000, sse=3065163.0, rms=1.58 022: dt: 0.5000, sse=3159964.5, rms=1.44 rms = 1.56, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=2852330.5, rms=1.20 024: dt: 0.2500, sse=2745482.5, rms=1.11 rms = 1.11, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=2706253.0, rms=1.11 rms = 1.10, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2690933.0, rms=1.10 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.3, 24 (2) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=2719204.8, rms=1.78 027: dt: 0.5000, sse=3232179.5, rms=1.12 rms = 1.27, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3026501.5, rms=0.96 rms = 0.92, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=2920557.5, rms=0.92 rms = 0.91, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=2928191.0, rms=0.91 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 2164 vertices erasing segment 1 (vno[0] = 45802) erasing segment 2 (vno[0] = 47859) erasing segment 3 (vno[0] = 70186) erasing segment 4 (vno[0] = 70208) erasing segment 5 (vno[0] = 74423) erasing segment 6 (vno[0] = 76328) erasing segment 7 (vno[0] = 76904) erasing segment 8 (vno[0] = 77804) erasing segment 9 (vno[0] = 79413) erasing segment 10 (vno[0] = 80271) erasing segment 11 (vno[0] = 82670) erasing segment 12 (vno[0] = 85006) writing cortex label to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.cortex.label... LabelWrite: saving to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.cortex.label writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.curv writing smoothed area to rh.area writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->4.76) (max @ vno 50644 --> 106680) face area 0.33 +- 0.16 (0.00-->4.37) refinement took 12.8 minutes #-------------------------------------------- #@# Smooth2 rh Fri Jul 15 15:46:47 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Fri Jul 15 15:46:57 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 43.0 mm, total surface area = 64828 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 1.8 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 229 vertices thresholded to be in k1 ~ [-0.24 0.41], k2 ~ [-0.14 0.06] total integrated curvature = 0.613*4pi (7.698) --> 0 handles ICI = 1.4, FI = 7.2, variation=129.049 148 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 138 vertices thresholded to be in [-0.15 0.19] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Fri Jul 15 15:51:06 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm CA149base 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 [ CA149base/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 [ 196 ] Gb_filter = 0 WARN: S lookup min: -1.023468 WARN: S explicit min: 0.000000 vertex = 487 #-------------------------------------------- #@# Sphere rh Fri Jul 15 15:51:23 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... gcamFindOptimalTimeStep: Complete in 179866.016 ms iter 0, gcam->neg = 39 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 97492.398 ms iter 1, dt=0.000000: new neg 5, old_neg 5, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0569: dt=6.400000, rms=0.366 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.366, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 165196.922 ms iter 0, gcam->neg = 43 after 64 iterations, nbhd size=2, neg = 0 0570: dt=0.720000, rms=0.365 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 182821.781 ms iter 0, gcam->neg = 35 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 69552.078 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0571: dt=0.720000, rms=0.365 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 157520.016 ms iter 0, gcam->neg = 37 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 89668.883 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0572: dt=1.008000, rms=0.365 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 192152.391 ms iter 0, gcam->neg = 34 after 61 iterations, nbhd size=3, neg = 0 0573: dt=0.246575, rms=0.365 (0.116%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 165179.688 ms iter 0, gcam->neg = 10 after 41 iterations, nbhd size=2, neg = 0 0574: dt=0.079880, rms=0.365 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 23 iterations, nbhd size=3, neg = 0 0575: dt=0.079880, rms=0.365 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 37 iterations, nbhd size=4, neg = 0 0576: dt=0.079880, rms=0.365 (0.064%), neg=0, invalid=766 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.43 hours scaling brain by 0.338... pass 1: epoch 1 of 3 starting distance error %40.13 pass 1: epoch 2 of 3 starting distance error %18.68 unfolding complete - removing small folds... starting distance error %18.63 removing remaining folds... final distance error %18.65 #-------------------------------------------- #@# Surf Reg rh Fri Jul 15 17:17:05 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_register -curv ../surf/rh.sphere /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif... iter 0, gcam->neg = 21 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 92471.734 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0577: dt=0.079880, rms=0.365 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.365, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 196638.281 ms iter 0, gcam->neg = 23 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 86618.297 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0578: dt=0.230769, rms=0.365 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.364, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 254529.688 ms 0579: dt=0.000109, rms=0.364 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 210250.609 ms iter 0, gcam->neg = 73 after 30 iterations, nbhd size=3, neg = 0 0580: dt=0.075252, rms=0.363 (0.260%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 206520.328 ms iter 0, gcam->neg = 2 after 15 iterations, nbhd size=2, neg = 0 0581: dt=0.005001, rms=0.363 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0582: dt=0.005001, rms=0.363 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0583: dt=0.005001, rms=0.363 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=2, neg = 0 0584: dt=0.005001, rms=0.363 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 35 iterations, nbhd size=1, neg = 0 0585: dt=0.005001, rms=0.363 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 20 iterations, nbhd size=3, neg = 0 0586: dt=0.005001, rms=0.363 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 16 iterations, nbhd size=2, neg = 0 0587: dt=0.005001, rms=0.362 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0588: dt=0.005001, rms=0.362 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 26 iterations, nbhd size=3, neg = 0 0589: dt=0.005001, rms=0.362 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0590: dt=0.005001, rms=0.362 (0.074%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 60 iterations, nbhd size=1, neg = 0 0591: dt=0.005001, rms=0.361 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 36 iterations, nbhd size=4, neg = 0 0592: dt=0.005001, rms=0.361 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 177745.828 ms 0593: dt=0.001750, rms=0.361 (0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.361, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 153797.125 ms 0594: dt=0.001500, rms=0.361 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 161808.719 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0595: dt=0.001000, rms=0.361 (0.003%), neg=0, invalid=766 0596: dt=0.001000, rms=0.361 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0597: dt=0.001000, rms=0.361 (0.005%), neg=0, invalid=766 writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.610 curvature mean = 0.024, std = 0.941 curvature mean = 0.018, std = 0.889 curvature mean = 0.009, std = 0.970 curvature mean = 0.006, std = 0.957 curvature mean = 0.007, std = 0.983 curvature mean = 0.002, std = 0.982 curvature mean = 0.007, std = 0.986 curvature mean = 0.000, std = 0.993 curvature mean = -0.027, std = 0.270 curvature mean = 0.004, std = 0.072 curvature mean = 0.048, std = 0.406 curvature mean = 0.004, std = 0.087 curvature mean = 0.017, std = 0.603 curvature mean = 0.004, std = 0.094 curvature mean = 0.008, std = 0.736 curvature mean = 0.004, std = 0.097 curvature mean = 0.002, std = 0.823 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri Jul 15 18:54:05 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri Jul 15 18:54:09 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mrisp_paint -a 5 /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Jul 15 18:54:14 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base rh ../surf/rh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 806 labels changed using aseg relabeling using gibbs priors... 000: 2468 changed, 106934 examined... 001: 535 changed, 10543 examined... 002: 129 changed, 3065 examined... 003: 64 changed, 777 examined... 004: 33 changed, 353 examined... 005: 9 changed, 186 examined... 006: 2 changed, 56 examined... 007: 0 changed, 12 examined... 168 labels changed using aseg 000: 80 total segments, 38 labels (194 vertices) changed 001: 43 total segments, 1 labels (1 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1117 vertices marked for relabeling... 1117 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 59 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Jul 15 18:56:14 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7076 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.2 +- 6.4 [70.0 --> 110.0] GM (86.0) : 83.9 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 108.4 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.4 (was 40) setting MAX_GRAY to 95.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=76 using class modes intead of means.... mean inside = 94.8, mean outside = 81.0 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->4.63) (max @ vno 39919 --> 46904) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.83 +- 1.04 3048 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 276 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 16 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=85.1, 50 (50) missing vertices, mean dist 0.2 [0.8 (%38.1)->0.8 (%61.9))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.24) (max @ vno 50644 --> 106680) face area 0.28 +- 0.13 (0.00-->3.20) mean absolute distance = 0.45 +- 0.84 2978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3114665.8, rms=8.09 001: dt: 0.5000, sse=3643488.5, rms=5.65 002: dt: 0.5000, sse=3796720.0, rms=4.09 003: dt: 0.5000, sse=3967666.5, rms=3.14 004: dt: 0.5000, sse=4062164.0, rms=2.60 005: dt: 0.5000, sse=4145953.8, rms=2.33 006: dt: 0.5000, sse=4160315.5, rms=2.20 007: dt: 0.5000, sse=4187330.8, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4184699.5, rms=2.11 009: dt: 0.2500, sse=2628285.5, rms=1.49 010: dt: 0.2500, sse=2473458.2, rms=1.39 rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2427971.8, rms=1.37 rms = 1.36, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2403428.5, rms=1.36 positioning took 2.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 256 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 22 points - only 0.00% unknown deleting segment 8 with 5 points - only 40.00% unknown deleting segment 9 with 148 points - only 52.03% unknown deleting segment 10 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=86.9, 58 (10) missing vertices, mean dist -0.2 [0.5 (%62.2)->0.3 (%37.8))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.10-->4.51) (max @ vno 50644 --> 106680) face area 0.35 +- 0.16 (0.00-->4.20) mean absolute distance = 0.37 +- 0.53 3210 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2725737.2, rms=3.59 013: dt: 0.5000, sse=2950717.8, rms=2.23 014: dt: 0.5000, sse=3172502.5, rms=1.80 015: dt: 0.5000, sse=3233262.5, rms=1.64 rms = 1.64, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=2826750.2, rms=1.39 017: dt: 0.2500, sse=2662212.2, rms=1.25 rms = 1.21, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=2615277.8, rms=1.21 rms = 1.20, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=2593846.0, rms=1.20 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 271 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 148 points - only 52.03% unknown deleting segment 6 with 23 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown mean border=89.3, 63 (4) missing vertices, mean dist -0.2 [0.4 (%69.4)->0.2 (%30.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 88847.758 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0598: dt=0.001000, rms=0.361 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.361, neg=0, invalid=766 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->4.69) (max @ vno 50644 --> 106680) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.28 +- 0.38 3032 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2795367.5, rms=3.44 020: dt: 0.5000, sse=2977493.8, rms=1.93 021: dt: 0.5000, sse=3109108.0, rms=1.59 022: dt: 0.5000, sse=3204135.2, rms=1.45 rms = 1.57, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=2894840.5, rms=1.21 024: dt: 0.2500, sse=2783224.5, rms=1.12 rms = 1.12, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=2745561.2, rms=1.12 rms = 1.11, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2732740.8, rms=1.11 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 276 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 148 points - only 52.03% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 20 points - only 0.00% unknown mean border=90.3, 86 (4) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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=2760861.0, rms=1.79 027: dt: 0.5000, sse=3287606.0, rms=1.13 rms = 1.28, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3076529.0, rms=0.97 rms = 0.93, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=2968223.2, rms=0.93 rms = 0.92, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=2976160.8, rms=0.92 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 11 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=64.9, 50 (50) missing vertices, mean dist 1.9 [3.0 (%0.0)->2.5 (%100.0))] %30 local maxima, %42 large gradients and %23 min vals, 997 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 gcamFindOptimalTimeStep: Complete in 198382.672 ms iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0599: dt=0.007000, rms=0.361 (0.024%), neg=0, invalid=766 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=16037579.0, rms=26.29 001: dt: 0.5000, sse=13046465.0, rms=23.37 002: dt: 0.5000, sse=10645415.0, rms=20.75 003: dt: 0.5000, sse=8822790.0, rms=18.43 004: dt: 0.5000, sse=7517294.5, rms=16.35 005: dt: 0.5000, sse=6534155.0, rms=14.47 006: dt: 0.5000, sse=5825918.0, rms=12.76 007: dt: 0.5000, sse=5300459.0, rms=11.15 008: dt: 0.5000, sse=4891596.5, rms=9.61 009: dt: 0.5000, sse=4606775.0, rms=8.13 010: dt: 0.5000, sse=4413434.0, rms=6.78 011: dt: 0.5000, sse=4355875.5, rms=5.64 012: dt: 0.5000, sse=4382588.0, rms=4.80 013: dt: 0.5000, sse=4416144.5, rms=4.25 014: dt: 0.5000, sse=4470795.5, rms=3.92 015: dt: 0.5000, sse=4511492.0, rms=3.72 016: dt: 0.5000, sse=4529339.5, rms=3.60 017: dt: 0.5000, sse=4553112.5, rms=3.51 018: dt: 0.5000, sse=4535463.0, rms=3.46 rms = 3.41, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=4564102.5, rms=3.41 020: dt: 0.2500, sse=2910253.8, rms=2.48 021: dt: 0.2500, sse=2732364.2, rms=2.22 022: dt: 0.2500, sse=2644788.0, rms=2.16 rms = 2.14, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2628345.8, rms=2.14 024: dt: 0.1250, sse=2525277.0, rms=2.04 rms = 2.04, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=2510971.2, rms=2.04 positioning took 5.7 minutes mean border=62.1, 542 (10) missing vertices, mean dist 0.2 [0.2 (%37.0)->0.4 (%63.0))] %49 local maxima, %30 large gradients and %16 min vals, 402 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 gcamFindOptimalTimeStep: Complete in 235555.094 ms iter 0, gcam->neg = 13 after 6 iterations, nbhd size=1, neg = 0 0600: dt=0.020000, rms=0.361 (0.067%), neg=0, invalid=766 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3039729.0, rms=4.77 026: dt: 0.5000, sse=3121807.0, rms=3.38 rms = 3.35, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=3819025.8, rms=3.35 028: dt: 0.2500, sse=2958818.8, rms=2.29 029: dt: 0.2500, sse=2914342.0, rms=2.05 030: dt: 0.2500, sse=2862978.8, rms=1.99 rms = 1.96, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2863831.0, rms=1.96 032: dt: 0.1250, sse=2769067.2, rms=1.87 rms = 1.86, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=2760932.5, rms=1.86 positioning took 1.7 minutes mean border=60.6, 742 (8) missing vertices, mean dist 0.1 [0.2 (%36.3)->0.3 (%63.7))] %63 local maxima, %16 large gradients and %16 min vals, 392 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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=2869268.0, rms=2.87 rms = 3.03, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=2766254.5, rms=2.29 035: dt: 0.2500, sse=2758365.2, rms=1.94 036: dt: 0.2500, sse=2817030.5, rms=1.85 rms = 1.82, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=2834974.0, rms=1.82 038: dt: 0.1250, sse=2779596.2, rms=1.77 rms = 1.76, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=2776151.0, rms=1.76 positioning took 1.4 minutes mean border=59.8, 1461 (7) missing vertices, mean dist 0.0 [0.2 (%43.5)->0.2 (%56.5))] %67 local maxima, %12 large gradients and %15 min vals, 377 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=2795401.0, rms=2.03 rms = 2.48, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=2745235.8, rms=1.81 041: dt: 0.2500, sse=2806928.0, rms=1.75 rms = 1.72, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=2841260.0, rms=1.72 rms = 1.68, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=2797050.8, rms=1.68 positioning took 1.0 minutes writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.area.pial vertex spacing 0.98 +- 0.39 (0.09-->8.45) (max @ vno 72733 --> 71888) face area 0.38 +- 0.28 (0.00-->6.96) measuring cortical thickness... gcamFindOptimalTimeStep: Complete in 208485.781 ms iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0601: dt=0.012000, rms=0.361 (0.039%), neg=0, invalid=766 writing cortical thickness estimate to 'thickness' file. 0 of 106934 vertices processed 25000 of 106934 vertices processed 50000 of 106934 vertices processed 75000 of 106934 vertices processed 100000 of 106934 vertices processed 0 of 106934 vertices processed 25000 of 106934 vertices processed 50000 of 106934 vertices processed 75000 of 106934 vertices processed 100000 of 106934 vertices processed thickness calculation complete, 1162:666 truncations. 52016 vertices at 0 distance 66434 vertices at 1 distance 50234 vertices at 2 distance 21136 vertices at 3 distance 8459 vertices at 4 distance 3346 vertices at 5 distance 1459 vertices at 6 distance 593 vertices at 7 distance 295 vertices at 8 distance 187 vertices at 9 distance 105 vertices at 10 distance 58 vertices at 11 distance 49 vertices at 12 distance 44 vertices at 13 distance 35 vertices at 14 distance 41 vertices at 15 distance 25 vertices at 16 distance 18 vertices at 17 distance 9 vertices at 18 distance 8 vertices at 19 distance 11 vertices at 20 distance writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.thickness positioning took 23.5 minutes #-------------------------------------------- #@# Surf Volume rh Fri Jul 15 19:19:48 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 ] #----------------------------------------- #@# Parcellation Stats rh Fri Jul 15 19:19:50 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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) 0602: dt=0.012000, rms=0.360 (0.037%), neg=0, invalid=766 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 1027 724 1648 2.335 0.375 0.101 0.021 6 0.9 bankssts 941 599 1946 3.103 0.577 0.144 0.038 16 1.5 caudalanteriorcingulate 2337 1598 4543 2.574 0.513 0.118 0.032 20 3.2 caudalmiddlefrontal 1960 1260 2239 1.740 0.488 0.158 0.051 31 4.4 cuneus 330 231 1332 3.788 0.767 0.092 0.024 2 0.3 entorhinal 3286 2221 6459 2.751 0.757 0.145 0.044 43 5.9 fusiform 6138 4147 11144 2.474 0.690 0.140 0.045 85 11.2 inferiorparietal 3548 2461 9025 3.203 0.778 0.162 0.081 77 14.3 inferiortemporal 1059 689 1788 2.533 0.720 0.141 0.047 16 1.9 isthmuscingulate 5831 3724 8719 2.151 0.603 0.145 0.046 72 11.1 lateraloccipital 2869 1925 5852 2.821 0.565 0.145 0.049 41 5.6 lateralorbitofrontal 3935 2613 4717 1.799 0.555 0.152 0.053 59 9.1 lingual 2196 1461 3916 2.484 0.652 0.152 0.077 63 5.7 medialorbitofrontal 3586 2474 8686 3.094 0.697 0.135 0.042 43 6.0 middletemporal 835 569 1866 2.850 0.744 0.111 0.031 7 1.1 parahippocampal 1862 1113 2664 2.256 0.615 0.098 0.022 14 1.8 paracentral 1574 1098 2989 2.499 0.475 0.118 0.032 13 2.0 parsopercularis 937 634 2287 3.035 0.626 0.152 0.055 13 2.0 parsorbitalis 1804 1195 3325 2.553 0.588 0.137 0.038 21 3.0 parstriangularis 1715 1131 1482 1.413 0.384 0.152 0.058 32 4.0 pericalcarine 5462 3374 7133 1.903 0.603 0.118 0.037 59 9.0 postcentral 1348 923 2439 2.604 0.611 0.150 0.048 21 2.6 posteriorcingulate 6138 3801 10230 2.472 0.605 0.112 0.033 65 9.4 precentral 4480 2942 7073 2.279 0.586 0.139 0.046 55 7.9 precuneus 924 589 2113 3.335 0.688 0.143 0.067 20 2.5 rostralanteriorcingulate 6301 4253 11271 2.378 0.640 0.157 0.057 104 14.0 rostralmiddlefrontal 7989 5338 16246 2.717 0.566 0.137 0.041 98 13.4 superiorfrontal 6530 4135 9611 2.118 0.533 0.125 0.038 76 10.0 superiorparietal 4111 2750 8957 2.813 0.669 0.113 0.029 35 4.8 superiortemporal 4213 2791 7334 2.441 0.565 0.135 0.037 51 6.5 supramarginal 402 268 997 2.818 0.592 0.198 0.085 9 1.3 frontalpole 595 416 2297 3.968 0.533 0.159 0.069 9 1.7 temporalpole 512 276 614 2.057 0.435 0.122 0.036 5 0.7 transversetemporal 3106 2021 6480 3.183 0.856 0.128 0.101 87 9.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Jul 15 19:20:33 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base rh ../surf/rh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 17 labels changed using aseg relabeling using gibbs priors... 000: 7647 changed, 106934 examined... 001: 1777 changed, 29234 examined... 002: 540 changed, 9027 examined... 003: 229 changed, 2913 examined... 004: 119 changed, 1352 examined... 005: 40 changed, 650 examined... 006: 20 changed, 239 examined... 007: 13 changed, 102 examined... 008: 7 changed, 68 examined... 009: 5 changed, 42 examined... 010: 2 changed, 25 examined... 011: 0 changed, 15 examined... 14 labels changed using aseg 000: 232 total segments, 150 labels (1678 vertices) changed 001: 94 total segments, 13 labels (94 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 100 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 696 vertices marked for relabeling... 696 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 2 minutes and 15 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Jul 15 19:22:50 EDT 2016 iter 0, gcam->neg = 8 after 28 iterations, nbhd size=4, neg = 0 0603: dt=0.012000, rms=0.360 (0.069%), neg=0, invalid=766 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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) iter 0, gcam->neg = 20 after 8 iterations, nbhd size=1, neg = 0 0604: dt=0.012000, rms=0.360 (0.096%), neg=0, invalid=766 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 954 645 1964 2.670 0.764 0.179 0.069 19 2.7 G_and_S_frontomargin 955 642 1762 2.548 0.656 0.157 0.051 12 2.0 G_and_S_occipital_inf 1290 743 1892 2.150 0.555 0.106 0.048 26 3.4 G_and_S_paracentral 1000 643 1882 2.592 0.560 0.148 0.058 18 2.8 G_and_S_subcentral 1192 775 2530 2.545 0.634 0.170 0.064 23 3.3 G_and_S_transv_frontopol 2348 1560 4284 2.733 0.754 0.133 0.044 31 4.1 G_and_S_cingul-Ant 1159 796 2330 2.803 0.549 0.126 0.035 14 1.7 G_and_S_cingul-Mid-Ant 1048 726 1763 2.424 0.542 0.127 0.032 10 1.4 G_and_S_cingul-Mid-Post 408 257 956 2.974 0.301 0.182 0.065 10 1.1 G_cingul-Post-dorsal 190 120 402 2.724 0.678 0.165 0.082 4 0.5 G_cingul-Post-ventral 1761 1138 1974 1.686 0.523 0.162 0.055 33 4.2 G_cuneus 1054 707 2354 2.584 0.418 0.136 0.041 13 1.8 G_front_inf-Opercular 363 229 884 2.932 0.442 0.145 0.052 5 0.8 G_front_inf-Orbital 913 603 2039 2.737 0.428 0.158 0.050 14 2.0 G_front_inf-Triangul 2528 1720 5477 2.571 0.483 0.153 0.056 42 5.6 G_front_middle 5497 3480 12083 2.829 0.550 0.151 0.052 95 12.2 G_front_sup 437 272 994 3.601 0.575 0.116 0.060 6 0.8 G_Ins_lg_and_S_cent_ins 555 336 1698 3.435 0.926 0.175 0.137 23 3.0 G_insular_short 1832 1176 3655 2.718 0.703 0.164 0.063 32 4.5 G_occipital_middle 1676 1008 2491 2.107 0.476 0.129 0.044 21 3.1 G_occipital_sup 1263 828 2580 2.551 0.608 0.154 0.052 19 2.7 G_oc-temp_lat-fusifor 2686 1737 3482 1.839 0.572 0.158 0.058 46 6.7 G_oc-temp_med-Lingual 1055 698 3130 3.440 0.678 0.120 0.146 45 2.5 G_oc-temp_med-Parahip 2137 1418 5433 3.044 0.559 0.162 0.067 39 5.7 G_orbital 2405 1598 5205 2.664 0.564 0.167 0.061 49 6.0 G_pariet_inf-Angular 2220 1450 4922 2.762 0.484 0.149 0.043 35 3.9 G_pariet_inf-Supramar 1879 1164 3445 2.396 0.517 0.141 0.048 30 3.5 G_parietal_sup 2108 1165 2939 2.047 0.438 0.121 0.040 26 3.8 G_postcentral 2498 1375 4969 2.728 0.516 0.105 0.030 22 3.1 G_precentral 1987 1271 3900 2.425 0.494 0.153 0.061 33 4.5 G_precuneus 683 447 1499 2.511 0.601 0.147 0.051 12 1.3 G_rectus 274 194 523 2.899 0.869 0.214 0.277 30 1.4 G_subcallosal 377 185 525 2.205 0.490 0.116 0.035 4 0.5 G_temp_sup-G_T_transv 1307 858 3737 3.083 0.526 0.143 0.045 19 2.2 G_temp_sup-Lateral 651 463 1653 3.393 0.658 0.097 0.024 3 0.6 G_temp_sup-Plan_polar 547 354 860 2.223 0.406 0.110 0.032 5 0.8 G_temp_sup-Plan_tempo 2132 1456 6025 3.223 0.739 0.181 0.113 64 12.1 G_temporal_inf 2310 1565 6420 3.200 0.665 0.152 0.053 36 5.0 G_temporal_middle 398 258 507 2.006 0.533 0.095 0.015 2 0.3 Lat_Fis-ant-Horizont 181 124 224 2.088 0.455 0.101 0.022 1 0.1 Lat_Fis-ant-Vertical 1167 779 1454 2.110 0.516 0.120 0.030 13 1.5 Lat_Fis-post 2548 1549 3165 1.861 0.528 0.150 0.055 35 5.7 Pole_occipital 1512 1046 5545 3.937 0.570 0.153 0.051 23 3.2 Pole_temporal 1866 1262 1853 1.635 0.583 0.144 0.050 28 3.7 S_calcarine 2750 1873 2881 1.692 0.557 0.111 0.027 17 3.1 S_central 1106 730 1475 2.130 0.534 0.102 0.026 7 1.1 S_cingul-Marginalis 426 292 762 2.980 0.533 0.108 0.030 3 0.5 S_circular_insula_ant 1195 810 2099 2.985 0.955 0.088 0.036 6 2.0 S_circular_insula_inf 1164 796 1773 2.813 0.531 0.109 0.032 7 1.7 S_circular_insula_sup 891 626 1520 2.747 0.617 0.108 0.021 7 0.9 S_collat_transv_ant 448 285 491 1.980 0.461 0.156 0.056 5 1.0 S_collat_transv_post 1428 982 2110 2.248 0.527 0.122 0.032 12 1.8 S_front_inf 1515 1028 2310 2.091 0.615 0.143 0.048 19 2.6 S_front_middle 2065 1448 3442 2.377 0.515 0.121 0.033 22 2.8 S_front_sup 352 236 398 2.197 0.314 0.124 0.029 3 0.4 S_interm_prim-Jensen 2621 1727 3350 2.029 0.467 0.110 0.026 19 2.8 S_intrapariet_and_P_trans 737 504 851 1.793 0.403 0.119 0.023 6 0.8 S_oc_middle_and_Lunatus 1269 860 1462 1.864 0.531 0.116 0.026 9 1.4 S_oc_sup_and_transversal 621 420 810 2.334 0.394 0.119 0.024 4 0.6 S_occipital_ant 518 361 997 3.005 0.693 0.169 0.057 8 1.3 S_oc-temp_lat 1435 1031 1987 2.253 0.569 0.126 0.035 12 2.1 S_oc-temp_med_and_Lingual 252 174 402 2.702 0.826 0.147 0.040 3 0.4 S_orbital_lateral 556 404 959 2.443 0.816 0.108 0.019 5 0.4 S_orbital_med-olfact 1288 870 2141 2.618 0.584 0.138 0.039 14 2.1 S_orbital-H_Shaped 1811 1205 2190 2.012 0.632 0.129 0.035 18 2.7 S_parieto_occipital 1175 743 1661 2.987 0.825 0.136 0.043 18 1.9 S_pericallosal 2166 1462 2454 1.856 0.480 0.113 0.026 16 2.4 S_postcentral 1347 949 2234 2.655 0.505 0.107 0.022 7 1.3 S_precentral-inf-part 878 581 1248 2.291 0.509 0.101 0.027 5 0.8 S_precentral-sup-part 116 72 184 3.289 0.338 0.186 0.046 2 0.2 S_suborbital 998 691 1422 2.161 0.576 0.136 0.034 10 1.3 S_subparietal 908 617 1518 3.104 0.723 0.128 0.034 8 1.2 S_temporal_inf 4245 2983 6581 2.335 0.537 0.104 0.022 26 4.0 S_temporal_sup 249 164 306 2.145 0.322 0.143 0.033 3 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Fri Jul 15 19:23:49 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon CA149base SUBJECTS_DIR is /data/belleville/ncorriveau/freesurfer/subjects iter 0, gcam->neg = 44 after 26 iterations, nbhd size=3, neg = 0 0605: dt=0.012000, rms=0.359 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 49 iterations, nbhd size=3, neg = 0 0606: dt=0.012000, rms=0.359 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 17 iterations, nbhd size=2, neg = 0 0607: dt=0.012000, rms=0.358 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 62 after 101 iterations, nbhd size=3, neg = 0 0608: dt=0.012000, rms=0.358 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 53 after 19 iterations, nbhd size=2, neg = 0 0609: dt=0.012000, rms=0.357 (0.144%), neg=0, invalid=766 iter 0, gcam->neg = 60 after 21 iterations, nbhd size=2, neg = 0 0610: dt=0.012000, rms=0.357 (0.139%), neg=0, invalid=766 iter 0, gcam->neg = 65 after 30 iterations, nbhd size=3, neg = 0 0611: dt=0.012000, rms=0.357 (0.127%), neg=0, invalid=766 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 = 30 writing volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Jul 15 19:49:12 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /opt/share/freesurfer/ASegStatsLUT.txt --subject CA149base iter 0, gcam->neg = 77 after 46 iterations, nbhd size=4, neg = 0 0612: dt=0.012000, rms=0.356 (0.096%), neg=0, invalid=766 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /opt/share/freesurfer/ASegStatsLUT.txt --subject CA149base sysname Linux hostname magma machine x86_64 user ncorriveau atlas_icv (eTIV) = 1262827 mm^3 (det: 1.542654 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 196601 rh white matter volume 194358 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 210949.663734, pTot = 389689.381366 c = 178739.717631 rh surface-based volumes (mm3): wTot = 210418.153042, pTot = 387841.072426 c = 177422.919384 Computing SupraTentVolCor SupraTentVolCor = 52889.000 SupraTentVol = 830419.454 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 4196 4196 4 5 Left-Inf-Lat-Vent 98 98 5 7 Left-Cerebellum-White-Matter 11370 11370 6 8 Left-Cerebellum-Cortex 42696 42696 7 10 Left-Thalamus-Proper 5091 5091 8 11 Left-Caudate 3134 3134 9 12 Left-Putamen 4376 4376 10 13 Left-Pallidum 1603 1603 11 14 3rd-Ventricle 973 973 12 15 4th-Ventricle iter 0, gcam->neg = 78 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 83122.688 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0613: dt=0.012000, rms=0.356 (0.000%), neg=0, invalid=766 948 948 13 16 Brain-Stem 17877 17877 14 17 Left-Hippocampus 4180 4180 15 18 Left-Amygdala 1405 1405 16 24 CSF 938 938 17 26 Left-Accumbens-area gcamFindOptimalTimeStep: Complete in 154617.359 ms 0614: dt=0.001750, rms=0.356 (0.002%), neg=0, invalid=766 517 517 18 28 Left-VentralDC 3598 3598 19 30 Left-vessel 42 42 20 31 Left-choroid-plexus 1290 1290 23 43 Right-Lateral-Ventricle gcamFindOptimalTimeStep: Complete in 141890.672 ms 0615: dt=0.001750, rms=0.356 (0.001%), neg=0, invalid=766 4505 4505 24 44 Right-Inf-Lat-Vent blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.356, neg=0, invalid=766 116 116 25 46 Right-Cerebellum-White-Matter 11128 11128 26 47 Right-Cerebellum-Cortex 44431 44431 27 49 Right-Thalamus-Proper 5591 5591 28 50 Right-Caudate 3167 3167 29 51 Right-Putamen gcamFindOptimalTimeStep: Complete in 171341.438 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0616: dt=0.004000, rms=0.356 (0.006%), neg=0, invalid=766 4542 4542 30 52 Right-Pallidum 1348 1348 31 53 Right-Hippocampus 4098 4098 32 54 Right-Amygdala 1757 1757 33 58 Right-Accumbens-area 629 629 34 60 Right-VentralDC 3615 3615 35 62 Right-vessel 28 28 36 63 Right-choroid-plexus 1597 1597 37 72 5th-Ventricle 6 6 38 77 WM-hypointensities 1377 1377 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 7 7 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 329 329 45 251 CC_Posterior 865 865 46 252 CC_Mid_Posterior 235 235 47 253 CC_Central 284 284 48 254 CC_Mid_Anterior gcamFindOptimalTimeStep: Complete in 257966.062 ms iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0617: dt=0.020036, rms=0.356 (0.031%), neg=0, invalid=766 293 293 49 255 CC_Anterior 535 535 Reporting on 45 segmentations SubCortGrayVol = 153655 #----------------------------------------- #@# AParc-to-ASeg Fri Jul 15 20:20:35 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --volmask SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 gcamFindOptimalTimeStep: Complete in 229346.469 ms 0618: dt=0.001750, rms=0.356 (0.003%), neg=0, invalid=766 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 347652 Used brute-force search on 0 voxels Writing output aseg to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --volmask --a2009s SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 = 347652 Used brute-force search on 0 voxels Writing output aseg to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Jul 15 20:29:59 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/ribbon.mgz Loading filled from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7086 vertices from left hemi Ripped 7053 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz Loading Ctx Seg File /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 49705.934 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0619: dt=0.001750, rms=0.356 (0.000%), neg=0, invalid=766 133 134 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.356, neg=0, invalid=766 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 gcamFindOptimalTimeStep: Complete in 123009.797 ms iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0620: dt=0.007000, rms=0.356 (0.022%), neg=0, invalid=766 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 716126 Used brute-force search on 31 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 4.000000 2 k 1.000000 3 k 1.000000 4 k 1459.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 1512.000000 3 k 1.000000 4 k 1.000000 Writing output aseg to mri/wmparc.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject CA149base --surf-wm-vol --ctab /opt/share/freesurfer/WMParcStatsLUT.txt --etiv gcamFindOptimalTimeStep: Complete in 145460.359 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0621: dt=0.003000, rms=0.355 (0.010%), neg=0, invalid=766 0622: dt=0.003000, rms=0.355 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0623: dt=0.003000, rms=0.355 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0624: dt=0.003000, rms=0.355 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0625: dt=0.003000, rms=0.355 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0626: dt=0.003000, rms=0.355 (0.036%), neg=0, invalid=766 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject CA149base --surf-wm-vol --ctab /opt/share/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname magma machine x86_64 user ncorriveau atlas_icv (eTIV) = 1262827 mm^3 (det: 1.542654 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 196601 rh white matter volume 194358 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz iter 0, gcam->neg = 9 after 21 iterations, nbhd size=3, neg = 0 0627: dt=0.003000, rms=0.355 (0.041%), neg=0, invalid=766 # nbrainmaskvoxels 1235595 # brainmaskvolume 1235595.0 # nbrainsegvoxels 190753 # brainsegvolume 190753.0 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 1 3001 wm-lh-bankssts 2977 2977 2 3002 wm-lh-caudalanteriorcingulate 2542 2542 3 3003 wm-lh-caudalmiddlefrontal 5419 5419 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2121 2121 6 3006 wm-lh-entorhinal 903 903 7 3007 wm-lh-fusiform iter 0, gcam->neg = 12 after 21 iterations, nbhd size=3, neg = 0 0628: dt=0.003000, rms=0.355 (0.045%), neg=0, invalid=766 5398 5398 8 3008 wm-lh-inferiorparietal 8262 8262 9 3009 wm-lh-inferiortemporal 5676 5676 10 3010 wm-lh-isthmuscingulate 3188 3188 11 3011 wm-lh-lateraloccipital 7465 7465 12 3012 wm-lh-lateralorbitofrontal 5150 5150 13 3013 wm-lh-lingual 4899 4899 iter 0, gcam->neg = 7 after 23 iterations, nbhd size=3, neg = 0 0629: dt=0.003000, rms=0.355 (0.048%), neg=0, invalid=766 14 3014 wm-lh-medialorbitofrontal 3591 3591 15 3015 wm-lh-middletemporal 3849 3849 16 3016 wm-lh-parahippocampal 1612 1612 17 3017 wm-lh-paracentral iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0630: dt=0.003000, rms=0.354 (0.051%), neg=0, invalid=766 3324 3324 18 3018 wm-lh-parsopercularis 3371 3371 19 3019 wm-lh-parsorbitalis 909 909 20 3020 wm-lh-parstriangularis iter 0, gcam->neg = 9 after 16 iterations, nbhd size=2, neg = 0 0631: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 2953 2953 21 3021 wm-lh-pericalcarine 2558 2558 22 3022 wm-lh-postcentral 6777 6777 23 3023 wm-lh-posteriorcingulate 3668 3668 24 3024 wm-lh-precentral iter 0, gcam->neg = 9 after 16 iterations, nbhd size=2, neg = 0 0632: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 11236 11236 25 3025 wm-lh-precuneus 7094 7094 26 3026 wm-lh-rostralanteriorcingulate 2005 2005 27 3027 wm-lh-rostralmiddlefrontal iter 0, gcam->neg = 9 after 20 iterations, nbhd size=3, neg = 0 0633: dt=0.003000, rms=0.354 (0.051%), neg=0, invalid=766 8979 8979 28 3028 wm-lh-superiorfrontal 14078 14078 29 3029 wm-lh-superiorparietal 10081 10081 30 3030 wm-lh-superiortemporal iter 0, gcam->neg = 9 after 15 iterations, nbhd size=2, neg = 0 0634: dt=0.003000, rms=0.354 (0.052%), neg=0, invalid=766 6021 6021 31 3031 wm-lh-supramarginal 7324 7324 32 3032 wm-lh-frontalpole iter 0, gcam->neg = 11 after 6 iterations, nbhd size=1, neg = 0 0635: dt=0.003000, rms=0.353 (0.054%), neg=0, invalid=766 196 196 33 3033 wm-lh-temporalpole 638 638 34 3034 wm-lh-transversetemporal 724 724 35 3035 wm-lh-insula 8380 8380 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2518 2518 120 4002 wm-rh-caudalanteriorcingulate 2309 2309 121 4003 wm-rh-caudalmiddlefrontal 4658 4658 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 2092 2092 124 4006 wm-rh-entorhinal 448 448 125 4007 wm-rh-fusiform iter 0, gcam->neg = 10 after 51 iterations, nbhd size=3, neg = 0 0636: dt=0.003000, rms=0.353 (0.051%), neg=0, invalid=766 5686 5686 126 4008 wm-rh-inferiorparietal blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.353, neg=0, invalid=766 8518 8518 127 4009 wm-rh-inferiortemporal 4886 4886 128 4010 wm-rh-isthmuscingulate 2608 2608 129 4011 wm-rh-lateraloccipital 8292 8292 130 4012 wm-rh-lateralorbitofrontal 5194 5194 131 4013 wm-rh-lingual 5480 5480 132 4014 wm-rh-medialorbitofrontal gcamFindOptimalTimeStep: Complete in 148486.422 ms 0637: dt=0.001750, rms=0.353 (0.005%), neg=0, invalid=766 2787 2787 133 4015 wm-rh-middletemporal 5093 5093 134 4016 wm-rh-parahippocampal 1623 1623 135 4017 wm-rh-paracentral 3541 3541 136 4018 wm-rh-parsopercularis 2566 2566 137 4019 wm-rh-parsorbitalis 1199 1199 138 4020 wm-rh-parstriangularis gcamFindOptimalTimeStep: Complete in 153928.203 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0638: dt=0.004000, rms=0.353 (0.011%), neg=0, invalid=766 2839 2839 139 4021 wm-rh-pericalcarine 2630 2630 140 4022 wm-rh-postcentral 6744 6744 141 4023 wm-rh-posteriorcingulate 3260 3260 142 4024 wm-rh-precentral 10745 10745 143 4025 wm-rh-precuneus 7269 7269 144 4026 wm-rh-rostralanteriorcingulate gcamFindOptimalTimeStep: Complete in 139310.641 ms iter 0, gcam->neg = 2 after 21 iterations, nbhd size=3, neg = 0 0639: dt=0.005001, rms=0.353 (0.013%), neg=0, invalid=766 1731 1731 145 4027 wm-rh-rostralmiddlefrontal 10202 10202 146 4028 wm-rh-superiorfrontal 13939 13939 147 4029 wm-rh-superiorparietal 9800 9800 148 4030 wm-rh-superiortemporal 5285 5285 149 4031 wm-rh-supramarginal 7267 7267 150 4032 wm-rh-frontalpole 403 403 151 4033 wm-rh-temporalpole gcamFindOptimalTimeStep: Complete in 189247.234 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0640: dt=0.006000, rms=0.353 (0.016%), neg=0, invalid=766 679 679 152 4034 wm-rh-transversetemporal 491 491 153 4035 wm-rh-insula 8040 8040 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 21990 21990 237 5002 Right-UnsegmentedWhiteMatter 22086 22086 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label #-------------------------------------------- #@# BA Labels lh Fri Jul 15 21:31:04 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject CA149base --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./lh.BA1.label 4290 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA2.label --trgsubject CA149base --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./lh.BA2.label 8148 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3a.label --trgsubject CA149base --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4077 points in source label. gcamFindOptimalTimeStep: Complete in 200784.750 ms iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0641: dt=0.007000, rms=0.353 (0.018%), neg=0, invalid=766 Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4164 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3b.label --trgsubject CA149base --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6162 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4a.label --trgsubject CA149base --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./lh.BA4a.label 5934 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4p.label --trgsubject CA149base --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4185 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA6.label --trgsubject CA149base --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./lh.BA6.label 14108 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA44.label --trgsubject CA149base --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.BA44.label 4398 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA45.label --trgsubject CA149base --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 399 Checking for and removing duplicates Writing label file ./lh.BA45.label 3821 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V1.label --trgsubject CA149base --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 721 Checking for and removing duplicates Writing label file ./lh.V1.label 5362 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V2.label --trgsubject CA149base --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 8114 points in source label. gcamFindOptimalTimeStep: Complete in 148557.016 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0642: dt=0.006000, rms=0.353 (0.015%), neg=0, invalid=766 Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 1586 Checking for and removing duplicates Writing label file ./lh.V2.label 9700 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.MT.label --trgsubject CA149base --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.MT.label 2171 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s CA149base --hemi lh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose Reading ctab /opt/share/freesurfer/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label cmdline mris_label2annot --s CA149base --hemi lh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose sysname Linux hostname magma machine x86_64 user ncorriveau subject CA149base hemi lh SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects ColorTable /opt/share/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 74632 unhit vertices Writing annot to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab CA149base lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /opt/share/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 985 529 1568 2.266 0.426 0.134 0.047 17 2.0 BA1 3297 2154 4941 2.203 0.552 0.108 0.032 27 4.2 BA2 944 647 808 1.571 0.461 0.140 0.037 9 1.5 BA3a 2129 1388 2816 1.845 0.674 0.119 0.033 21 3.2 BA3b 1416 732 2028 2.353 0.588 0.100 0.044 21 2.0 BA4a 1080 694 1711 2.500 0.475 0.099 0.034 14 1.4 BA4p 7735 4896 15079 2.665 0.513 0.120 0.043 87 14.5 BA6 2049 1380 3847 2.641 0.423 0.133 0.035 23 3.0 BA44 2568 1739 4662 2.343 0.558 0.128 0.036 28 3.7 BA45 2701 1786 2846 1.533 0.493 0.159 0.063 62 7.8 V1 6825 4419 8762 1.916 0.588 0.157 0.053 102 14.8 V2 1377 920 2435 2.345 0.500 0.124 0.043 17 1.9 MT #-------------------------------------------- #@# BA Labels rh Fri Jul 15 21:36:06 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA1.label --trgsubject CA149base --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3962 points in source label. iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0643: dt=0.006000, rms=0.353 (0.015%), neg=0, invalid=766 Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./rh.BA1.label 4168 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA2.label --trgsubject CA149base --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 260 Checking for and removing duplicates Writing label file ./rh.BA2.label 6947 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3a.label --trgsubject CA149base --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4076 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3b.label --trgsubject CA149base --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4717 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4a.label --trgsubject CA149base --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5891 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4p.label --trgsubject CA149base --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4591 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA6.label --trgsubject CA149base --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 12256 points in source label. iter 0, gcam->neg = 12 after 31 iterations, nbhd size=4, neg = 0 0644: dt=0.006000, rms=0.353 (0.026%), neg=0, invalid=766 Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA6.label 12521 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA44.label --trgsubject CA149base --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./rh.BA44.label 7178 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA45.label --trgsubject CA149base --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 447 Checking for and removing duplicates Writing label file ./rh.BA45.label 5802 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V1.label --trgsubject CA149base --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 981 Checking for and removing duplicates Writing label file ./rh.V1.label 5708 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V2.label --trgsubject CA149base --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 1878 Checking for and removing duplicates Writing label file ./rh.V2.label 9894 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.MT.label --trgsubject CA149base --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 178 Checking for and removing duplicates Writing label file ./rh.MT.label 2110 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s CA149base --hemi rh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose Reading ctab /opt/share/freesurfer/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label cmdline mris_label2annot --s CA149base --hemi rh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose sysname Linux hostname magma machine x86_64 user ncorriveau subject CA149base hemi rh SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects ColorTable /opt/share/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 73806 unhit vertices Writing annot to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab CA149base rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... iter 0, gcam->neg = 8 after 22 iterations, nbhd size=3, neg = 0 0645: dt=0.006000, rms=0.353 (0.039%), neg=0, invalid=766 reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /opt/share/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 906 486 1403 2.187 0.365 0.129 0.046 11 1.8 BA1 2881 1885 3783 1.973 0.517 0.113 0.029 24 3.4 BA2 924 650 748 1.433 0.350 0.140 0.037 8 1.4 BA3a 1820 1116 2014 1.626 0.511 0.114 0.039 23 3.3 BA3b 1339 783 2082 2.353 0.483 0.095 0.039 25 3.1 BA4a 1134 741 1574 2.140 0.458 0.103 0.025 6 1.2 BA4p 5985 3670 11907 2.770 0.519 0.115 0.032 56 8.0 BA6 2940 2011 5247 2.534 0.503 0.118 0.031 25 3.9 BA44 3328 2245 6507 2.578 0.623 0.142 0.044 42 6.1 BA45 3308 2119 3416 1.547 0.481 0.147 0.055 52 7.7 V1 6998 4508 8770 1.904 0.530 0.155 0.054 109 15.4 V2 1565 1071 2426 2.249 0.567 0.130 0.031 15 2.2 MT /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Jul 15 21:41:13 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o CA149base label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject CA149base. processing subject lh.EC_average... reading output surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 860 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label CA149base lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 306 191 976 3.215 0.584 0.099 0.023 2 0.3 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Jul 15 21:41:57 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o CA149base label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject CA149base. processing subject rh.EC_average... reading output surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 630 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label CA149base rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 225 143 792 3.447 0.564 0.085 0.030 1 0.3 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s CA149base finished without error at Fri Jul 15 21:42:37 EDT 2016 iter 0, gcam->neg = 18 after 35 iterations, nbhd size=3, neg = 0 0646: dt=0.006000, rms=0.353 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 18 iterations, nbhd size=2, neg = 0 0647: dt=0.006000, rms=0.352 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 31 iterations, nbhd size=4, neg = 0 0648: dt=0.006000, rms=0.352 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 21 iterations, nbhd size=2, neg = 0 0649: dt=0.006000, rms=0.352 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 31 after 17 iterations, nbhd size=2, neg = 0 0650: dt=0.006000, rms=0.352 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 19 iterations, nbhd size=2, neg = 0 0651: dt=0.006000, rms=0.351 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 38 iterations, nbhd size=4, neg = 0 0652: dt=0.006000, rms=0.351 (0.064%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 26 hours, 6 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Inv Fri Jul 15 21:58:03 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Jul 15 22:01:09 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/share/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/share/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 12119142 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 3 minutes and 34 seconds. #-------------------------------------- #@# SkullLTA Fri Jul 15 22:04:45 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/share/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/share/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=12.0 skull bounding box = (52, 51, 45) --> (204, 226, 230) using (103, 109, 138) as brain centroid... mean wm in atlas = 126, using box (84,87,115) --> (121, 130,160) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10306.9, old_max_log_p =-10351.7 (thresh=-10341.3) 1.177 0.042 -0.022 -24.081; 0.006 1.319 0.389 -100.340; 0.045 -0.298 0.999 10.823; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10306.9, old_max_log_p =-10306.9 (thresh=-10296.6) 1.177 0.042 -0.022 -24.081; 0.006 1.319 0.389 -100.340; 0.045 -0.298 0.999 10.823; 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=-10292.4, old_max_log_p =-10306.9 (thresh=-10296.6) 1.149 -0.086 -0.053 -3.635; 0.120 1.363 0.293 -106.249; 0.048 -0.155 0.976 -1.265; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10292.2, old_max_log_p =-10292.4 (thresh=-10282.1) 1.172 -0.091 -0.021 -9.814; 0.119 1.367 0.261 -100.742; 0.014 -0.106 0.968 -2.282; 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=-10288.0, old_max_log_p =-10292.2 (thresh=-10281.9) 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 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 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 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: 006: -log(p) = 10288.0 tol 0.000010 Resulting transform: 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10288.0 (old=-10351.7) transform before final EM align: 1.173 -0.093 -0.005 -12.227; 0.119 1.370 0.254 -100.105; -0.004 -0.093 0.972 -2.109; 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 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.17302 -0.09299 -0.00531 -12.22673; 0.11859 1.36959 0.25359 -100.10512; -0.00407 -0.09326 0.97213 -2.10890; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1144886.8 after pass:transform: ( 1.17, -0.09, -0.01, -12.23) ( 0.12, 1.37, 0.25, -100.11) ( -0.00, -0.09, 0.97, -2.11) dfp_em_step_func: 008: -log(p) = 1144886.6 after pass:transform: ( 1.17, -0.09, -0.01, -12.23) ( 0.12, 1.37, 0.25, -100.11) ( -0.00, -0.09, 0.97, -2.11) dfp_em_step_func: 009: -log(p) = 1144879.6 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 010: -log(p) = 1144874.8 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... dfp_em_step_func: 011: -log(p) = 1144874.5 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... dfp_em_step_func: 012: -log(p) = 1144874.2 after pass:transform: ( 1.18, -0.09, -0.00, -12.23) ( 0.11, 1.37, 0.25, -100.11) ( -0.01, -0.10, 0.97, -2.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 1144874.2 tol 0.000000 final transform: 1.178 -0.088 -0.003 -12.227; 0.114 1.366 0.248 -100.105; -0.012 -0.103 0.971 -2.109; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 62 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Fri Jul 15 23:07:44 EDT 2016 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname magma machine x86_64 user ncorriveau Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /opt/share/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 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /opt/share/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /opt/share/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 = 0.14205 (23) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1063 voxels, overlap=0.375) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1063 voxels, peak = 22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.14912 (22) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (1301 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (1301 voxels, peak = 19), gca=19.0 gca peak = 0.28003 (97) mri peak = 0.15045 (108) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (394 voxels, overlap=0.041) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (394 voxels, peak = 104), gca=104.3 gca peak = 0.18160 (96) mri peak = 0.16043 (107) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (374 voxels, overlap=0.074) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (374 voxels, peak = 106), gca=105.6 gca peak = 0.27536 (62) mri peak = 0.09225 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1005 voxels, overlap=0.240) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1005 voxels, peak = 71), gca=71.3 gca peak = 0.32745 (63) mri peak = 0.11376 (72) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (979 voxels, overlap=0.413) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (979 voxels, peak = 71), gca=70.9 gca peak = 0.08597 (105) mri peak = 0.11210 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (28895 voxels, overlap=0.499) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (28895 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.10834 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26012 voxels, overlap=0.504) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (26012 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04324 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (34745 voxels, overlap=0.626) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (34745 voxels, peak = 72), gca=72.4 gca peak = 0.08598 (64) mri peak = 0.04422 (71) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (32986 voxels, overlap=0.573) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (32986 voxels, peak = 72), gca=72.0 gca peak = 0.24164 (71) mri peak = 0.12121 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (756 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.17 x + 0.0 (756 voxels, peak = 83), gca=83.4 gca peak = 0.18227 (75) mri peak = 0.12791 (83) Left_Caudate (11): linear fit = 1.10 x + 0.0 (749 voxels, overlap=0.516) Left_Caudate (11): linear fit = 1.10 x + 0.0 (749 voxels, peak = 82), gca=82.5 gca peak = 0.10629 (62) mri peak = 0.05837 (67) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23363 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23363 voxels, peak = 70), gca=69.8 gca peak = 0.11668 (59) mri peak = 0.05601 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24936 voxels, overlap=0.872) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24936 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.12519 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5454 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5454 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.12860 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5324 voxels, overlap=0.826) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5324 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.12667 (69) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (407 voxels, overlap=0.001) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (407 voxels, peak = 70), gca=70.4 gca peak = 0.42394 (62) mri peak = 0.14970 (70) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (499 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (499 voxels, peak = 68), gca=68.2 gca peak = 0.10041 (96) mri peak = 0.09064 (98) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3079 voxels, overlap=0.872) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3079 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.08243 (98) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3312 voxels, overlap=0.516) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3312 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.06803 (95) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1804 voxels, overlap=0.630) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1804 voxels, peak = 89), gca=89.1 gca peak = 0.09624 (82) mri peak = 0.07530 (92) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1607 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1607 voxels, peak = 88), gca=88.2 gca peak = 0.07543 (88) mri peak = 0.06208 (88) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10410 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10410 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.10407 (104) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1256 voxels, overlap=0.363) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1256 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.08530 (103) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1362 voxels, overlap=0.410) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1362 voxels, peak = 101), gca=101.2 gca peak = 0.21361 (36) mri peak = 0.17246 (24) gca peak = 0.26069 (23) mri peak = 0.18750 (25) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (96 voxels, overlap=0.696) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (96 voxels, peak = 21), gca=21.3 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 1.12 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.90 x + 0.0 Left_Pallidum too bright - rescaling by 1.005 (from 1.100) to 106.2 (was 105.6) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14514 (23) mri peak = 0.14205 (23) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=0.864) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 23), gca=23.0 gca peak = 0.15050 (19) mri peak = 0.14912 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1301 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1301 voxels, peak = 19), gca=19.5 gca peak = 0.24146 (105) mri peak = 0.15045 (108) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, peak = 105), gca=105.0 gca peak = 0.17034 (107) mri peak = 0.16043 (107) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (374 voxels, overlap=0.818) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (374 voxels, peak = 104), gca=104.3 gca peak = 0.25238 (71) mri peak = 0.09225 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1005 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1005 voxels, peak = 71), gca=71.0 gca peak = 0.31227 (71) mri peak = 0.11376 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (979 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (979 voxels, peak = 71), gca=71.0 gca peak = 0.08006 (112) mri peak = 0.11210 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28895 voxels, overlap=0.671) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28895 voxels, peak = 112), gca=112.0 gca peak = 0.08505 (108) mri peak = 0.10834 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26012 voxels, overlap=0.639) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (26012 voxels, peak = 108), gca=108.0 gca peak = 0.06954 (72) mri peak = 0.04324 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34745 voxels, overlap=0.901) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34745 voxels, peak = 70), gca=70.2 gca peak = 0.07883 (72) mri peak = 0.04422 (71) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (32986 voxels, overlap=0.899) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (32986 voxels, peak = 70), gca=70.2 gca peak = 0.21717 (83) mri peak = 0.12121 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (756 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (756 voxels, peak = 83), gca=83.0 gca peak = 0.13780 (82) mri peak = 0.12791 (83) Left_Caudate (11): linear fit = 0.98 x + 0.0 (749 voxels, overlap=0.741) Left_Caudate (11): linear fit = 0.98 x + 0.0 (749 voxels, peak = 80), gca=80.0 gca peak = 0.09301 (70) mri peak = 0.05837 (67) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23363 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23363 voxels, peak = 70), gca=70.0 gca peak = 0.12039 (64) mri peak = 0.05601 (65) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (24936 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (24936 voxels, peak = 66), gca=65.6 gca peak = 0.16848 (92) mri peak = 0.12519 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5454 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5454 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.12860 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5324 voxels, overlap=0.970) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5324 voxels, peak = 91), gca=91.0 gca peak = 0.30566 (70) mri peak = 0.12667 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (407 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (407 voxels, peak = 70), gca=70.0 gca peak = 0.35282 (69) mri peak = 0.14970 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (499 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (499 voxels, peak = 69), gca=69.0 gca peak = 0.09784 (97) mri peak = 0.09064 (98) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3079 voxels, overlap=0.930) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3079 voxels, peak = 97), gca=97.0 gca peak = 0.09781 (97) mri peak = 0.08243 (98) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3312 voxels, overlap=0.899) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3312 voxels, peak = 97), gca=97.0 gca peak = 0.08109 (91) mri peak = 0.06803 (95) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1804 voxels, overlap=0.973) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1804 voxels, peak = 91), gca=91.0 gca peak = 0.09427 (88) mri peak = 0.07530 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1607 voxels, overlap=0.984) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1607 voxels, peak = 88), gca=88.0 gca peak = 0.07247 (90) mri peak = 0.06208 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10410 voxels, overlap=0.853) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10410 voxels, peak = 90), gca=90.0 gca peak = 0.13771 (104) mri peak = 0.10407 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1256 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1256 voxels, peak = 104), gca=104.0 gca peak = 0.12455 (102) mri peak = 0.08530 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1362 voxels, overlap=0.868) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1362 voxels, peak = 102), gca=102.0 gca peak = 0.22647 (34) mri peak = 0.17246 (24) gca peak = 0.23444 (21) mri peak = 0.18750 (25) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (96 voxels, overlap=0.808) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (96 voxels, peak = 21), gca=21.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.23325 (40) gca peak Third_Ventricle = 0.22647 (34) gca peak CSF = 0.25620 (35) gca peak Left_Accumbens_area = 0.51667 (77) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.27366 (84) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (38) gca peak WM_hypointensities = 0.14892 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34481 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Right_Pallidum too bright - rescaling by 1.016 (from 1.000) to 106.7 (was 105.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 18188 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 285 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 52314 changed. image ll: -2.052, PF=1.000 pass 2: 7485 changed. pass 3: 2577 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 67 minutes and 22 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/cc_up.lta CA149base will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/transforms/cc_up.lta reading aseg from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.auto_noCCseg.mgz reading norm from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/norm.mgz 27429 voxels in left wm, 27563 in right wm, xrange [122, 131] searching rotation angles z=[-3 11], y=[-9 5] searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 global minimum found at slice 126.2, rotations (-2.43, 3.67) final transformation (x=126.2, yr=-2.433, zr=3.666): 0.997 -0.064 -0.042 15.026; 0.064 0.998 -0.003 0.516; 0.042 -0.000 0.999 -0.248; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 139 119 eigenvectors: -0.001 0.010 1.000; -0.131 -0.991 0.010; 0.991 -0.131 0.002; error in mid anterior detected - correcting... writing aseg with callosum to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.2 minutes #-------------------------------------- #@# Merge ASeg Sat Jul 16 00:17:39 EDT 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Jul 16 00:17:39 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 985 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 9 minutes and 49 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 109 gm peak at 76 (76), valley at 35 (35) csf peak at 20, setting threshold to 57 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 36 (36) csf peak at 20, setting threshold to 58 #-------------------------------------------- #@# Mask BFS Sat Jul 16 00:27:40 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1234975 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Jul 16 00:27:50 EDT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname magma machine x86_64 user ncorriveau input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname magma machine x86_64 user ncorriveau input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.2 +- 6.6 [80.0 --> 125.0] GM (76.0) : 74.5 +- 9.4 [30.0 --> 96.0] setting bottom of white matter range to 83.9 setting top of gray matter range to 93.3 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... 1463 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1897 filled 0 bright non-wm voxels segmented. 1096 diagonally connected voxels added... white matter segmentation took 4.4 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 1.91 minutes reading wm segmentation from wm.seg.mgz... 18 voxels added to wm to prevent paths from MTL structures to cortex 1501 additional wm voxels added 0 additional wm voxels added SEG EDIT: 28854 voxels turned on, 34266 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 99 new 99 115,126,128 old 99 new 99 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 15 found - 15 modified | TOTAL: 25 pass 2 (xy-): 0 found - 15 modified | TOTAL: 25 pass 1 (yz+): 15 found - 15 modified | TOTAL: 40 pass 2 (yz+): 0 found - 15 modified | TOTAL: 40 pass 1 (yz-): 12 found - 12 modified | TOTAL: 52 pass 2 (yz-): 0 found - 12 modified | TOTAL: 52 pass 1 (xz+): 14 found - 14 modified | TOTAL: 66 pass 2 (xz+): 0 found - 14 modified | TOTAL: 66 pass 1 (xz-): 11 found - 11 modified | TOTAL: 77 pass 2 (xz-): 0 found - 11 modified | TOTAL: 77 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 11 found - 11 modified | TOTAL: 23 pass 2 (+++): 0 found - 11 modified | TOTAL: 23 pass 1 (+++): 4 found - 4 modified | TOTAL: 27 pass 2 (+++): 0 found - 4 modified | TOTAL: 27 pass 1 (+++): 0 found - 0 modified | TOTAL: 27 Iteration Number : 1 pass 1 (++): 19 found - 19 modified | TOTAL: 19 pass 2 (++): 0 found - 19 modified | TOTAL: 19 pass 1 (+-): 29 found - 29 modified | TOTAL: 48 pass 2 (+-): 0 found - 29 modified | TOTAL: 48 pass 1 (--): 26 found - 26 modified | TOTAL: 74 pass 2 (--): 0 found - 26 modified | TOTAL: 74 pass 1 (-+): 20 found - 20 modified | TOTAL: 94 pass 2 (-+): 0 found - 20 modified | TOTAL: 94 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 207 (out of 457998: 0.045197) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Sat Jul 16 00:35:22 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.166 -0.119 -0.069 4.089; 0.159 1.222 0.356 -102.686; 0.049 -0.322 1.080 3.103; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1264 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (129, 105, 97), TAL = (-1.0, -31.0, 23.0) talairach voxel to voxel transform 0.845 0.089 0.025 5.581; -0.091 0.743 -0.251 77.491; -0.065 0.218 0.850 20.011; 0.000 0.000 0.000 1.000; segmentation indicates cc at (129, 105, 97) --> (-1.0, -31.0, 23.0) done. writing output to filled.mgz... filling took 2.9 minutes talairach cc position changed to (-1.00, -31.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(17.00, -31.00, 23.00) SRC: (111.03, 121.13, 118.07) search lh wm seed point around talairach space (-19.00, -31.00, 23.00), SRC: (141.44, 117.86, 115.72) 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 Sat Jul 16 00:38:19 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 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+): 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 220752: 0.003171) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 70: 3334 vertices, 3530 faces slice 80: 11801 vertices, 12122 faces slice 90: 21827 vertices, 22137 faces slice 100: 31521 vertices, 31850 faces slice 110: 40701 vertices, 41022 faces slice 120: 50310 vertices, 50637 faces slice 130: 60027 vertices, 60359 faces slice 140: 69024 vertices, 69347 faces slice 150: 78151 vertices, 78452 faces slice 160: 86634 vertices, 86895 faces slice 170: 93508 vertices, 93788 faces slice 180: 99436 vertices, 99649 faces slice 190: 104402 vertices, 104567 faces slice 200: 107461 vertices, 107559 faces slice 210: 108302 vertices, 108324 faces slice 220: 108302 vertices, 108324 faces slice 230: 108302 vertices, 108324 faces slice 240: 108302 vertices, 108324 faces slice 250: 108302 vertices, 108324 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... 108302 voxel in cpt #1: X=-22 [v=108302,e=324972,f=216648] located at (-24.370428, -3.206571, 8.361665) For the whole surface: X=-22 [v=108302,e=324972,f=216648] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Jul 16 00:38:50 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Sat Jul 16 00:39:00 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts avg radius = 43.3 mm, total surface area = 58061 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.6 minutes Not saving sulc step 000: RMS=0.095 (target=0.015) step 005: RMS=0.069 (target=0.015) step 010: RMS=0.051 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (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=0.024 (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 Sat Jul 16 00:40:39 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.12 +- 0.60 (0.00-->7.42) (max @ vno 80562 --> 80581) face area 0.03 +- 0.04 (-0.14-->0.65) scaling brain by 0.361... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.781, avgs=0 005/300: dt: 0.9000, rms radial error=175.524, avgs=0 010/300: dt: 0.9000, rms radial error=174.972, avgs=0 015/300: dt: 0.9000, rms radial error=174.246, avgs=0 020/300: dt: 0.9000, rms radial error=173.418, avgs=0 025/300: dt: 0.9000, rms radial error=172.532, avgs=0 030/300: dt: 0.9000, rms radial error=171.613, avgs=0 035/300: dt: 0.9000, rms radial error=170.680, avgs=0 040/300: dt: 0.9000, rms radial error=169.741, avgs=0 045/300: dt: 0.9000, rms radial error=168.798, avgs=0 050/300: dt: 0.9000, rms radial error=167.856, avgs=0 055/300: dt: 0.9000, rms radial error=166.916, avgs=0 060/300: dt: 0.9000, rms radial error=165.979, avgs=0 065/300: dt: 0.9000, rms radial error=165.047, avgs=0 070/300: dt: 0.9000, rms radial error=164.119, avgs=0 075/300: dt: 0.9000, rms radial error=163.196, avgs=0 080/300: dt: 0.9000, rms radial error=162.278, avgs=0 085/300: dt: 0.9000, rms radial error=161.365, avgs=0 090/300: dt: 0.9000, rms radial error=160.456, avgs=0 095/300: dt: 0.9000, rms radial error=159.552, avgs=0 100/300: dt: 0.9000, rms radial error=158.653, avgs=0 105/300: dt: 0.9000, rms radial error=157.759, avgs=0 110/300: dt: 0.9000, rms radial error=156.870, avgs=0 115/300: dt: 0.9000, rms radial error=155.988, avgs=0 120/300: dt: 0.9000, rms radial error=155.112, avgs=0 125/300: dt: 0.9000, rms radial error=154.241, avgs=0 130/300: dt: 0.9000, rms radial error=153.375, avgs=0 135/300: dt: 0.9000, rms radial error=152.513, avgs=0 140/300: dt: 0.9000, rms radial error=151.656, avgs=0 145/300: dt: 0.9000, rms radial error=150.804, avgs=0 150/300: dt: 0.9000, rms radial error=149.956, avgs=0 155/300: dt: 0.9000, rms radial error=149.113, avgs=0 160/300: dt: 0.9000, rms radial error=148.275, avgs=0 165/300: dt: 0.9000, rms radial error=147.441, avgs=0 170/300: dt: 0.9000, rms radial error=146.611, avgs=0 175/300: dt: 0.9000, rms radial error=145.786, avgs=0 180/300: dt: 0.9000, rms radial error=144.965, avgs=0 185/300: dt: 0.9000, rms radial error=144.149, avgs=0 190/300: dt: 0.9000, rms radial error=143.338, avgs=0 195/300: dt: 0.9000, rms radial error=142.531, avgs=0 200/300: dt: 0.9000, rms radial error=141.728, avgs=0 205/300: dt: 0.9000, rms radial error=140.930, avgs=0 210/300: dt: 0.9000, rms radial error=140.136, avgs=0 215/300: dt: 0.9000, rms radial error=139.347, avgs=0 220/300: dt: 0.9000, rms radial error=138.562, avgs=0 225/300: dt: 0.9000, rms radial error=137.781, avgs=0 230/300: dt: 0.9000, rms radial error=137.005, avgs=0 235/300: dt: 0.9000, rms radial error=136.233, avgs=0 240/300: dt: 0.9000, rms radial error=135.465, avgs=0 245/300: dt: 0.9000, rms radial error=134.702, avgs=0 250/300: dt: 0.9000, rms radial error=133.943, avgs=0 255/300: dt: 0.9000, rms radial error=133.188, avgs=0 260/300: dt: 0.9000, rms radial error=132.437, avgs=0 265/300: dt: 0.9000, rms radial error=131.690, avgs=0 270/300: dt: 0.9000, rms radial error=130.948, avgs=0 275/300: dt: 0.9000, rms radial error=130.210, avgs=0 280/300: dt: 0.9000, rms radial error=129.476, avgs=0 285/300: dt: 0.9000, rms radial error=128.746, avgs=0 290/300: dt: 0.9000, rms radial error=128.020, avgs=0 295/300: dt: 0.9000, rms radial error=127.299, avgs=0 300/300: dt: 0.9000, rms radial error=126.581, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11933.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 1761.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00025 epoch 3 (K=160.0), pass 1, starting sse = 138.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00645 epoch 4 (K=640.0), pass 1, starting sse = 6.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00621 final dwriting spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours istance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sat Jul 16 00:49:30 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 CA149base 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-22 (nv=108302, nf=216648, ne=324972, g=12) 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... 1245 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7081 (-4.3541) -vertex loglikelihood: -5.7394 (-2.8697) -normal dot loglikelihood: -3.6279 (-3.6279) -quad curv loglikelihood: -6.4271 (-3.2135) Total Loglikelihood : -24.5025 CORRECTING DEFECT 0 (vertices=21, convex hull=25) After retessellation of defect 0, euler #=-9 (107518,322201,214674) : difference with theory (-12) = -3 CORRECTING DEFECT 1 (vertices=37, convex hull=76) After retessellation of defect 1, euler #=-8 (107527,322259,214724) : difference with theory (-11) = -3 CORRECTING DEFECT 2 (vertices=8, convex hull=15) After retessellation of defect 2, euler #=-7 (107528,322266,214731) : difference with theory (-10) = -3 CORRECTING DEFECT 3 (vertices=31, convex hull=51) After retessellation of defect 3, euler #=-6 (107547,322345,214792) : difference with theory (-9) = -3 CORRECTING DEFECT 4 (vertices=26, convex hull=21) After retessellation of defect 4, euler #=-5 (107551,322360,214804) : difference with theory (-8) = -3 CORRECTING DEFECT 5 (vertices=195, convex hull=61) After retessellation of defect 5, euler #=-4 (107562,322421,214855) : difference with theory (-7) = -3 CORRECTING DEFECT 6 (vertices=37, convex hull=70) After retessellation of defect 6, euler #=-3 (107582,322505,214920) : difference with theory (-6) = -3 CORRECTING DEFECT 7 (vertices=75, convex hull=81) After retessellation of defect 7, euler #=-3 (107615,322649,215031) : difference with theory (-5) = -2 CORRECTING DEFECT 8 (vertices=127, convex hull=148) After retessellation of defect 8, euler #=-3 (107661,322855,215191) : difference with theory (-4) = -1 CORRECTING DEFECT 9 (vertices=28, convex hull=47) After retessellation of defect 9, euler #=-2 (107675,322911,215234) : difference with theory (-3) = -1 CORRECTING DEFECT 10 (vertices=28, convex hull=23) After retessellation of defect 10, euler #=-2 (107681,322940,215257) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=63, convex hull=40) After retessellation of defect 11, euler #=-1 (107687,322973,215285) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=66) After retessellation of defect 12, euler #=0 (107697,323028,215331) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=31, convex hull=56) After retessellation of defect 13, euler #=1 (107711,323093,215383) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=48, convex hull=82) After retessellation of defect 14, euler #=2 (107738,323208,215472) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.05-->5.54) (max @ vno 75908 --> 75920) 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 (0.05-->5.54) (max @ vno 75908 --> 75920) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 55 mutations (33.5%), 109 crossovers (66.5%), 52 vertices were eliminated building final representation... 564 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=107738, nf=215472, ne=323208, g=0) writing corrected surface to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.0 minutes 0 defective edges removing intersecting faces 000: 58 intersecting 001: 6 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 107738 - 323208 + 215472 = 2 --> 0 holes F =2V-4: 215472 = 215476-4 (0) 2E=3F: 646416 = 646416 (0) total defect index = 0 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 13 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Jul 16 01:11:43 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7462 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 83.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.7 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.81) (max @ vno 81921 --> 107629) face area 0.28 +- 0.12 (0.00-->1.13) mean absolute distance = 0.86 +- 1.06 2979 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=75 using class modes intead of means.... mean inside = 95.0, mean outside = 81.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.5, 9 (9) missing vertices, mean dist 0.3 [0.8 (%35.4)->0.9 (%64.6))] %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->3.85) (max @ vno 81921 --> 107629) face area 0.28 +- 0.13 (0.00-->1.66) mean absolute distance = 0.45 +- 0.85 2929 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3291322.8, rms=8.56 001: dt: 0.5000, sse=3703650.5, rms=6.06 002: dt: 0.5000, sse=3847908.5, rms=4.39 003: dt: 0.5000, sse=4049931.2, rms=3.31 004: dt: 0.5000, sse=4129320.2, rms=2.68 005: dt: 0.5000, sse=4214587.5, rms=2.35 006: dt: 0.5000, sse=4212396.5, rms=2.21 007: dt: 0.5000, sse=4252234.5, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4245008.0, rms=2.11 009: dt: 0.2500, sse=2622303.2, rms=1.48 010: dt: 0.2500, sse=2473091.0, rms=1.40 rms = 1.38, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2429420.2, rms=1.38 rms = 1.37, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2401884.0, rms=1.37 positioning took 2.4 minutes 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=86.4, 24 (1) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %56 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.06-->4.07) (max @ vno 70431 --> 69542) face area 0.35 +- 0.16 (0.00-->2.45) mean absolute distance = 0.38 +- 0.53 3452 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2744818.2, rms=3.78 013: dt: 0.5000, sse=2963821.5, rms=2.38 014: dt: 0.5000, sse=3192575.5, rms=1.88 015: dt: 0.5000, sse=3234785.8, rms=1.67 rms = 1.65, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=3480803.5, rms=1.65 017: dt: 0.2500, sse=2708241.5, rms=1.24 018: dt: 0.2500, sse=2605611.8, rms=1.19 rms = 1.18, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2577163.5, rms=1.18 rms = 1.18, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2555069.5, rms=1.18 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 12 (1) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->4.50) (max @ vno 70431 --> 69542) face area 0.34 +- 0.16 (0.00-->2.55) mean absolute distance = 0.28 +- 0.37 2898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2808080.8, rms=3.79 021: dt: 0.5000, sse=2953509.5, rms=2.07 022: dt: 0.5000, sse=3108183.2, rms=1.65 023: dt: 0.5000, sse=3214451.8, rms=1.49 rms = 1.60, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=2867498.8, rms=1.22 025: dt: 0.2500, sse=2744902.5, rms=1.11 rms = 1.10, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2708585.8, rms=1.10 rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2690677.2, rms=1.10 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=90.3, 11 (0) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.2 (%39.2))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=2722549.5, rms=1.85 028: dt: 0.5000, sse=3230767.2, rms=1.15 rms = 1.30, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3020761.5, rms=0.97 030: dt: 0.2500, sse=2913785.8, rms=0.91 rms = 0.90, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2932323.0, rms=0.90 rms = 0.91, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=2932323.0, rms=0.90 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 2088 vertices erasing segment 1 (vno[0] = 65137) erasing segment 2 (vno[0] = 77469) erasing segment 3 (vno[0] = 78212) erasing segment 4 (vno[0] = 79130) erasing segment 5 (vno[0] = 79140) erasing segment 6 (vno[0] = 79962) erasing segment 7 (vno[0] = 81767) erasing segment 8 (vno[0] = 82568) erasing segment 9 (vno[0] = 83391) erasing segment 10 (vno[0] = 85016) erasing segment 11 (vno[0] = 85048) erasing segment 12 (vno[0] = 107676) writing cortex label to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.cortex.label... LabelWrite: saving to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.cortex.label writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->4.54) (max @ vno 70431 --> 69542) face area 0.33 +- 0.16 (0.00-->2.54) refinement took 10.6 minutes #-------------------------------------------- #@# Smooth2 lh Sat Jul 16 01:22:22 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Sat Jul 16 01:22:31 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 43.5 mm, total surface area = 65234 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.110 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (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=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 1.8 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 259 vertices thresholded to be in k1 ~ [-0.21 0.43], k2 ~ [-0.11 0.07] total integrated curvature = 0.612*4pi (7.688) --> 0 handles ICI = 1.5, FI = 7.3, variation=133.964 135 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 = 0.001 131 vertices thresholded to be in [-0.14 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Sat Jul 16 01:26:24 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm CA149base 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 [ CA149base/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 [ 174 ] Gb_filter = 0 WARN: S lookup min: -0.068964 WARN: S explicit min: 0.000000 vertex = 1430 #-------------------------------------------- #@# Sphere lh Sat Jul 16 01:26:38 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 2.01 hours scaling brain by 0.339... pass 1: epoch 1 of 3 starting distance error %18.65 pass 1: epoch 2 of 3 starting distance error %18.64 unfolding complete - removing small folds... starting distance error %18.59 removing remaining folds... final distance error %18.61 expanding nbhd size to 1 #-------------------------------------------- #@# Surf Reg lh Sat Jul 16 03:27:24 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_register -curv ../surf/lh.sphere /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.615 curvature mean = 0.030, std = 0.936 curvature mean = 0.018, std = 0.890 curvature mean = 0.015, std = 0.972 curvature mean = 0.006, std = 0.958 curvature mean = 0.014, std = 0.986 curvature mean = 0.003, std = 0.983 curvature mean = 0.013, std = 0.990 curvature mean = 0.000, std = 0.993 curvature mean = -0.025, std = 0.272 curvature mean = 0.003, std = 0.068 curvature mean = 0.046, std = 0.404 curvature mean = 0.003, std = 0.082 curvature mean = 0.016, std = 0.598 curvature mean = 0.003, std = 0.088 curvature mean = 0.009, std = 0.725 curvature mean = 0.003, std = 0.092 curvature mean = 0.003, std = 0.812 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat Jul 16 04:30:44 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sat Jul 16 04:30:49 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mrisp_paint -a 5 /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/share/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat Jul 16 04:30:53 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base lh ../surf/lh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 844 labels changed using aseg relabeling using gibbs priors... 000: 2442 changed, 107738 examined... 001: 568 changed, 10616 examined... 002: 127 changed, 3190 examined... 003: 47 changed, 763 examined... 004: 24 changed, 296 examined... 005: 7 changed, 146 examined... 006: 3 changed, 45 examined... 007: 0 changed, 21 examined... 170 labels changed using aseg 000: 105 total segments, 65 labels (175 vertices) changed 001: 41 total segments, 2 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1419 vertices marked for relabeling... 1419 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 39 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Jul 16 04:32:33 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7462 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 83.7 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.7 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.1 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=75 using class modes intead of means.... mean inside = 95.0, mean outside = 81.1 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->2.81) (max @ vno 81921 --> 107629) face area 0.28 +- 0.12 (0.00-->1.13) mean absolute distance = 0.86 +- 1.06 3018 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 206 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 23 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=84.5, 9 (9) missing vertices, mean dist 0.3 [0.9 (%35.4)->0.9 (%64.6))] %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->3.85) (max @ vno 81921 --> 107629) face area 0.28 +- 0.13 (0.00-->1.66) mean absolute distance = 0.45 +- 0.86 2978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3295717.5, rms=8.55 001: dt: 0.5000, sse=3713652.5, rms=6.06 002: dt: 0.5000, sse=3857956.2, rms=4.38 003: dt: 0.5000, sse=4058731.0, rms=3.31 004: dt: 0.5000, sse=4139295.8, rms=2.67 005: dt: 0.5000, sse=4224950.0, rms=2.35 006: dt: 0.5000, sse=4223366.0, rms=2.21 007: dt: 0.5000, sse=4263232.0, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4255626.5, rms=2.11 009: dt: 0.2500, sse=2632026.5, rms=1.48 010: dt: 0.2500, sse=2482888.8, rms=1.40 rms = 1.39, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2439602.2, rms=1.39 rms = 1.37, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2412031.5, rms=1.37 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 150 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown deleting segment 10 with 103 points - only 20.39% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=86.4, 26 (1) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %57 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.06-->4.07) (max @ vno 70431 --> 69542) face area 0.35 +- 0.16 (0.00-->2.17) mean absolute distance = 0.38 +- 0.53 3520 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2763453.0, rms=3.78 013: dt: 0.5000, sse=2982197.5, rms=2.38 014: dt: 0.5000, sse=3214474.8, rms=1.88 015: dt: 0.5000, sse=3257349.0, rms=1.67 rms = 1.65, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=3504993.5, rms=1.65 017: dt: 0.2500, sse=2730598.2, rms=1.25 018: dt: 0.2500, sse=2627259.0, rms=1.19 rms = 1.19, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2599168.2, rms=1.19 rms = 1.18, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2577158.8, rms=1.18 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 181 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 81 points - only 25.93% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown mean border=89.2, 21 (1) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->4.50) (max @ vno 70431 --> 69542) face area 0.34 +- 0.16 (0.00-->2.33) mean absolute distance = 0.28 +- 0.37 2965 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2830717.8, rms=3.78 021: dt: 0.5000, sse=2976108.8, rms=2.07 022: dt: 0.5000, sse=3132238.5, rms=1.65 023: dt: 0.5000, sse=3236581.5, rms=1.49 rms = 1.60, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=2889254.2, rms=1.23 025: dt: 0.2500, sse=2766427.2, rms=1.12 rms = 1.11, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2730579.0, rms=1.11 rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2713168.8, rms=1.10 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 190 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 78 points - only 26.92% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown mean border=90.3, 34 (0) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.2 (%39.2))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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=2745304.8, rms=1.86 028: dt: 0.5000, sse=3258741.2, rms=1.16 rms = 1.31, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3048059.2, rms=0.98 030: dt: 0.2500, sse=2941546.5, rms=0.92 rms = 0.91, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2960732.0, rms=0.91 rms = 0.91, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=2960732.0, rms=0.91 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=63.9, 23 (23) missing vertices, mean dist 1.9 [3.7 (%0.0)->2.5 (%100.0))] %33 local maxima, %41 large gradients and %22 min vals, 757 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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=17218796.0, rms=27.26 001: dt: 0.5000, sse=14020590.0, rms=24.26 002: dt: 0.5000, sse=11444568.0, rms=21.58 003: dt: 0.5000, sse=9468405.0, rms=19.19 004: dt: 0.5000, sse=8044845.0, rms=17.06 005: dt: 0.5000, sse=6992998.0, rms=15.12 006: dt: 0.5000, sse=6196389.0, rms=13.35 007: dt: 0.5000, sse=5553184.5, rms=11.60 008: dt: 0.5000, sse=5032635.0, rms=9.87 009: dt: 0.5000, sse=4679310.0, rms=8.18 010: dt: 0.5000, sse=4470950.0, rms=6.70 011: dt: 0.5000, sse=4413658.0, rms=5.52 012: dt: 0.5000, sse=4461597.0, rms=4.76 013: dt: 0.5000, sse=4539051.0, rms=4.31 014: dt: 0.5000, sse=4582165.5, rms=4.04 015: dt: 0.5000, sse=4604929.5, rms=3.88 016: dt: 0.5000, sse=4648533.0, rms=3.77 017: dt: 0.5000, sse=4622838.5, rms=3.68 018: dt: 0.5000, sse=4645615.0, rms=3.63 019: dt: 0.5000, sse=4633281.5, rms=3.58 rms = 3.55, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=4672408.0, rms=3.55 021: dt: 0.2500, sse=2927254.8, rms=2.55 022: dt: 0.2500, sse=2725787.2, rms=2.27 023: dt: 0.2500, sse=2632736.0, rms=2.20 rms = 2.17, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=2596539.8, rms=2.17 025: dt: 0.1250, sse=2482972.2, rms=2.06 rms = 2.04, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2474079.8, rms=2.04 positioning took 4.9 minutes mean border=61.0, 562 (3) missing vertices, mean dist 0.2 [0.2 (%35.6)->0.4 (%64.4))] %51 local maxima, %29 large gradients and %15 min vals, 353 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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=3026981.0, rms=4.88 027: dt: 0.5000, sse=3132055.5, rms=3.37 rms = 3.48, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=2876624.2, rms=2.63 029: dt: 0.2500, sse=2858784.5, rms=2.24 030: dt: 0.2500, sse=2829848.8, rms=2.09 031: dt: 0.2500, sse=2818531.5, rms=2.03 rms = 2.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=2827632.5, rms=2.00 033: dt: 0.1250, sse=2750646.5, rms=1.91 rms = 1.90, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=2744104.0, rms=1.90 positioning took 1.4 minutes mean border=59.4, 658 (3) missing vertices, mean dist 0.1 [0.2 (%35.4)->0.3 (%64.6))] %64 local maxima, %16 large gradients and %15 min vals, 342 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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=2849652.2, rms=2.87 rms = 3.14, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=2747334.0, rms=2.27 036: dt: 0.2500, sse=2766987.2, rms=1.96 037: dt: 0.2500, sse=2821522.5, rms=1.88 rms = 1.86, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=2836499.5, rms=1.86 039: dt: 0.1250, sse=2785453.0, rms=1.80 rms = 1.79, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=2778287.0, rms=1.79 positioning took 1.0 minutes mean border=58.6, 1399 (3) missing vertices, mean dist 0.0 [0.2 (%43.6)->0.2 (%56.4))] %69 local maxima, %11 large gradients and %14 min vals, 310 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=2798088.5, rms=2.07 rms = 2.55, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=2749086.2, rms=1.85 042: dt: 0.2500, sse=2817024.0, rms=1.78 rms = 1.75, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=2836532.5, rms=1.75 rms = 1.71, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=2796414.2, rms=1.71 positioning took 0.7 minutes writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.area.pial vertex spacing 0.98 +- 0.39 (0.02-->6.53) (max @ vno 50951 --> 50950) face area 0.38 +- 0.27 (0.00-->6.72) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 107738 vertices processed 25000 of 107738 vertices processed 50000 of 107738 vertices processed 75000 of 107738 vertices processed 100000 of 107738 vertices processed 0 of 107738 vertices processed 25000 of 107738 vertices processed 50000 of 107738 vertices processed 75000 of 107738 vertices processed 100000 of 107738 vertices processed thickness calculation complete, 821:637 truncations. 51847 vertices at 0 distance 69833 vertices at 1 distance 50889 vertices at 2 distance 20084 vertices at 3 distance 7714 vertices at 4 distance 3038 vertices at 5 distance 1190 vertices at 6 distance 472 vertices at 7 distance 244 vertices at 8 distance 148 vertices at 9 distance 76 vertices at 10 distance 59 vertices at 11 distance 39 vertices at 12 distance 48 vertices at 13 distance 40 vertices at 14 distance 40 vertices at 15 distance 25 vertices at 16 distance 28 vertices at 17 distance 16 vertices at 18 distance 20 vertices at 19 distance 16 vertices at 20 distance writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.thickness positioning took 18.6 minutes #-------------------------------------------- #@# Surf Volume lh Sat Jul 16 04:51:11 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 ] #----------------------------------------- #@# Parcellation Stats lh Sat Jul 16 04:51:13 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1325 906 2253 2.499 0.520 0.101 0.023 7 1.3 bankssts 1006 649 2109 3.494 0.541 0.154 0.044 19 1.7 caudalanteriorcingulate 2729 1797 5100 2.584 0.494 0.124 0.038 26 4.2 caudalmiddlefrontal 1882 1168 2037 1.732 0.465 0.165 0.055 34 4.4 cuneus 567 381 1693 3.327 0.729 0.126 0.034 5 0.8 entorhinal 3580 2459 7213 2.653 0.759 0.149 0.048 47 6.7 fusiform 5401 3554 9186 2.345 0.558 0.133 0.060 84 15.6 inferiorparietal 3971 2702 8853 2.938 0.755 0.147 0.045 59 7.1 inferiortemporal 1210 768 2044 2.647 0.677 0.139 0.052 17 2.0 isthmuscingulate 5674 3618 8942 2.270 0.568 0.149 0.051 83 11.2 lateraloccipital 2960 1958 5624 2.694 0.500 0.137 0.046 37 5.6 lateralorbitofrontal 3808 2573 4500 1.689 0.533 0.150 0.049 49 7.9 lingual 2432 1636 4486 2.523 0.712 0.147 0.124 58 7.3 medialorbitofrontal 3041 2099 7571 2.939 0.693 0.143 0.046 45 5.7 middletemporal 860 580 2122 3.082 0.814 0.103 0.026 6 0.8 parahippocampal 1924 1146 2579 2.104 0.525 0.106 0.029 14 2.4 paracentral 2148 1438 3907 2.496 0.526 0.120 0.031 22 2.7 parsopercularis 862 539 2032 2.935 0.544 0.153 0.062 16 1.9 parsorbitalis 1687 1130 2894 2.260 0.593 0.122 0.029 16 2.0 parstriangularis 1438 947 1250 1.445 0.411 0.158 0.068 42 4.7 pericalcarine 5675 3584 7931 1.994 0.597 0.119 0.035 61 8.7 postcentral 1596 1037 2844 2.593 0.583 0.148 0.076 31 5.4 posteriorcingulate 6086 3750 10193 2.529 0.540 0.116 0.042 77 9.6 precentral 4297 2844 6672 2.207 0.558 0.137 0.039 53 6.8 precuneus 1245 825 2626 2.820 0.824 0.145 0.052 22 2.4 rostralanteriorcingulate 5590 3822 10119 2.423 0.581 0.158 0.055 91 12.1 rostralmiddlefrontal 8119 5437 16189 2.641 0.550 0.137 0.046 106 16.4 superiorfrontal 6268 4062 9446 2.129 0.517 0.115 0.031 59 7.7 superiorparietal 4305 2858 9371 2.880 0.735 0.116 0.032 41 5.8 superiortemporal 4412 2954 8443 2.653 0.504 0.139 0.043 56 7.2 supramarginal 175 131 471 2.632 0.406 0.179 0.058 3 0.3 frontalpole 607 426 2562 4.026 0.474 0.164 0.074 12 1.6 temporalpole 636 386 992 2.372 0.424 0.124 0.038 6 1.0 transversetemporal 3136 2032 6572 3.228 0.887 0.140 0.072 54 8.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Jul 16 04:51:49 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base lh ../surf/lh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 31 labels changed using aseg relabeling using gibbs priors... 000: 7462 changed, 107738 examined... 001: 1761 changed, 28734 examined... 002: 515 changed, 9052 examined... 003: 215 changed, 2858 examined... 004: 92 changed, 1212 examined... 005: 38 changed, 509 examined... 006: 18 changed, 209 examined... 007: 7 changed, 97 examined... 008: 8 changed, 50 examined... 009: 5 changed, 35 examined... 010: 1 changed, 24 examined... 011: 0 changed, 5 examined... 22 labels changed using aseg 000: 224 total segments, 141 labels (1199 vertices) changed 001: 89 total segments, 7 labels (33 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 95 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 951 vertices marked for relabeling... 951 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 48 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Jul 16 04:53:38 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 771 581 1492 2.443 0.694 0.176 0.053 13 1.7 G_and_S_frontomargin 1303 860 2150 2.281 0.614 0.147 0.048 17 2.5 G_and_S_occipital_inf 1320 719 1801 2.055 0.552 0.106 0.028 15 1.6 G_and_S_paracentral 1195 814 2364 2.571 0.359 0.155 0.046 17 2.3 G_and_S_subcentral 557 390 1251 2.486 0.484 0.181 0.055 11 1.2 G_and_S_transv_frontopol 2232 1532 4304 2.658 0.693 0.142 0.044 32 3.9 G_and_S_cingul-Ant 1315 881 2451 2.964 0.587 0.145 0.042 20 2.3 G_and_S_cingul-Mid-Ant 1309 898 2184 2.431 0.490 0.138 0.038 15 2.0 G_and_S_cingul-Mid-Post 472 293 1057 3.011 0.329 0.178 0.072 10 1.6 G_cingul-Post-dorsal 317 181 479 2.490 0.770 0.117 0.037 3 0.4 G_cingul-Post-ventral 1578 951 1874 1.810 0.508 0.172 0.064 32 4.3 G_cuneus 1113 737 2505 2.709 0.404 0.143 0.041 16 1.9 G_front_inf-Opercular 263 151 667 3.029 0.493 0.144 0.083 6 0.7 G_front_inf-Orbital 1031 676 2159 2.501 0.500 0.136 0.036 13 1.5 G_front_inf-Triangul 3165 2080 6901 2.628 0.502 0.159 0.063 56 7.6 G_front_middle 5490 3493 12031 2.733 0.538 0.139 0.054 83 13.2 G_front_sup 510 290 1035 3.111 0.622 0.174 0.123 20 2.5 G_Ins_lg_and_S_cent_ins 637 391 1929 3.935 0.775 0.163 0.097 14 2.3 G_insular_short 1675 1035 3278 2.577 0.438 0.148 0.068 33 4.2 G_occipital_middle 1325 848 2148 2.205 0.525 0.128 0.036 15 2.0 G_occipital_sup 1333 901 2789 2.647 0.641 0.152 0.052 19 2.7 G_oc-temp_lat-fusifor 2989 1961 3635 1.708 0.555 0.160 0.055 44 7.0 G_oc-temp_med-Lingual 1120 757 3540 3.444 0.748 0.124 0.036 11 1.5 G_oc-temp_med-Parahip 2253 1433 5120 2.860 0.534 0.152 0.059 38 5.3 G_orbital 2047 1318 4448 2.705 0.524 0.161 0.097 56 10.2 G_pariet_inf-Angular 2354 1546 5325 2.807 0.435 0.149 0.051 38 4.7 G_pariet_inf-Supramar 2063 1327 3771 2.271 0.507 0.115 0.037 23 2.8 G_parietal_sup 2246 1318 3455 2.147 0.523 0.119 0.040 28 4.0 G_postcentral 2337 1236 4563 2.775 0.456 0.113 0.061 44 4.7 G_precentral 1984 1286 3897 2.445 0.459 0.147 0.043 31 3.4 G_precuneus 897 605 2118 2.637 0.607 0.164 0.071 19 2.8 G_rectus 355 220 520 2.411 0.837 0.181 0.491 26 2.7 G_subcallosal 527 300 898 2.412 0.394 0.125 0.044 6 1.0 G_temp_sup-G_T_transv 1592 1021 4519 3.188 0.594 0.139 0.040 21 2.7 G_temp_sup-Lateral 513 357 1476 3.821 0.506 0.115 0.030 4 0.6 G_temp_sup-Plan_polar 684 481 1359 2.481 0.557 0.111 0.037 6 1.0 G_temp_sup-Plan_tempo 2162 1453 5903 3.201 0.667 0.167 0.056 44 4.6 G_temporal_inf 1952 1330 5449 3.055 0.536 0.157 0.057 36 4.4 G_temporal_middle 336 226 374 1.785 0.515 0.099 0.017 2 0.2 Lat_Fis-ant-Horizont 301 218 394 1.978 0.460 0.099 0.020 1 0.3 Lat_Fis-ant-Vertical 936 638 1128 2.132 0.486 0.121 0.038 7 1.2 Lat_Fis-post 1928 1202 2815 2.071 0.573 0.162 0.059 30 4.7 Pole_occipital 1497 1041 5465 3.792 0.721 0.159 0.062 25 3.6 Pole_temporal 1849 1259 1812 1.573 0.556 0.146 0.056 45 5.0 S_calcarine 2852 1916 3171 1.843 0.663 0.111 0.029 20 3.6 S_central 1035 684 1290 1.987 0.492 0.115 0.028 9 1.2 S_cingul-Marginalis 406 287 710 3.007 0.564 0.114 0.036 2 0.6 S_circular_insula_ant 1388 955 2400 2.937 0.893 0.085 0.019 5 1.0 S_circular_insula_inf 1645 1139 2533 2.545 0.622 0.119 0.031 12 2.2 S_circular_insula_sup 962 672 1554 2.526 0.671 0.121 0.027 9 1.1 S_collat_transv_ant 245 164 245 1.884 0.406 0.152 0.048 3 0.5 S_collat_transv_post 1652 1124 2310 2.211 0.431 0.119 0.032 15 2.0 S_front_inf 990 672 1370 2.154 0.587 0.134 0.040 12 1.6 S_front_middle 2110 1452 3247 2.475 0.475 0.115 0.027 14 2.5 S_front_sup 325 243 439 2.410 0.546 0.134 0.026 2 0.5 S_interm_prim-Jensen 2347 1537 2883 1.997 0.479 0.113 0.026 18 2.4 S_intrapariet_and_P_trans 894 581 1263 2.420 0.460 0.149 0.051 12 1.7 S_oc_middle_and_Lunatus 1037 696 1176 1.861 0.420 0.102 0.022 5 1.0 S_oc_sup_and_transversal 406 295 635 2.214 0.304 0.116 0.025 3 0.4 S_occipital_ant 626 422 867 2.447 0.411 0.155 0.043 9 1.0 S_oc-temp_lat 1417 984 1966 2.179 0.623 0.120 0.031 11 1.7 S_oc-temp_med_and_Lingual 292 210 487 2.414 0.541 0.153 0.042 3 0.6 S_orbital_lateral 769 534 1270 2.600 0.760 0.143 0.078 13 1.8 S_orbital_med-olfact 874 604 1365 2.428 0.443 0.126 0.032 7 1.2 S_orbital-H_Shaped 1691 1133 1821 1.818 0.544 0.129 0.036 16 2.6 S_parieto_occipital 983 614 1400 3.001 0.987 0.155 0.092 24 3.6 S_pericallosal 2502 1659 3438 2.196 0.574 0.114 0.027 20 2.9 S_postcentral 1357 898 2100 2.529 0.473 0.116 0.028 10 1.7 S_precentral-inf-part 982 694 1422 2.334 0.475 0.103 0.020 5 0.9 S_precentral-sup-part 482 328 823 2.859 0.819 0.117 0.039 5 0.5 S_suborbital 856 574 1271 2.356 0.494 0.135 0.049 8 1.3 S_subparietal 1155 814 1805 2.557 0.532 0.124 0.027 8 1.5 S_temporal_inf 4229 2851 6288 2.304 0.556 0.107 0.027 29 4.7 S_temporal_sup 310 223 444 2.661 0.539 0.122 0.026 3 0.3 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Sat Jul 16 04:54:26 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 = 2 (out of 220413: 0.000907) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 70: 1871 vertices, 2014 faces slice 80: 8130 vertices, 8403 faces slice 90: 17828 vertices, 18160 faces slice 100: 27899 vertices, 28237 faces slice 110: 37324 vertices, 37608 faces slice 120: 47308 vertices, 47645 faces slice 130: 56924 vertices, 57274 faces slice 140: 66296 vertices, 66633 faces slice 150: 75298 vertices, 75636 faces slice 160: 83910 vertices, 84223 faces slice 170: 90966 vertices, 91210 faces slice 180: 97108 vertices, 97315 faces slice 190: 102267 vertices, 102467 faces slice 200: 106187 vertices, 106301 faces slice 210: 107700 vertices, 107718 faces slice 220: 107700 vertices, 107718 faces slice 230: 107700 vertices, 107718 faces slice 240: 107700 vertices, 107718 faces slice 250: 107700 vertices, 107718 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... 107700 voxel in cpt #1: X=-18 [v=107700,e=323154,f=215436] located at (27.432730, -0.096760, 4.756945) For the whole surface: X=-18 [v=107700,e=323154,f=215436] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat Jul 16 04:54:50 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Sat Jul 16 04:54:58 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts avg radius = 42.8 mm, total surface area = 57540 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.5 minutes Not saving sulc step 000: RMS=0.096 (target=0.015) step 005: RMS=0.070 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.043 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (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 rh Sat Jul 16 04:56:28 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.12 +- 0.60 (0.00-->6.52) (max @ vno 49973 --> 50874) face area 0.03 +- 0.04 (-0.33-->0.80) scaling brain by 0.361... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.839, avgs=0 005/300: dt: 0.9000, rms radial error=175.580, avgs=0 010/300: dt: 0.9000, rms radial error=175.025, avgs=0 015/300: dt: 0.9000, rms radial error=174.295, avgs=0 020/300: dt: 0.9000, rms radial error=173.464, avgs=0 025/300: dt: 0.9000, rms radial error=172.577, avgs=0 030/300: dt: 0.9000, rms radial error=171.663, avgs=0 035/300: dt: 0.9000, rms radial error=170.732, avgs=0 040/300: dt: 0.9000, rms radial error=169.794, avgs=0 045/300: dt: 0.9000, rms radial error=168.853, avgs=0 050/300: dt: 0.9000, rms radial error=167.914, avgs=0 055/300: dt: 0.9000, rms radial error=166.977, avgs=0 060/300: dt: 0.9000, rms radial error=166.043, avgs=0 065/300: dt: 0.9000, rms radial error=165.114, avgs=0 070/300: dt: 0.9000, rms radial error=164.189, avgs=0 075/300: dt: 0.9000, rms radial error=163.269, avgs=0 080/300: dt: 0.9000, rms radial error=162.353, avgs=0 085/300: dt: 0.9000, rms radial error=161.442, avgs=0 090/300: dt: 0.9000, rms radial error=160.536, avgs=0 095/300: dt: 0.9000, rms radial error=159.635, avgs=0 100/300: dt: 0.9000, rms radial error=158.739, avgs=0 105/300: dt: 0.9000, rms radial error=157.848, avgs=0 110/300: dt: 0.9000, rms radial error=156.962, avgs=0 115/300: dt: 0.9000, rms radial error=156.081, avgs=0 120/300: dt: 0.9000, rms radial error=155.204, avgs=0 125/300: dt: 0.9000, rms radial error=154.333, avgs=0 130/300: dt: 0.9000, rms radial error=153.466, avgs=0 135/300: dt: 0.9000, rms radial error=152.604, avgs=0 140/300: dt: 0.9000, rms radial error=151.747, avgs=0 145/300: dt: 0.9000, rms radial error=150.895, avgs=0 150/300: dt: 0.9000, rms radial error=150.048, avgs=0 155/300: dt: 0.9000, rms radial error=149.204, avgs=0 160/300: dt: 0.9000, rms radial error=148.366, avgs=0 165/300: dt: 0.9000, rms radial error=147.532, avgs=0 170/300: dt: 0.9000, rms radial error=146.703, avgs=0 175/300: dt: 0.9000, rms radial error=145.878, avgs=0 180/300: dt: 0.9000, rms radial error=145.058, avgs=0 185/300: dt: 0.9000, rms radial error=144.242, avgs=0 190/300: dt: 0.9000, rms radial error=143.431, avgs=0 195/300: dt: 0.9000, rms radial error=142.624, avgs=0 200/300: dt: 0.9000, rms radial error=141.821, avgs=0 205/300: dt: 0.9000, rms radial error=141.023, avgs=0 210/300: dt: 0.9000, rms radial error=140.230, avgs=0 215/300: dt: 0.9000, rms radial error=139.440, avgs=0 220/300: dt: 0.9000, rms radial error=138.655, avgs=0 225/300: dt: 0.9000, rms radial error=137.875, avgs=0 230/300: dt: 0.9000, rms radial error=137.098, avgs=0 235/300: dt: 0.9000, rms radial error=136.326, avgs=0 240/300: dt: 0.9000, rms radial error=135.558, avgs=0 245/300: dt: 0.9000, rms radial error=134.795, avgs=0 250/300: dt: 0.9000, rms radial error=134.035, avgs=0 255/300: dt: 0.9000, rms radial error=133.280, avgs=0 260/300: dt: 0.9000, rms radial error=132.530, avgs=0 265/300: dt: 0.9000, rms radial error=131.783, avgs=0 270/300: dt: 0.9000, rms radial error=131.040, avgs=0 275/300: dt: 0.9000, rms radial error=130.302, avgs=0 280/300: dt: 0.9000, rms radial error=129.568, avgs=0 285/300: dt: 0.9000, rms radial error=128.838, avgs=0 290/300: dt: 0.9000, rms radial error=128.112, avgs=0 295/300: dt: 0.9000, rms radial error=127.390, avgs=0 300/300: dt: 0.9000, rms radial error=126.672, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11866.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 1750.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00031 epoch 3 (K=160.0), pass 1, starting sse = 142.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/12 = 0.01110 epoch 4 (K=640.0), pass 1, starting sse = 6.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/15 = 0.01283 final dwriting spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.18 hours istance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat Jul 16 05:07:29 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 CA149base 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-18 (nv=107700, nf=215436, ne=323154, g=10) 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 5 iterations marking ambiguous vertices... 1589 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 5 -merging segment 17 into 5 19 defects to be corrected 0 vertices coincident reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7448 (-4.3724) -vertex loglikelihood: -5.7542 (-2.8771) -normal dot loglikelihood: -3.6713 (-3.6713) -quad curv loglikelihood: -6.4561 (-3.2281) Total Loglikelihood : -24.6264 CORRECTING DEFECT 0 (vertices=200, convex hull=217) After retessellation of defect 0, euler #=-18 (106686,319664,212960) : difference with theory (-16) = 2 CORRECTING DEFECT 1 (vertices=14, convex hull=29) After retessellation of defect 1, euler #=-17 (106691,319688,212980) : difference with theory (-15) = 2 CORRECTING DEFECT 2 (vertices=55, convex hull=46) After retessellation of defect 2, euler #=-16 (106701,319735,213018) : difference with theory (-14) = 2 CORRECTING DEFECT 3 (vertices=67, convex hull=100) After retessellation of defect 3, euler #=-15 (106742,319903,213146) : difference with theory (-13) = 2 CORRECTING DEFECT 4 (vertices=8, convex hull=19) After retessellation of defect 4, euler #=-14 (106746,319920,213160) : difference with theory (-12) = 2 CORRECTING DEFECT 5 (vertices=291, convex hull=221) After retessellation of defect 5, euler #=-11 (106835,320299,213453) : difference with theory (-11) = 0 CORRECTING DEFECT 6 (vertices=9, convex hull=29) Warning - incorrect dp selected!!!!(-84.030656 >= -84.030663 ) After retessellation of defect 6, euler #=-10 (106837,320313,213466) : difference with theory (-10) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=76) After retessellation of defect 7, euler #=-9 (106850,320378,213519) : difference with theory (-9) = 0 CORRECTING DEFECT 8 (vertices=30, convex hull=54) After retessellation of defect 8, euler #=-8 (106867,320448,213573) : difference with theory (-8) = 0 CORRECTING DEFECT 9 (vertices=14, convex hull=21) After retessellation of defect 9, euler #=-7 (106869,320461,213585) : difference with theory (-7) = 0 CORRECTING DEFECT 10 (vertices=42, convex hull=76) After retessellation of defect 10, euler #=-6 (106878,320516,213632) : difference with theory (-6) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=23) After retessellation of defect 11, euler #=-5 (106880,320528,213643) : difference with theory (-5) = 0 CORRECTING DEFECT 12 (vertices=26, convex hull=22) After retessellation of defect 12, euler #=-4 (106884,320546,213658) : difference with theory (-4) = 0 CORRECTING DEFECT 13 (vertices=34, convex hull=54) After retessellation of defect 13, euler #=-3 (106895,320599,213701) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=11, convex hull=23) After retessellation of defect 14, euler #=-2 (106896,320608,213710) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=114, convex hull=63) After retessellation of defect 15, euler #=-1 (106906,320664,213757) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=10, convex hull=25) After retessellation of defect 16, euler #=0 (106908,320677,213769) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=32, convex hull=65) After retessellation of defect 17, euler #=1 (106928,320763,213836) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=28, convex hull=40) After retessellation of defect 18, euler #=2 (106934,320796,213864) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.07-->8.34) (max @ vno 39919 --> 46904) 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 (0.07-->8.34) (max @ vno 39919 --> 46904) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 90 mutations (35.9%), 161 crossovers (64.1%), 102 vertices were eliminated building final representation... 766 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=106934, nf=213864, ne=320796, g=0) writing corrected surface to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 33.9 minutes 0 defective edges removing intersecting faces 000: 140 intersecting 001: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 106934 - 320796 + 213864 = 2 --> 0 holes F =2V-4: 213864 = 213868-4 (0) 2E=3F: 641592 = 641592 (0) total defect index = 0 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Jul 16 05:41:35 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7076 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.2 +- 6.4 [70.0 --> 110.0] GM (86.0) : 83.9 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 108.4 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.4 (was 40) setting MAX_GRAY to 95.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->4.63) (max @ vno 39919 --> 46904) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.82 +- 1.04 2997 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=76 using class modes intead of means.... mean inside = 94.8, mean outside = 81.0 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 3 vertex label from ripped group mean border=85.1, 49 (49) missing vertices, mean dist 0.2 [0.8 (%38.1)->0.8 (%61.9))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.24) (max @ vno 50644 --> 106680) face area 0.28 +- 0.13 (0.00-->3.20) mean absolute distance = 0.44 +- 0.83 2892 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3107924.5, rms=8.09 001: dt: 0.5000, sse=3630637.8, rms=5.65 002: dt: 0.5000, sse=3785014.8, rms=4.09 003: dt: 0.5000, sse=3954610.8, rms=3.14 004: dt: 0.5000, sse=4050235.0, rms=2.60 005: dt: 0.5000, sse=4133877.8, rms=2.32 006: dt: 0.5000, sse=4147756.8, rms=2.20 007: dt: 0.5000, sse=4173903.2, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4171583.5, rms=2.11 009: dt: 0.2500, sse=2615376.5, rms=1.48 010: dt: 0.2500, sse=2460308.8, rms=1.39 rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2415770.5, rms=1.37 rms = 1.35, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2391620.2, rms=1.35 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.9, 26 (6) missing vertices, mean dist -0.2 [0.5 (%62.3)->0.3 (%37.7))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.10-->4.51) (max @ vno 50644 --> 106680) face area 0.35 +- 0.16 (0.00-->4.20) mean absolute distance = 0.37 +- 0.52 3119 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2687874.8, rms=3.58 013: dt: 0.5000, sse=2909154.8, rms=2.21 014: dt: 0.5000, sse=3126316.5, rms=1.79 015: dt: 0.5000, sse=3189664.5, rms=1.62 rms = 1.63, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=2785005.8, rms=1.38 017: dt: 0.2500, sse=2623047.8, rms=1.23 rms = 1.20, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=2577220.5, rms=1.20 rms = 1.18, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=2554407.2, rms=1.18 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.3, 23 (3) missing vertices, mean dist -0.2 [0.4 (%69.5)->0.2 (%30.5))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->4.69) (max @ vno 50644 --> 106680) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.28 +- 0.37 2959 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2756407.2, rms=3.44 020: dt: 0.5000, sse=2932529.0, rms=1.92 021: dt: 0.5000, sse=3065163.0, rms=1.58 022: dt: 0.5000, sse=3159964.5, rms=1.44 rms = 1.56, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=2852330.5, rms=1.20 024: dt: 0.2500, sse=2745482.5, rms=1.11 rms = 1.11, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=2706253.0, rms=1.11 rms = 1.10, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2690933.0, rms=1.10 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.3, 24 (2) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=2719204.8, rms=1.78 027: dt: 0.5000, sse=3232179.5, rms=1.12 rms = 1.27, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3026501.5, rms=0.96 rms = 0.92, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=2920557.5, rms=0.92 rms = 0.91, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=2928191.0, rms=0.91 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 2164 vertices erasing segment 1 (vno[0] = 45802) erasing segment 2 (vno[0] = 47859) erasing segment 3 (vno[0] = 70186) erasing segment 4 (vno[0] = 70208) erasing segment 5 (vno[0] = 74423) erasing segment 6 (vno[0] = 76328) erasing segment 7 (vno[0] = 76904) erasing segment 8 (vno[0] = 77804) erasing segment 9 (vno[0] = 79413) erasing segment 10 (vno[0] = 80271) erasing segment 11 (vno[0] = 82670) erasing segment 12 (vno[0] = 85006) writing cortex label to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.cortex.label... LabelWrite: saving to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.cortex.label writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.curv writing smoothed area to rh.area writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->4.76) (max @ vno 50644 --> 106680) face area 0.33 +- 0.16 (0.00-->4.37) refinement took 7.8 minutes #-------------------------------------------- #@# Smooth2 rh Sat Jul 16 05:49:24 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Sat Jul 16 05:49:30 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 43.0 mm, total surface area = 64828 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 1.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 227 vertices thresholded to be in k1 ~ [-0.24 0.43], k2 ~ [-0.15 0.06] total integrated curvature = 0.612*4pi (7.685) --> 0 handles ICI = 1.4, FI = 7.2, variation=129.147 149 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 133 vertices thresholded to be in [-0.15 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats rh Sat Jul 16 05:52:29 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm CA149base 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 [ CA149base/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 [ 196 ] Gb_filter = 0 WARN: S lookup min: -1.023468 WARN: S explicit min: 0.000000 vertex = 487 #-------------------------------------------- #@# Sphere rh Sat Jul 16 05:52:41 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 0.90 hours scaling brain by 0.338... pass 1: epoch 1 of 3 starting distance error %40.13 pass 1: epoch 2 of 3 starting distance error %18.68 unfolding complete - removing small folds... starting distance error %18.63 removing remaining folds... final distance error %18.65 #-------------------------------------------- #@# Surf Reg rh Sat Jul 16 06:46:51 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_register -curv ../surf/rh.sphere /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.610 curvature mean = 0.024, std = 0.941 curvature mean = 0.018, std = 0.889 curvature mean = 0.009, std = 0.970 curvature mean = 0.006, std = 0.957 curvature mean = 0.007, std = 0.983 curvature mean = 0.002, std = 0.982 curvature mean = 0.007, std = 0.986 curvature mean = 0.000, std = 0.993 curvature mean = -0.027, std = 0.270 curvature mean = 0.004, std = 0.072 curvature mean = 0.048, std = 0.406 curvature mean = 0.004, std = 0.087 curvature mean = 0.017, std = 0.603 curvature mean = 0.004, std = 0.094 curvature mean = 0.008, std = 0.736 curvature mean = 0.004, std = 0.097 curvature mean = 0.002, std = 0.823 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat Jul 16 07:42:48 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Sat Jul 16 07:42:52 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mrisp_paint -a 5 /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/share/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Sat Jul 16 07:42:55 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base rh ../surf/rh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 806 labels changed using aseg relabeling using gibbs priors... 000: 2468 changed, 106934 examined... 001: 535 changed, 10543 examined... 002: 129 changed, 3065 examined... 003: 64 changed, 777 examined... 004: 33 changed, 353 examined... 005: 9 changed, 186 examined... 006: 2 changed, 56 examined... 007: 0 changed, 12 examined... 168 labels changed using aseg 000: 80 total segments, 38 labels (194 vertices) changed 001: 43 total segments, 1 labels (1 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1117 vertices marked for relabeling... 1117 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 27 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat Jul 16 07:44:23 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs CA149base 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/brain.finalsurfs.mgz... reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... 7076 bright wm thresholded. 1 bright non-wm voxels segmented. reading original surface position from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.orig... computing class statistics... border white: 207784 voxels (1.24%) border gray 219857 voxels (1.31%) WM (95.0): 96.2 +- 6.4 [70.0 --> 110.0] GM (86.0) : 83.9 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 108.4 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 54.4 (was 40) setting MAX_GRAY to 95.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=76 using class modes intead of means.... mean inside = 94.8, mean outside = 81.0 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->4.63) (max @ vno 39919 --> 46904) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.83 +- 1.04 3048 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 276 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 16 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=85.1, 50 (50) missing vertices, mean dist 0.2 [0.8 (%38.1)->0.8 (%61.9))] %52 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.24) (max @ vno 50644 --> 106680) face area 0.28 +- 0.13 (0.00-->3.20) mean absolute distance = 0.45 +- 0.84 2978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3114665.8, rms=8.09 001: dt: 0.5000, sse=3643488.5, rms=5.65 002: dt: 0.5000, sse=3796720.0, rms=4.09 003: dt: 0.5000, sse=3967666.5, rms=3.14 004: dt: 0.5000, sse=4062164.0, rms=2.60 005: dt: 0.5000, sse=4145953.8, rms=2.33 006: dt: 0.5000, sse=4160315.5, rms=2.20 007: dt: 0.5000, sse=4187330.8, rms=2.14 rms = 2.11, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=4184699.5, rms=2.11 009: dt: 0.2500, sse=2628285.5, rms=1.49 010: dt: 0.2500, sse=2473458.2, rms=1.39 rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2427971.8, rms=1.37 rms = 1.36, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2403428.5, rms=1.36 positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 256 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 22 points - only 0.00% unknown deleting segment 8 with 5 points - only 40.00% unknown deleting segment 9 with 148 points - only 52.03% unknown deleting segment 10 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown mean border=86.9, 58 (10) missing vertices, mean dist -0.2 [0.5 (%62.2)->0.3 (%37.8))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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 (0.10-->4.51) (max @ vno 50644 --> 106680) face area 0.35 +- 0.16 (0.00-->4.20) mean absolute distance = 0.37 +- 0.53 3210 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2725737.2, rms=3.59 013: dt: 0.5000, sse=2950717.8, rms=2.23 014: dt: 0.5000, sse=3172502.5, rms=1.80 015: dt: 0.5000, sse=3233262.5, rms=1.64 rms = 1.64, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=2826750.2, rms=1.39 017: dt: 0.2500, sse=2662212.2, rms=1.25 rms = 1.21, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=2615277.8, rms=1.21 rms = 1.20, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=2593846.0, rms=1.20 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 271 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 148 points - only 52.03% unknown deleting segment 6 with 23 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown mean border=89.3, 63 (4) missing vertices, mean dist -0.2 [0.4 (%69.4)->0.2 (%30.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->4.69) (max @ vno 50644 --> 106680) face area 0.34 +- 0.16 (0.00-->4.34) mean absolute distance = 0.28 +- 0.38 3032 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2795367.5, rms=3.44 020: dt: 0.5000, sse=2977493.8, rms=1.93 021: dt: 0.5000, sse=3109108.0, rms=1.59 022: dt: 0.5000, sse=3204135.2, rms=1.45 rms = 1.57, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=2894840.5, rms=1.21 024: dt: 0.2500, sse=2783224.5, rms=1.12 rms = 1.12, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=2745561.2, rms=1.12 rms = 1.11, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2732740.8, rms=1.11 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 276 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 148 points - only 52.03% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 20 points - only 0.00% unknown mean border=90.3, 86 (4) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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=2760861.0, rms=1.79 027: dt: 0.5000, sse=3287606.0, rms=1.13 rms = 1.28, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3076529.0, rms=0.97 rms = 0.93, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=2968223.2, rms=0.93 rms = 0.92, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=2976160.8, rms=0.92 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 11 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=64.9, 50 (50) missing vertices, mean dist 1.9 [3.0 (%0.0)->2.5 (%100.0))] %30 local maxima, %42 large gradients and %23 min vals, 997 gradients ignored tol=1.0e-04, sigma=2.0, host=magma, 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=16037579.0, rms=26.29 001: dt: 0.5000, sse=13046465.0, rms=23.37 002: dt: 0.5000, sse=10645415.0, rms=20.75 003: dt: 0.5000, sse=8822790.0, rms=18.43 004: dt: 0.5000, sse=7517294.5, rms=16.35 005: dt: 0.5000, sse=6534155.0, rms=14.47 006: dt: 0.5000, sse=5825918.0, rms=12.76 007: dt: 0.5000, sse=5300459.0, rms=11.15 008: dt: 0.5000, sse=4891596.5, rms=9.61 009: dt: 0.5000, sse=4606775.0, rms=8.13 010: dt: 0.5000, sse=4413434.0, rms=6.78 011: dt: 0.5000, sse=4355875.5, rms=5.64 012: dt: 0.5000, sse=4382588.0, rms=4.80 013: dt: 0.5000, sse=4416144.5, rms=4.25 014: dt: 0.5000, sse=4470795.5, rms=3.92 015: dt: 0.5000, sse=4511492.0, rms=3.72 016: dt: 0.5000, sse=4529339.5, rms=3.60 017: dt: 0.5000, sse=4553112.5, rms=3.51 018: dt: 0.5000, sse=4535463.0, rms=3.46 rms = 3.41, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=4564102.5, rms=3.41 020: dt: 0.2500, sse=2910253.8, rms=2.48 021: dt: 0.2500, sse=2732364.2, rms=2.22 022: dt: 0.2500, sse=2644788.0, rms=2.16 rms = 2.14, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2628345.8, rms=2.14 024: dt: 0.1250, sse=2525277.0, rms=2.04 rms = 2.04, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=2510971.2, rms=2.04 positioning took 3.8 minutes mean border=62.1, 542 (10) missing vertices, mean dist 0.2 [0.2 (%37.0)->0.4 (%63.0))] %49 local maxima, %30 large gradients and %16 min vals, 402 gradients ignored tol=1.0e-04, sigma=1.0, host=magma, 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=3039729.0, rms=4.77 026: dt: 0.5000, sse=3121807.0, rms=3.38 rms = 3.35, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=3819025.8, rms=3.35 028: dt: 0.2500, sse=2958818.8, rms=2.29 029: dt: 0.2500, sse=2914342.0, rms=2.05 030: dt: 0.2500, sse=2862978.8, rms=1.99 rms = 1.96, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=2863831.0, rms=1.96 032: dt: 0.1250, sse=2769067.2, rms=1.87 rms = 1.86, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=2760932.5, rms=1.86 positioning took 1.3 minutes mean border=60.6, 742 (8) missing vertices, mean dist 0.1 [0.2 (%36.3)->0.3 (%63.7))] %63 local maxima, %16 large gradients and %16 min vals, 392 gradients ignored tol=1.0e-04, sigma=0.5, host=magma, 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=2869268.0, rms=2.87 rms = 3.03, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=2766254.5, rms=2.29 035: dt: 0.2500, sse=2758365.2, rms=1.94 036: dt: 0.2500, sse=2817030.5, rms=1.85 rms = 1.82, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=2834974.0, rms=1.82 038: dt: 0.1250, sse=2779596.2, rms=1.77 rms = 1.76, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=2776151.0, rms=1.76 positioning took 1.0 minutes mean border=59.8, 1461 (7) missing vertices, mean dist 0.0 [0.2 (%43.5)->0.2 (%56.5))] %67 local maxima, %12 large gradients and %15 min vals, 377 gradients ignored tol=1.0e-04, sigma=0.2, host=magma, 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=2795401.0, rms=2.03 rms = 2.48, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=2745235.8, rms=1.81 041: dt: 0.2500, sse=2806928.0, rms=1.75 rms = 1.72, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=2841260.0, rms=1.72 rms = 1.68, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=2797050.8, rms=1.68 positioning took 0.7 minutes writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.area.pial vertex spacing 0.98 +- 0.39 (0.09-->8.45) (max @ vno 72733 --> 71888) face area 0.38 +- 0.28 (0.00-->6.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 106934 vertices processed 25000 of 106934 vertices processed 50000 of 106934 vertices processed 75000 of 106934 vertices processed 100000 of 106934 vertices processed 0 of 106934 vertices processed 25000 of 106934 vertices processed 50000 of 106934 vertices processed 75000 of 106934 vertices processed 100000 of 106934 vertices processed thickness calculation complete, 1162:666 truncations. 52016 vertices at 0 distance 66434 vertices at 1 distance 50234 vertices at 2 distance 21136 vertices at 3 distance 8459 vertices at 4 distance 3346 vertices at 5 distance 1459 vertices at 6 distance 593 vertices at 7 distance 295 vertices at 8 distance 187 vertices at 9 distance 105 vertices at 10 distance 58 vertices at 11 distance 49 vertices at 12 distance 44 vertices at 13 distance 35 vertices at 14 distance 41 vertices at 15 distance 25 vertices at 16 distance 18 vertices at 17 distance 9 vertices at 18 distance 8 vertices at 19 distance 11 vertices at 20 distance writing curvature file /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.thickness positioning took 16.9 minutes #-------------------------------------------- #@# Surf Volume rh Sat Jul 16 08:01:18 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 ] #----------------------------------------- #@# Parcellation Stats rh Sat Jul 16 08:01:20 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 1027 724 1648 2.335 0.375 0.101 0.021 6 0.9 bankssts 941 599 1946 3.103 0.577 0.144 0.038 16 1.5 caudalanteriorcingulate 2337 1598 4543 2.574 0.513 0.118 0.032 20 3.2 caudalmiddlefrontal 1960 1260 2239 1.740 0.488 0.158 0.051 31 4.4 cuneus 330 231 1332 3.788 0.767 0.092 0.024 2 0.3 entorhinal 3286 2221 6459 2.751 0.757 0.145 0.044 43 5.9 fusiform 6138 4147 11144 2.474 0.690 0.140 0.045 85 11.2 inferiorparietal 3548 2461 9025 3.203 0.778 0.162 0.081 77 14.3 inferiortemporal 1059 689 1788 2.533 0.720 0.141 0.047 16 1.9 isthmuscingulate 5831 3724 8719 2.151 0.603 0.145 0.046 72 11.1 lateraloccipital 2869 1925 5852 2.821 0.565 0.145 0.049 41 5.6 lateralorbitofrontal 3935 2613 4717 1.799 0.555 0.152 0.053 59 9.1 lingual 2196 1461 3916 2.484 0.652 0.152 0.077 63 5.7 medialorbitofrontal 3586 2474 8686 3.094 0.697 0.135 0.042 43 6.0 middletemporal 835 569 1866 2.850 0.744 0.111 0.031 7 1.1 parahippocampal 1862 1113 2664 2.256 0.615 0.098 0.022 14 1.8 paracentral 1574 1098 2989 2.499 0.475 0.118 0.032 13 2.0 parsopercularis 937 634 2287 3.035 0.626 0.152 0.055 13 2.0 parsorbitalis 1804 1195 3325 2.553 0.588 0.137 0.038 21 3.0 parstriangularis 1715 1131 1482 1.413 0.384 0.152 0.058 32 4.0 pericalcarine 5462 3374 7133 1.903 0.603 0.118 0.037 59 9.0 postcentral 1348 923 2439 2.604 0.611 0.150 0.048 21 2.6 posteriorcingulate 6138 3801 10230 2.472 0.605 0.112 0.033 65 9.4 precentral 4480 2942 7073 2.279 0.586 0.139 0.046 55 7.9 precuneus 924 589 2113 3.335 0.688 0.143 0.067 20 2.5 rostralanteriorcingulate 6301 4253 11271 2.378 0.640 0.157 0.057 104 14.0 rostralmiddlefrontal 7989 5338 16246 2.717 0.566 0.137 0.041 98 13.4 superiorfrontal 6530 4135 9611 2.118 0.533 0.125 0.038 76 10.0 superiorparietal 4111 2750 8957 2.813 0.669 0.113 0.029 35 4.8 superiortemporal 4213 2791 7334 2.441 0.565 0.135 0.037 51 6.5 supramarginal 402 268 997 2.818 0.592 0.198 0.085 9 1.3 frontalpole 595 416 2297 3.968 0.533 0.159 0.069 9 1.7 temporalpole 512 276 614 2.057 0.435 0.122 0.036 5 0.7 transversetemporal 3106 2021 6480 3.183 0.856 0.128 0.101 87 9.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat Jul 16 08:02:08 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 CA149base rh ../surf/rh.sphere.reg /opt/share/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /opt/share/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... 17 labels changed using aseg relabeling using gibbs priors... 000: 7647 changed, 106934 examined... 001: 1777 changed, 29234 examined... 002: 540 changed, 9027 examined... 003: 229 changed, 2913 examined... 004: 119 changed, 1352 examined... 005: 40 changed, 650 examined... 006: 20 changed, 239 examined... 007: 13 changed, 102 examined... 008: 7 changed, 68 examined... 009: 5 changed, 42 examined... 010: 2 changed, 25 examined... 011: 0 changed, 15 examined... 14 labels changed using aseg 000: 232 total segments, 150 labels (1678 vertices) changed 001: 94 total segments, 13 labels (94 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 100 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 696 vertices marked for relabeling... 696 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat Jul 16 08:03:49 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 CA149base rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 954 645 1964 2.670 0.764 0.179 0.069 19 2.7 G_and_S_frontomargin 955 642 1762 2.548 0.656 0.157 0.051 12 2.0 G_and_S_occipital_inf 1290 743 1892 2.150 0.555 0.106 0.048 26 3.4 G_and_S_paracentral 1000 643 1882 2.592 0.560 0.148 0.058 18 2.8 G_and_S_subcentral 1192 775 2530 2.545 0.634 0.170 0.064 23 3.3 G_and_S_transv_frontopol 2348 1560 4284 2.733 0.754 0.133 0.044 31 4.1 G_and_S_cingul-Ant 1159 796 2330 2.803 0.549 0.126 0.035 14 1.7 G_and_S_cingul-Mid-Ant 1048 726 1763 2.424 0.542 0.127 0.032 10 1.4 G_and_S_cingul-Mid-Post 408 257 956 2.974 0.301 0.182 0.065 10 1.1 G_cingul-Post-dorsal 190 120 402 2.724 0.678 0.165 0.082 4 0.5 G_cingul-Post-ventral 1761 1138 1974 1.686 0.523 0.162 0.055 33 4.2 G_cuneus 1054 707 2354 2.584 0.418 0.136 0.041 13 1.8 G_front_inf-Opercular 363 229 884 2.932 0.442 0.145 0.052 5 0.8 G_front_inf-Orbital 913 603 2039 2.737 0.428 0.158 0.050 14 2.0 G_front_inf-Triangul 2528 1720 5477 2.571 0.483 0.153 0.056 42 5.6 G_front_middle 5497 3480 12083 2.829 0.550 0.151 0.052 95 12.2 G_front_sup 437 272 994 3.601 0.575 0.116 0.060 6 0.8 G_Ins_lg_and_S_cent_ins 555 336 1698 3.435 0.926 0.175 0.137 23 3.0 G_insular_short 1832 1176 3655 2.718 0.703 0.164 0.063 32 4.5 G_occipital_middle 1676 1008 2491 2.107 0.476 0.129 0.044 21 3.1 G_occipital_sup 1263 828 2580 2.551 0.608 0.154 0.052 19 2.7 G_oc-temp_lat-fusifor 2686 1737 3482 1.839 0.572 0.158 0.058 46 6.7 G_oc-temp_med-Lingual 1055 698 3130 3.440 0.678 0.120 0.146 45 2.5 G_oc-temp_med-Parahip 2137 1418 5433 3.044 0.559 0.162 0.067 39 5.7 G_orbital 2405 1598 5205 2.664 0.564 0.167 0.061 49 6.0 G_pariet_inf-Angular 2220 1450 4922 2.762 0.484 0.149 0.043 35 3.9 G_pariet_inf-Supramar 1879 1164 3445 2.396 0.517 0.141 0.048 30 3.5 G_parietal_sup 2108 1165 2939 2.047 0.438 0.121 0.040 26 3.8 G_postcentral 2498 1375 4969 2.728 0.516 0.105 0.030 22 3.1 G_precentral 1987 1271 3900 2.425 0.494 0.153 0.061 33 4.5 G_precuneus 683 447 1499 2.511 0.601 0.147 0.051 12 1.3 G_rectus 274 194 523 2.899 0.869 0.214 0.277 30 1.4 G_subcallosal 377 185 525 2.205 0.490 0.116 0.035 4 0.5 G_temp_sup-G_T_transv 1307 858 3737 3.083 0.526 0.143 0.045 19 2.2 G_temp_sup-Lateral 651 463 1653 3.393 0.658 0.097 0.024 3 0.6 G_temp_sup-Plan_polar 547 354 860 2.223 0.406 0.110 0.032 5 0.8 G_temp_sup-Plan_tempo 2132 1456 6025 3.223 0.739 0.181 0.113 64 12.1 G_temporal_inf 2310 1565 6420 3.200 0.665 0.152 0.053 36 5.0 G_temporal_middle 398 258 507 2.006 0.533 0.095 0.015 2 0.3 Lat_Fis-ant-Horizont 181 124 224 2.088 0.455 0.101 0.022 1 0.1 Lat_Fis-ant-Vertical 1167 779 1454 2.110 0.516 0.120 0.030 13 1.5 Lat_Fis-post 2548 1549 3165 1.861 0.528 0.150 0.055 35 5.7 Pole_occipital 1512 1046 5545 3.937 0.570 0.153 0.051 23 3.2 Pole_temporal 1866 1262 1853 1.635 0.583 0.144 0.050 28 3.7 S_calcarine 2750 1873 2881 1.692 0.557 0.111 0.027 17 3.1 S_central 1106 730 1475 2.130 0.534 0.102 0.026 7 1.1 S_cingul-Marginalis 426 292 762 2.980 0.533 0.108 0.030 3 0.5 S_circular_insula_ant 1195 810 2099 2.985 0.955 0.088 0.036 6 2.0 S_circular_insula_inf 1164 796 1773 2.813 0.531 0.109 0.032 7 1.7 S_circular_insula_sup 891 626 1520 2.747 0.617 0.108 0.021 7 0.9 S_collat_transv_ant 448 285 491 1.980 0.461 0.156 0.056 5 1.0 S_collat_transv_post 1428 982 2110 2.248 0.527 0.122 0.032 12 1.8 S_front_inf 1515 1028 2310 2.091 0.615 0.143 0.048 19 2.6 S_front_middle 2065 1448 3442 2.377 0.515 0.121 0.033 22 2.8 S_front_sup 352 236 398 2.197 0.314 0.124 0.029 3 0.4 S_interm_prim-Jensen 2621 1727 3350 2.029 0.467 0.110 0.026 19 2.8 S_intrapariet_and_P_trans 737 504 851 1.793 0.403 0.119 0.023 6 0.8 S_oc_middle_and_Lunatus 1269 860 1462 1.864 0.531 0.116 0.026 9 1.4 S_oc_sup_and_transversal 621 420 810 2.334 0.394 0.119 0.024 4 0.6 S_occipital_ant 518 361 997 3.005 0.693 0.169 0.057 8 1.3 S_oc-temp_lat 1435 1031 1987 2.253 0.569 0.126 0.035 12 2.1 S_oc-temp_med_and_Lingual 252 174 402 2.702 0.826 0.147 0.040 3 0.4 S_orbital_lateral 556 404 959 2.443 0.816 0.108 0.019 5 0.4 S_orbital_med-olfact 1288 870 2141 2.618 0.584 0.138 0.039 14 2.1 S_orbital-H_Shaped 1811 1205 2190 2.012 0.632 0.129 0.035 18 2.7 S_parieto_occipital 1175 743 1661 2.987 0.825 0.136 0.043 18 1.9 S_pericallosal 2166 1462 2454 1.856 0.480 0.113 0.026 16 2.4 S_postcentral 1347 949 2234 2.655 0.505 0.107 0.022 7 1.3 S_precentral-inf-part 878 581 1248 2.291 0.509 0.101 0.027 5 0.8 S_precentral-sup-part 116 72 184 3.289 0.338 0.186 0.046 2 0.2 S_suborbital 998 691 1422 2.161 0.576 0.136 0.034 10 1.3 S_subparietal 908 617 1518 3.104 0.723 0.128 0.034 8 1.2 S_temporal_inf 4245 2983 6581 2.335 0.537 0.104 0.022 26 4.0 S_temporal_sup 249 164 306 2.145 0.322 0.143 0.033 3 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Sat Jul 16 08:04:37 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon CA149base SUBJECTS_DIR is /data/belleville/ncorriveau/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 30 writing volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat Jul 16 08:19:54 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /opt/share/freesurfer/ASegStatsLUT.txt --subject CA149base $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /opt/share/freesurfer/ASegStatsLUT.txt --subject CA149base sysname Linux hostname magma machine x86_64 user ncorriveau atlas_icv (eTIV) = 1262827 mm^3 (det: 1.542654 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 196601 rh white matter volume 194358 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 210949.663734, pTot = 389689.381366 c = 178739.717631 rh surface-based volumes (mm3): wTot = 210418.153042, pTot = 387841.072426 c = 177422.919384 Computing SupraTentVolCor SupraTentVolCor = 52889.000 SupraTentVol = 830419.454 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 4196 4196 4 5 Left-Inf-Lat-Vent 98 98 5 7 Left-Cerebellum-White-Matter 11370 11370 6 8 Left-Cerebellum-Cortex 42696 42696 7 10 Left-Thalamus-Proper 5091 5091 8 11 Left-Caudate 3134 3134 9 12 Left-Putamen 4376 4376 10 13 Left-Pallidum 1603 1603 11 14 3rd-Ventricle 973 973 12 15 4th-Ventricle 948 948 13 16 Brain-Stem 17877 17877 14 17 Left-Hippocampus 4180 4180 15 18 Left-Amygdala 1405 1405 16 24 CSF 938 938 17 26 Left-Accumbens-area 517 517 18 28 Left-VentralDC 3598 3598 19 30 Left-vessel 42 42 20 31 Left-choroid-plexus 1290 1290 23 43 Right-Lateral-Ventricle 4505 4505 24 44 Right-Inf-Lat-Vent 116 116 25 46 Right-Cerebellum-White-Matter 11128 11128 26 47 Right-Cerebellum-Cortex 44431 44431 27 49 Right-Thalamus-Proper 5591 5591 28 50 Right-Caudate 3167 3167 29 51 Right-Putamen 4542 4542 30 52 Right-Pallidum 1348 1348 31 53 Right-Hippocampus 4098 4098 32 54 Right-Amygdala 1757 1757 33 58 Right-Accumbens-area 629 629 34 60 Right-VentralDC 3615 3615 35 62 Right-vessel 28 28 36 63 Right-choroid-plexus 1597 1597 37 72 5th-Ventricle 6 6 38 77 WM-hypointensities 1377 1377 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 7 7 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 329 329 45 251 CC_Posterior 865 865 46 252 CC_Mid_Posterior 235 235 47 253 CC_Central 284 284 48 254 CC_Mid_Anterior 293 293 49 255 CC_Anterior 535 535 Reporting on 45 segmentations SubCortGrayVol = 153655 #----------------------------------------- #@# AParc-to-ASeg Sat Jul 16 08:42:51 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --volmask SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 = 347652 Used brute-force search on 0 voxels Writing output aseg to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --volmask --a2009s SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 = 347652 Used brute-force search on 0 voxels Writing output aseg to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sat Jul 16 08:53:39 EDT 2016 /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_aparc2aseg --s CA149base --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects subject CA149base outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aparc+aseg.mgz Reading lh white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading lh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial Loading lh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading rh pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial Loading rh annotations from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/ribbon.mgz Loading filled from /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7086 vertices from left hemi Ripped 7053 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 /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/aseg.mgz Loading Ctx Seg File /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 = 716126 Used brute-force search on 31 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 4.000000 2 k 1.000000 3 k 1.000000 4 k 1459.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 1512.000000 3 k 1.000000 4 k 1.000000 Writing output aseg to mri/wmparc.mgz /data/belleville/ncorriveau/freesurfer/subjects/CA149base mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject CA149base --surf-wm-vol --ctab /opt/share/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject CA149base --surf-wm-vol --ctab /opt/share/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname magma machine x86_64 user ncorriveau atlas_icv (eTIV) = 1262827 mm^3 (det: 1.542654 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 196601 rh white matter volume 194358 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1235595 # brainmaskvolume 1235595.0 # nbrainsegvoxels 190753 # brainsegvolume 190753.0 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 1 3001 wm-lh-bankssts 2977 2977 2 3002 wm-lh-caudalanteriorcingulate 2542 2542 3 3003 wm-lh-caudalmiddlefrontal 5419 5419 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2121 2121 6 3006 wm-lh-entorhinal 903 903 7 3007 wm-lh-fusiform 5398 5398 8 3008 wm-lh-inferiorparietal 8262 8262 9 3009 wm-lh-inferiortemporal 5676 5676 10 3010 wm-lh-isthmuscingulate 3188 3188 11 3011 wm-lh-lateraloccipital 7465 7465 12 3012 wm-lh-lateralorbitofrontal 5150 5150 13 3013 wm-lh-lingual 4899 4899 14 3014 wm-lh-medialorbitofrontal 3591 3591 15 3015 wm-lh-middletemporal 3849 3849 16 3016 wm-lh-parahippocampal 1612 1612 17 3017 wm-lh-paracentral 3324 3324 18 3018 wm-lh-parsopercularis 3371 3371 19 3019 wm-lh-parsorbitalis 909 909 20 3020 wm-lh-parstriangularis 2953 2953 21 3021 wm-lh-pericalcarine 2558 2558 22 3022 wm-lh-postcentral 6777 6777 23 3023 wm-lh-posteriorcingulate 3668 3668 24 3024 wm-lh-precentral 11236 11236 25 3025 wm-lh-precuneus 7094 7094 26 3026 wm-lh-rostralanteriorcingulate 2005 2005 27 3027 wm-lh-rostralmiddlefrontal 8979 8979 28 3028 wm-lh-superiorfrontal 14078 14078 29 3029 wm-lh-superiorparietal 10081 10081 30 3030 wm-lh-superiortemporal 6021 6021 31 3031 wm-lh-supramarginal 7324 7324 32 3032 wm-lh-frontalpole 196 196 33 3033 wm-lh-temporalpole 638 638 34 3034 wm-lh-transversetemporal 724 724 35 3035 wm-lh-insula 8380 8380 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2518 2518 120 4002 wm-rh-caudalanteriorcingulate 2309 2309 121 4003 wm-rh-caudalmiddlefrontal 4658 4658 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 2092 2092 124 4006 wm-rh-entorhinal 448 448 125 4007 wm-rh-fusiform 5686 5686 126 4008 wm-rh-inferiorparietal 8518 8518 127 4009 wm-rh-inferiortemporal 4886 4886 128 4010 wm-rh-isthmuscingulate 2608 2608 129 4011 wm-rh-lateraloccipital 8292 8292 130 4012 wm-rh-lateralorbitofrontal 5194 5194 131 4013 wm-rh-lingual 5480 5480 132 4014 wm-rh-medialorbitofrontal 2787 2787 133 4015 wm-rh-middletemporal 5093 5093 134 4016 wm-rh-parahippocampal 1623 1623 135 4017 wm-rh-paracentral 3541 3541 136 4018 wm-rh-parsopercularis 2566 2566 137 4019 wm-rh-parsorbitalis 1199 1199 138 4020 wm-rh-parstriangularis 2839 2839 139 4021 wm-rh-pericalcarine 2630 2630 140 4022 wm-rh-postcentral 6744 6744 141 4023 wm-rh-posteriorcingulate 3260 3260 142 4024 wm-rh-precentral 10745 10745 143 4025 wm-rh-precuneus 7269 7269 144 4026 wm-rh-rostralanteriorcingulate 1731 1731 145 4027 wm-rh-rostralmiddlefrontal 10202 10202 146 4028 wm-rh-superiorfrontal 13939 13939 147 4029 wm-rh-superiorparietal 9800 9800 148 4030 wm-rh-superiortemporal 5285 5285 149 4031 wm-rh-supramarginal 7267 7267 150 4032 wm-rh-frontalpole 403 403 151 4033 wm-rh-temporalpole 679 679 152 4034 wm-rh-transversetemporal 491 491 153 4035 wm-rh-insula 8040 8040 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 21990 21990 237 5002 Right-UnsegmentedWhiteMatter 22086 22086 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label #-------------------------------------------- #@# BA Labels lh Sat Jul 16 09:29:37 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject CA149base --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./lh.BA1.label 4290 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA2.label --trgsubject CA149base --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 239 Checking for and removing duplicates Writing label file ./lh.BA2.label 8148 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3a.label --trgsubject CA149base --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4164 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3b.label --trgsubject CA149base --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6162 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4a.label --trgsubject CA149base --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./lh.BA4a.label 5934 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4p.label --trgsubject CA149base --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4185 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA6.label --trgsubject CA149base --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./lh.BA6.label 14108 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA44.label --trgsubject CA149base --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.BA44.label 4398 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA45.label --trgsubject CA149base --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 399 Checking for and removing duplicates Writing label file ./lh.BA45.label 3821 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V1.label --trgsubject CA149base --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 721 Checking for and removing duplicates Writing label file ./lh.V1.label 5362 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V2.label --trgsubject CA149base --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 1586 Checking for and removing duplicates Writing label file ./lh.V2.label 9700 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.MT.label --trgsubject CA149base --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.MT.label 2171 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s CA149base --hemi lh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose Reading ctab /opt/share/freesurfer/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label cmdline mris_label2annot --s CA149base --hemi lh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose sysname Linux hostname magma machine x86_64 user ncorriveau subject CA149base hemi lh SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects ColorTable /opt/share/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 74632 unhit vertices Writing annot to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab CA149base lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /opt/share/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 985 529 1568 2.266 0.426 0.134 0.047 17 2.0 BA1 3297 2154 4941 2.203 0.552 0.108 0.032 27 4.2 BA2 944 647 808 1.571 0.461 0.140 0.037 9 1.5 BA3a 2129 1388 2816 1.845 0.674 0.119 0.033 21 3.2 BA3b 1416 732 2028 2.353 0.588 0.100 0.044 21 2.0 BA4a 1080 694 1711 2.500 0.475 0.099 0.034 14 1.4 BA4p 7735 4896 15079 2.665 0.513 0.120 0.043 87 14.5 BA6 2049 1380 3847 2.641 0.423 0.133 0.035 23 3.0 BA44 2568 1739 4662 2.343 0.558 0.128 0.036 28 3.7 BA45 2701 1786 2846 1.533 0.493 0.159 0.063 62 7.8 V1 6825 4419 8762 1.916 0.588 0.157 0.053 102 14.8 V2 1377 920 2435 2.345 0.500 0.124 0.043 17 1.9 MT #-------------------------------------------- #@# BA Labels rh Sat Jul 16 09:33:06 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA1.label --trgsubject CA149base --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./rh.BA1.label 4168 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA2.label --trgsubject CA149base --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 260 Checking for and removing duplicates Writing label file ./rh.BA2.label 6947 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3a.label --trgsubject CA149base --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4076 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3b.label --trgsubject CA149base --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4717 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4a.label --trgsubject CA149base --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5891 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4p.label --trgsubject CA149base --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4591 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA6.label --trgsubject CA149base --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA6.label 12521 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA44.label --trgsubject CA149base --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./rh.BA44.label 7178 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA45.label --trgsubject CA149base --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 447 Checking for and removing duplicates Writing label file ./rh.BA45.label 5802 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V1.label --trgsubject CA149base --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 981 Checking for and removing duplicates Writing label file ./rh.V1.label 5708 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V2.label --trgsubject CA149base --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 1878 Checking for and removing duplicates Writing label file ./rh.V2.label 9894 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.MT.label --trgsubject CA149base --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = CA149base 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 /data/belleville/ncorriveau/freesurfer/subjects FREESURFER_HOME /opt/share/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/belleville/ncorriveau/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white Reading target registration /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 Number of reverse mapping hits = 178 Checking for and removing duplicates Writing label file ./rh.MT.label 2110 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s CA149base --hemi rh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose Reading ctab /opt/share/freesurfer/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label cmdline mris_label2annot --s CA149base --hemi rh --ctab /opt/share/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 --a BA --maxstatwinner --noverbose sysname Linux hostname magma machine x86_64 user ncorriveau subject CA149base hemi rh SUBJECTS_DIR /data/belleville/ncorriveau/freesurfer/subjects ColorTable /opt/share/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 73806 unhit vertices Writing annot to /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab CA149base rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /opt/share/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 906 486 1403 2.187 0.365 0.129 0.046 11 1.8 BA1 2881 1885 3783 1.973 0.517 0.113 0.029 24 3.4 BA2 924 650 748 1.433 0.350 0.140 0.037 8 1.4 BA3a 1820 1116 2014 1.626 0.511 0.114 0.039 23 3.3 BA3b 1339 783 2082 2.353 0.483 0.095 0.039 25 3.1 BA4a 1134 741 1574 2.140 0.458 0.103 0.025 6 1.2 BA4p 5985 3670 11907 2.770 0.519 0.115 0.032 56 8.0 BA6 2940 2011 5247 2.534 0.503 0.118 0.031 25 3.9 BA44 3328 2245 6507 2.578 0.623 0.142 0.044 42 6.1 BA45 3308 2119 3416 1.547 0.481 0.147 0.055 52 7.7 V1 6998 4508 8770 1.904 0.530 0.155 0.054 109 15.4 V2 1565 1071 2426 2.249 0.567 0.130 0.031 15 2.2 MT /data/belleville/ncorriveau/freesurfer/subjects/CA149base/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sat Jul 16 09:36:51 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o CA149base label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject CA149base. processing subject lh.EC_average... reading output surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 860 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label CA149base lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/lh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 306 191 976 3.215 0.584 0.099 0.023 2 0.3 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sat Jul 16 09:37:24 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o CA149base label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject CA149base. processing subject rh.EC_average... reading output surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 630 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label CA149base rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /data/belleville/ncorriveau/freesurfer/subjects/CA149base/mri/wm.mgz... reading input surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.white... reading input pial surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/surf/rh.pial... reading input white surface /data/belleville/ncorriveau/freesurfer/subjects/CA149base/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 225 143 792 3.447 0.564 0.085 0.030 1 0.3 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s CA149base finished without error at Sat Jul 16 09:37:56 EDT 2016