Thu May 7 11:59:22 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m /autofs/space/plato_002/users/freesurfer/bin/recon-all -all -nuintensitycor-3T -i R01L019_MD_12m-1.mgz -i R01L019_MD_12m-2.mgz -subjid R01L019_MD_12m subjid R01L019_MD_12m setenv SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-107 2.6.32-504.8.1.el6.x86_64 #1 SMP Wed Jan 28 21:11:36 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 256658 total used free shared buffers cached Mem: 32877376 18143772 14733604 4 6408 15307304 -/+ buffers/cache: 2830060 30047316 Swap: 67108860 119040 66989820 ######################################## 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: 2015/05/07-15:59:23-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/07-15:59:23-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/07-15:59:24-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:25-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:25-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:26-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:26-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:26-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:27-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:27-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:28-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:28-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:29-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:29-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:30-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:30-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:30-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:31-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:31-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:32-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:32-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:33-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:33-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:33-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:34-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:34-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:35-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:35-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:35-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:36-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:36-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:37-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/07-15:59:37-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/07-15:59:38-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:38-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:38-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:39-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/07-15:59:39-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: mlapoint Machine: compute-0-107 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-1.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-1.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-1.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (-0.0442402, -0.994559, 0.0943157) j_ras = (-0.0106679, -0.0939324, -0.995521) k_ras = (-0.998964, 0.0450482, 0.00645425) writing to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz... /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-2.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-2.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m-2.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (-0.0442402, -0.994559, 0.0943157) j_ras = (-0.0106679, -0.0939324, -0.995521) k_ras = (-0.998964, 0.0450482, 0.00645425) writing to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu May 7 11:59:59 EDT 2015 Found 2 runs /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_robust_template --mov /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz --average 1 --template /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001-iscale.txt /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002-iscale.txt --subsample 200 --lta /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.lta /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz as movable/source volume. --mov: Using /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz'... reading source '/autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/002.mgz ) to TP 1 ( /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1.05469, 1.05469, 1.2)mm and dim (240, 256, 176) Dst: (1.05469, 1.05469, 1.2)mm and dim (240, 256, 176) Asserting both images: 1.05469mm isotropic and (240, 256, 201) voxels Original : (1.05469, 1.05469, 1.2) mm size and (240, 256, 176) voxels. Resampled: (1.05469, 1.05469, 1.05469) mm size and (240, 256, 201) voxels. Reslicing using trilinear interpolation Original : (1.05469, 1.05469, 1.2) mm size and (240, 256, 176) voxels. Resampled: (1.05469, 1.05469, 1.05469) mm size and (240, 256, 201) voxels. Reslicing using trilinear interpolation Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 60 , 64 , 50 ) -- gpT ( 60 , 64 , 50 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 16 ( 0.305494 ), max sat: 0 ( -1 ), sat diff: -16 -- Iteration: 2 trying sat: 32 min sat: 16 ( 0.305494 ), max sat: 32 ( 0.117905 ), sat diff: 16 -- Iteration: 3 trying sat: 24 min sat: 24 ( 0.180397 ), max sat: 32 ( 0.117905 ), sat diff: 8 -- Iteration: 4 trying sat: 28 min sat: 24 ( 0.180397 ), max sat: 28 ( 0.141437 ), sat diff: 4 -- Iteration: 5 trying sat: 26 min sat: 24 ( 0.180397 ), max sat: 26 ( 0.155475 ), sat diff: 2 -- Iteration: 6 trying sat: 25 min sat: 24 ( 0.180397 ), max sat: 25 ( 0.164347 ), sat diff: 1 -- Iteration: 7 trying sat: 24.5 - final SAT: 24.5 ( it: 7 , weight check 0.168925 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -2.3639252598275 0 1.0000000000000 0 -19.9082716289500 0 0 1.0000000000000 -0.3941193841166 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 30 32 25 ) T( 30 32 25 ) Iteration(f): 1 -- diff. to prev. transform: 2.867 Iteration(f): 2 -- diff. to prev. transform: 1.80354 Iteration(f): 3 -- diff. to prev. transform: 1.03015 Iteration(f): 4 -- diff. to prev. transform: 0.429592 Iteration(f): 5 -- diff. to prev. transform: 0.127534 max it: 5 reached! Resolution: 2 S( 60 64 50 ) T( 60 64 50 ) Iteration(f): 1 -- diff. to prev. transform: 4.29758 Iteration(f): 2 -- diff. to prev. transform: 0.213381 Iteration(f): 3 -- diff. to prev. transform: 0.214801 Iteration(f): 4 -- diff. to prev. transform: 0.0658403 Iteration(f): 5 -- diff. to prev. transform: 0.0694096 max it: 5 reached! Resolution: 1 S( 120 128 100 ) T( 120 128 100 ) Iteration(f): 1 -- diff. to prev. transform: 2.53735 Iteration(f): 2 -- diff. to prev. transform: 0.032001 Iteration(f): 3 -- diff. to prev. transform: 0.00153097 < 0.01 :-) Resolution: 0 S( 240 256 201 ) T( 240 256 201 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.854002 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.0245611 Iteration(f): 3 (subsample 200) -- diff. to prev. transform: 0.00118764 < 0.01 :-) - final transform: Tf = [ ... 0.9999938016051 -0.0034225096697 0.0008265463443 0.3013088559954 0.0034215131144 0.9999934216676 0.0012041052482 -0.8523684377538 -0.0008306619689 -0.0012012697455 0.9999989334753 0.1792804147621 0 0 0 1.0000000000000 ] - final iscale: If = 1.4971 Adjusting final transform due to non isotropic voxels ... warping movs and creating initial template... allow intensity scaling using median Writing final template: /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 2 minutes and 0 seconds. /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig.mgz --conform mri_convert /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/rawavg.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (-0.0442402, -0.994559, 0.0943157) j_ras = (-0.0106679, -0.0939324, -0.995521) k_ras = (-0.998964, 0.0450482, 0.00645425) Original Data has (1.05469, 1.05469, 1.2) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/talairach.xfm /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 7 12:02:18 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu May 7 12:03:50 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6661, pval=0.3663 >= threshold=0.0050) awk -f /autofs/space/plato_002/users/freesurfer/bin/extract_talairach_avi_QA.awk /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/talairach_avi.log TalAviQA: 0.97355 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Thu May 7 12:03:51 EDT 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri /autofs/space/plato_002/users/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux compute-0-107 2.6.32-504.8.1.el6.x86_64 #1 SMP Wed Jan 28 21:11:36 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Thu May 7 12:03:51 EDT 2015 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.22335 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22335/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22335/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=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (-1, -7.45058e-08, -1.89058e-07) j_ras = (-2.14204e-08, 1.97324e-08, -1) k_ras = (1.00583e-07, 1, -2.20898e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.22335/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu May 7 12:03:57 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.22335/nu0.mnc ./tmp.mri_nu_correct.mni.22335/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.22335/0/ -iterations 1000 -distance 50 [mlapoint@compute-0-107:/autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/] [2015-05-07 12:03:57] running: /autofs/space/plato_002/users/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.22335/0/ ./tmp.mri_nu_correct.mni.22335/nu0.mnc ./tmp.mri_nu_correct.mni.22335/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 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 29 CV of field change: 0.000943542 [mlapoint@compute-0-107:/autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/] [2015-05-07 12:04:52] running: /autofs/space/plato_002/users/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.22335/nu0.mnc ./tmp.mri_nu_correct.mni.22335/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.22335/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.22335/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.22335/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.22335/ones.mgz sysname Linux hostname compute-0-107 machine x86_64 user mlapoint input ./tmp.mri_nu_correct.mni.22335/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.22335/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.22335/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.22335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22335/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.22335/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.22335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22335/input.mean.dat sysname Linux hostname compute-0-107 machine x86_64 user mlapoint Loading ./tmp.mri_nu_correct.mni.22335/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.22335/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.22335/ones.mgz --i ./tmp.mri_nu_correct.mni.22335/nu1.mnc --sum ./tmp.mri_nu_correct.mni.22335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22335/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.22335/ones.mgz --i ./tmp.mri_nu_correct.mni.22335/nu1.mnc --sum ./tmp.mri_nu_correct.mni.22335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.22335/output.mean.dat sysname Linux hostname compute-0-107 machine x86_64 user mlapoint Loading ./tmp.mri_nu_correct.mni.22335/ones.mgz Loading ./tmp.mri_nu_correct.mni.22335/nu1.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.22335/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.22335/nu1.mnc ./tmp.mri_nu_correct.mni.22335/nu1.mnc mul 1.01977767947601992037 Saving result to './tmp.mri_nu_correct.mni.22335/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.22335/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.22335/nu1.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.22335/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.45058e-08, -1.89058e-07) j_ras = (-2.14204e-08, 1.97324e-08, -1) k_ras = (1.00583e-07, 1, -2.20898e-08) INFO: transform src into the like-volume: orig.mgz Reslicing using trilinear interpolation writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 11 seconds. mapping ( 7, 117) to ( 3, 110) Thu May 7 12:06:13 EDT 2015 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Thu May 7 12:06:13 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... 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 T1.mgz 3D bias adjustment took 2 minutes and 23 seconds. MRIsplineNormalize(): npeaks = 17 Starting OpenSpline(): npoints = 17 white matter peak found at 111 white matter peak found at 106 gm peak at 62 (62), valley at 34 (34) csf peak at 31, setting threshold to 51 white matter peak found at 111 white matter peak found at 110 gm peak at 56 (56), valley at 33 (33) csf peak at 28, setting threshold to 46 #-------------------------------------------- #@# Skull Stripping Thu May 7 12:08:37 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_em_register -skull nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/autofs/space/plato_002/users/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.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=7.0 skull bounding box = (47, 26, 26) --> (209, 255, 255) using (101, 102, 141) as brain centroid... mean wm in atlas = 126, using box (81,74,113) --> (120, 130,169) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 initial log_p = -10395.9 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-5.1, 8.5, -2.8): log p = -10345.169 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10341.3, old_max_log_p =-10345.2 (thresh=-10334.8) 1.000 0.000 0.000 -5.114; 0.000 1.066 0.140 -14.163; 0.000 -0.121 0.917 19.780; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10326.6, old_max_log_p =-10341.3 (thresh=-10330.9) 1.037 0.036 0.005 -12.788; -0.035 1.126 0.148 -15.322; 0.000 -0.123 0.934 16.348; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10326.6, old_max_log_p =-10326.6 (thresh=-10316.3) 1.037 0.036 0.005 -12.788; -0.035 1.126 0.148 -15.322; 0.000 -0.123 0.934 16.348; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10322.9, old_max_log_p =-10326.6 (thresh=-10316.3) 1.040 0.044 0.014 -14.642; -0.043 1.127 0.148 -14.357; -0.009 -0.123 0.932 17.139; 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 1.04025 0.04420 0.01389 -14.64173; -0.04283 1.12691 0.14821 -14.35748; -0.00874 -0.12288 0.93250 17.13875; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04025 0.04420 0.01389 -14.64173; -0.04283 1.12691 0.14821 -14.35748; -0.00874 -0.12288 0.93250 17.13875; 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) = 10322.9 tol 0.000010 Resulting transform: 1.040 0.044 0.014 -14.642; -0.043 1.127 0.148 -14.357; -0.009 -0.123 0.932 17.139; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10322.9 (old=-10395.9) transform before final EM align: 1.040 0.044 0.014 -14.642; -0.043 1.127 0.148 -14.357; -0.009 -0.123 0.932 17.139; 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 1.04025 0.04420 0.01389 -14.64173; -0.04283 1.12691 0.14821 -14.35748; -0.00874 -0.12288 0.93250 17.13875; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04025 0.04420 0.01389 -14.64173; -0.04283 1.12691 0.14821 -14.35748; -0.00874 -0.12288 0.93250 17.13875; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1145719.5 after pass:transform: ( 1.04, 0.04, 0.01, -14.64) ( -0.04, 1.13, 0.15, -14.36) ( -0.01, -0.12, 0.93, 17.14) 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: 008: -log(p) = 1145712.1 after pass:transform: ( 1.04, 0.04, 0.01, -14.64) ( -0.04, 1.13, 0.15, -14.36) ( -0.01, -0.12, 0.93, 17.14) 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... 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: 010: -log(p) = 1145712.1 tol 0.000000 final transform: 1.040 0.044 0.014 -14.642; -0.042 1.128 0.149 -14.357; -0.010 -0.125 0.932 17.139; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 19 minutes and 27 seconds. mri_watershed -T1 -brain_atlas /autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=108 z=116 r=96 first estimation of the main basin volume: 3772967 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=153, y=86, z=84, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=22689674542 voxels, voxel volume =1.000 = 22689674542 mmm3 = 22689675.264 cm3 done. PostAnalyze...Basin Prior 109 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=110, z=112, r=10859 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=14, CSF_MAX=57 , nb = 43524 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=132 , nb = 2538 LEFT_CER CSF_MIN=0, CSF_intensity=32, CSF_MAX=73 , nb = 2286 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=53 , nb = 18450 LEFT_BRAIN CSF_MIN=0, CSF_intensity=12, CSF_MAX=56 , nb = 18684 OTHER CSF_MIN=0, CSF_intensity=23, CSF_MAX=39 , nb = 1566 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 57, 48, 43, 74 after analyzing : 39, 48, 48, 54 RIGHT_CER before analyzing : 132, 62, 48, 76 after analyzing : 36, 62, 62, 65 LEFT_CER before analyzing : 73, 59, 50, 80 after analyzing : 52, 59, 59, 64 RIGHT_BRAIN before analyzing : 53, 47, 43, 74 after analyzing : 38, 47, 47, 53 LEFT_BRAIN before analyzing : 56, 48, 43, 72 after analyzing : 39, 48, 48, 54 OTHER before analyzing : 39, 58, 77, 93 after analyzing : 39, 70, 77, 75 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 69.470, std = 8.633 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.01, sigma = 4.54 after rotation: sse = 3.01, sigma = 4.54 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.23, its var is 4.32 before Erosion-Dilatation 0.45% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mri_strip_skull: done peeling brain Brain Size = 1661598 voxels, voxel volume = 1.000 mm3 = 1661598 mmm3 = 1661.598 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu May 7 12:28:41 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/autofs/space/plato_002/users/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 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (60, 47, 28) --> (199, 186, 201) using (106, 93, 115) as brain centroid... mean wm in atlas = 107, using box (89,76,94) --> (123, 110,136) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -7440.6 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-6.3, 7.4, -9.7): log p = -7262.037 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7171.5, old_max_log_p =-7262.0 (thresh=-7254.8) 1.000 0.000 0.000 -6.250; 0.000 1.135 0.169 -27.108; 0.000 -0.112 0.997 3.184; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7171.5, old_max_log_p =-7171.5 (thresh=-7164.3) 1.000 0.000 0.000 -6.250; 0.000 1.135 0.169 -27.108; 0.000 -0.112 0.997 3.184; 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=-7074.9, old_max_log_p =-7171.5 (thresh=-7164.3) 1.017 0.036 0.015 -12.500; -0.034 1.175 0.310 -39.218; 0.005 -0.249 0.949 25.451; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7068.7, old_max_log_p =-7074.9 (thresh=-7067.8) 0.998 0.035 0.014 -9.888; -0.034 1.175 0.310 -39.218; 0.005 -0.249 0.949 25.451; 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=-7045.8, old_max_log_p =-7068.7 (thresh=-7061.7) 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.260 0.949 29.870; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7044.5, old_max_log_p =-7045.8 (thresh=-7038.7) 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7044.5 tol 0.000010 Resulting transform: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7044.5 (old=-7440.6) transform before final EM align: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 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: 010: -log(p) = 840374.6 tol 0.000000 final transform: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 20 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize Thu May 7 12:49:20 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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 nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (60, 47, 28) --> (199, 186, 201) using (106, 93, 115) as brain centroid... mean wm in atlas = 107, using box (89,76,94) --> (123, 110,136) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 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 (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 220.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 220.0 0 of 80 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 100.0 --> 220.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 220.0 0 of 22 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 98.0 --> 220.0 0 of 18 (0.0%) samples deleted using 179 total control points for intensity normalization... bias field = 0.953 +- 0.094 0 of 179 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 205.0 0 of 102 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 205.0 0 of 136 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 205.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 205.0 5 of 50 (10.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 82.0 --> 205.0 0 of 86 (0.0%) samples deleted using 424 total control points for intensity normalization... bias field = 0.974 +- 0.055 0 of 419 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 199.0 0 of 181 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 199.0 0 of 205 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 199.0 0 of 67 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 199.0 0 of 80 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 76.0 --> 199.0 0 of 177 (0.0%) samples deleted using 710 total control points for intensity normalization... bias field = 0.995 +- 0.042 0 of 710 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 2 seconds. #-------------------------------------- #@# CA Reg Thu May 7 12:51:22 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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) = 1.20 (predicted orig area = 6.7) 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=0.888, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43492.715 ms 0001: dt=129.472000, rms=0.833 (6.189%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43928.160 ms 0002: dt=92.480000, rms=0.822 (1.342%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46181.438 ms 0003: dt=369.920000, rms=0.800 (2.710%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44471.008 ms 0004: dt=55.488000, rms=0.792 (0.971%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45700.109 ms 0005: dt=73.984000, rms=0.790 (0.212%), neg=0, invalid=766 0006: dt=73.984000, rms=0.787 (0.373%), neg=0, invalid=766 0007: dt=73.984000, rms=0.782 (0.602%), neg=0, invalid=766 0008: dt=73.984000, rms=0.777 (0.700%), neg=0, invalid=766 0009: dt=73.984000, rms=0.771 (0.720%), neg=0, invalid=766 0010: dt=73.984000, rms=0.766 (0.752%), neg=0, invalid=766 0011: dt=73.984000, rms=0.759 (0.834%), neg=0, invalid=766 0012: dt=73.984000, rms=0.753 (0.834%), neg=0, invalid=766 0013: dt=73.984000, rms=0.747 (0.787%), neg=0, invalid=766 0014: dt=73.984000, rms=0.742 (0.681%), neg=0, invalid=766 0015: dt=73.984000, rms=0.738 (0.576%), neg=0, invalid=766 0016: dt=73.984000, rms=0.733 (0.570%), neg=0, invalid=766 0017: dt=73.984000, rms=0.729 (0.547%), neg=0, invalid=766 0018: dt=73.984000, rms=0.726 (0.476%), neg=0, invalid=766 0019: dt=73.984000, rms=0.723 (0.420%), neg=0, invalid=766 0020: dt=73.984000, rms=0.720 (0.390%), neg=0, invalid=766 0021: dt=73.984000, rms=0.717 (0.417%), neg=0, invalid=766 0022: dt=73.984000, rms=0.714 (0.428%), neg=0, invalid=766 0023: dt=73.984000, rms=0.711 (0.389%), neg=0, invalid=766 0024: dt=73.984000, rms=0.709 (0.328%), neg=0, invalid=766 0025: dt=73.984000, rms=0.707 (0.286%), neg=0, invalid=766 0026: dt=73.984000, rms=0.705 (0.282%), neg=0, invalid=766 0027: dt=73.984000, rms=0.703 (0.284%), neg=0, invalid=766 0028: dt=73.984000, rms=0.701 (0.263%), neg=0, invalid=766 0029: dt=73.984000, rms=0.699 (0.250%), neg=0, invalid=766 0030: dt=73.984000, rms=0.698 (0.222%), neg=0, invalid=766 0031: dt=73.984000, rms=0.696 (0.223%), neg=0, invalid=766 0032: dt=73.984000, rms=0.695 (0.193%), neg=0, invalid=766 0033: dt=73.984000, rms=0.693 (0.174%), neg=0, invalid=766 0034: dt=73.984000, rms=0.692 (0.191%), neg=0, invalid=766 0035: dt=73.984000, rms=0.691 (0.185%), neg=0, invalid=766 0036: dt=73.984000, rms=0.690 (0.129%), neg=0, invalid=766 0037: dt=73.984000, rms=0.689 (0.109%), neg=0, invalid=766 0038: dt=73.984000, rms=0.688 (0.134%), neg=0, invalid=766 0039: dt=73.984000, rms=0.687 (0.136%), neg=0, invalid=766 0040: dt=73.984000, rms=0.687 (0.113%), neg=0, invalid=766 0041: dt=73.984000, rms=0.686 (0.117%), neg=0, invalid=766 0042: dt=73.984000, rms=0.685 (0.120%), neg=0, invalid=766 0043: dt=73.984000, rms=0.684 (0.124%), neg=0, invalid=766 0044: dt=73.984000, rms=0.683 (0.102%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48644.746 ms 0045: dt=443.904000, rms=0.683 (0.041%), neg=0, invalid=766 0046: dt=443.904000, rms=0.683 (-0.168%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42752.488 ms 0047: dt=92.480000, rms=0.683 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44070.773 ms 0048: dt=517.888000, rms=0.682 (0.197%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42421.297 ms 0049: dt=0.000000, rms=0.682 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.690, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40229.488 ms 0050: dt=145.152000, rms=0.681 (1.277%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37837.699 ms 0051: dt=82.944000, rms=0.672 (1.418%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37571.320 ms 0052: dt=15.552000, rms=0.669 (0.401%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39426.098 ms 0053: dt=9.072000, rms=0.668 (0.097%), neg=0, invalid=766 0054: dt=9.072000, rms=0.668 (0.051%), neg=0, invalid=766 0055: dt=9.072000, rms=0.667 (0.084%), neg=0, invalid=766 0056: dt=9.072000, rms=0.667 (0.138%), neg=0, invalid=766 0057: dt=9.072000, rms=0.665 (0.205%), neg=0, invalid=766 0058: dt=9.072000, rms=0.663 (0.300%), neg=0, invalid=766 0059: dt=9.072000, rms=0.661 (0.365%), neg=0, invalid=766 0060: dt=9.072000, rms=0.658 (0.381%), neg=0, invalid=766 0061: dt=9.072000, rms=0.656 (0.377%), neg=0, invalid=766 0062: dt=9.072000, rms=0.653 (0.363%), neg=0, invalid=766 0063: dt=9.072000, rms=0.651 (0.336%), neg=0, invalid=766 0064: dt=9.072000, rms=0.649 (0.325%), neg=0, invalid=766 0065: dt=9.072000, rms=0.647 (0.318%), neg=0, invalid=766 0066: dt=9.072000, rms=0.645 (0.333%), neg=0, invalid=766 0067: dt=9.072000, rms=0.643 (0.342%), neg=0, invalid=766 0068: dt=9.072000, rms=0.640 (0.331%), neg=0, invalid=766 0069: dt=9.072000, rms=0.639 (0.303%), neg=0, invalid=766 0070: dt=9.072000, rms=0.637 (0.278%), neg=0, invalid=766 0071: dt=9.072000, rms=0.635 (0.248%), neg=0, invalid=766 0072: dt=9.072000, rms=0.634 (0.224%), neg=0, invalid=766 0073: dt=9.072000, rms=0.632 (0.207%), neg=0, invalid=766 0074: dt=9.072000, rms=0.631 (0.207%), neg=0, invalid=766 0075: dt=9.072000, rms=0.630 (0.213%), neg=0, invalid=766 0076: dt=9.072000, rms=0.628 (0.216%), neg=0, invalid=766 0077: dt=9.072000, rms=0.627 (0.210%), neg=0, invalid=766 0078: dt=9.072000, rms=0.626 (0.192%), neg=0, invalid=766 0079: dt=9.072000, rms=0.625 (0.165%), neg=0, invalid=766 0080: dt=9.072000, rms=0.624 (0.146%), neg=0, invalid=766 0081: dt=9.072000, rms=0.623 (0.137%), neg=0, invalid=766 0082: dt=9.072000, rms=0.622 (0.131%), neg=0, invalid=766 0083: dt=9.072000, rms=0.621 (0.133%), neg=0, invalid=766 0084: dt=9.072000, rms=0.621 (0.127%), neg=0, invalid=766 0085: dt=9.072000, rms=0.620 (0.124%), neg=0, invalid=766 0086: dt=9.072000, rms=0.619 (0.115%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48002.594 ms 0087: dt=145.152000, rms=0.619 (0.079%), neg=0, invalid=766 0088: dt=145.152000, rms=0.619 (-0.859%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45832.441 ms 0089: dt=31.104000, rms=0.618 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47991.969 ms 0090: dt=9.072000, rms=0.618 (0.010%), neg=0, invalid=766 0091: dt=9.072000, rms=0.618 (0.005%), neg=0, invalid=766 0092: dt=9.072000, rms=0.618 (0.008%), neg=0, invalid=766 0093: dt=9.072000, rms=0.618 (0.001%), neg=0, invalid=766 0094: dt=9.072000, rms=0.618 (0.005%), neg=0, invalid=766 0095: dt=9.072000, rms=0.618 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45303.027 ms 0096: dt=2.800000, rms=0.644 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50361.879 ms 0097: dt=1.200000, rms=0.644 (0.004%), neg=0, invalid=766 0098: dt=1.200000, rms=0.644 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46821.859 ms 0099: dt=0.000000, rms=0.644 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47270.336 ms 0100: dt=4.924471, rms=0.704 (2.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44319.625 ms 0101: dt=1.500000, rms=0.704 (0.034%), neg=0, invalid=766 0102: dt=1.500000, rms=0.704 (-0.033%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41441.730 ms 0103: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.792, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46405.473 ms 0104: dt=1.067485, rms=0.788 (0.547%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41477.223 ms 0105: dt=0.448000, rms=0.785 (0.284%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44337.254 ms 0106: dt=1.944444, rms=0.781 (0.524%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42946.535 ms 0107: dt=1.024000, rms=0.781 (0.083%), neg=0, invalid=766 0108: dt=1.024000, rms=0.780 (0.081%), neg=0, invalid=766 0109: dt=1.024000, rms=0.780 (-0.024%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.780, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42495.141 ms 0110: dt=1.055118, rms=0.779 (0.124%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40327.422 ms 0111: dt=0.000000, rms=0.779 (0.003%), neg=0, invalid=766 0112: dt=0.100000, rms=0.779 (-0.006%), 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=0.715, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42952.402 ms 0113: dt=0.448000, rms=0.696 (2.770%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37169.867 ms 0114: dt=0.000000, rms=0.696 (0.004%), neg=0, invalid=766 0115: dt=0.050000, rms=0.696 (-0.356%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.696, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37246.875 ms 0116: dt=0.000000, rms=0.696 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13333 (21) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2829 voxels, overlap=0.355) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2829 voxels, peak = 18), gca=18.0 gca peak = 0.14022 (22) mri peak = 0.13267 (22) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2037 voxels, overlap=0.666) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2037 voxels, peak = 19), gca=19.2 gca peak = 0.24234 (100) mri peak = 0.09976 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (414 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (414 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.10552 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (414 voxels, overlap=0.516) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (414 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.06384 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (829 voxels, overlap=0.039) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (829 voxels, peak = 72), gca=72.4 gca peak = 0.29892 (64) mri peak = 0.05544 (74) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (733 voxels, overlap=0.177) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (733 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.08450 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68273 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68273 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.07787 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (65634 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (65634 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03394 (67) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (25796 voxels, overlap=0.726) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (25796 voxels, peak = 69), gca=69.3 gca peak = 0.13270 (63) mri peak = 0.03150 (79) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (26474 voxels, overlap=0.251) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (26474 voxels, peak = 76), gca=75.6 gca peak = 0.15182 (70) mri peak = 0.13176 (79) Right_Caudate (50): linear fit = 1.12 x + 0.0 (490 voxels, overlap=0.203) Right_Caudate (50): linear fit = 1.12 x + 0.0 (490 voxels, peak = 79), gca=78.8 gca peak = 0.14251 (76) mri peak = 0.11433 (86) Left_Caudate (11): linear fit = 1.05 x + 0.0 (618 voxels, overlap=0.614) Left_Caudate (11): linear fit = 1.05 x + 0.0 (618 voxels, peak = 80), gca=79.8 gca peak = 0.12116 (60) mri peak = 0.04418 (68) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20345 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20345 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04208 (68) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (26188 voxels, overlap=0.511) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (26188 voxels, peak = 69), gca=68.6 gca peak = 0.22684 (88) mri peak = 0.08690 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9996 voxels, overlap=0.769) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9996 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.09166 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9090 voxels, overlap=0.730) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9090 voxels, peak = 91), gca=91.3 gca peak = 0.25455 (62) mri peak = 0.08278 (76) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (302 voxels, overlap=0.402) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (302 voxels, peak = 71), gca=71.3 gca peak = 0.39668 (62) mri peak = 0.09286 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (281 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (281 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.06250 (103) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4632 voxels, overlap=0.868) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4632 voxels, peak = 98), gca=97.6 gca peak = 0.12071 (89) mri peak = 0.06557 (100) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3814 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3814 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.05669 (88) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2791 voxels, overlap=0.780) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2791 voxels, peak = 90), gca=90.2 gca peak = 0.15214 (84) mri peak = 0.07075 (88) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2669 voxels, overlap=0.675) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2669 voxels, peak = 90), gca=90.3 gca peak = 0.08983 (85) mri peak = 0.08257 (93) Brain_Stem (16): linear fit = 1.08 x + 0.0 (11867 voxels, overlap=0.741) Brain_Stem (16): linear fit = 1.08 x + 0.0 (11867 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.10567 (99) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1055 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1055 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.08736 (102) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1148 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1148 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) mri peak = 0.10485 (23) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (68 voxels, overlap=0.192) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (68 voxels, peak = 25), gca=25.2 gca peak = 0.13542 (27) mri peak = 0.10496 (23) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (548 voxels, overlap=0.558) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (548 voxels, peak = 22), gca=22.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) 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 1.16 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.79 x + 0.0 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=0.735, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56571.113 ms 0117: dt=92.480000, rms=0.726 (1.254%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42748.117 ms 0118: dt=92.480000, rms=0.724 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48065.371 ms 0119: dt=129.472000, rms=0.719 (0.768%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43030.246 ms 0120: dt=32.368000, rms=0.718 (0.049%), neg=0, invalid=766 0121: dt=32.368000, rms=0.718 (0.069%), neg=0, invalid=766 0122: dt=32.368000, rms=0.717 (0.109%), neg=0, invalid=766 0123: dt=32.368000, rms=0.716 (0.163%), neg=0, invalid=766 0124: dt=32.368000, rms=0.714 (0.226%), neg=0, invalid=766 0125: dt=32.368000, rms=0.713 (0.252%), neg=0, invalid=766 0126: dt=32.368000, rms=0.711 (0.234%), neg=0, invalid=766 0127: dt=32.368000, rms=0.710 (0.199%), neg=0, invalid=766 0128: dt=32.368000, rms=0.708 (0.185%), neg=0, invalid=766 0129: dt=32.368000, rms=0.707 (0.178%), neg=0, invalid=766 0130: dt=32.368000, rms=0.706 (0.186%), neg=0, invalid=766 0131: dt=32.368000, rms=0.704 (0.206%), neg=0, invalid=766 0132: dt=32.368000, rms=0.702 (0.241%), neg=0, invalid=766 0133: dt=32.368000, rms=0.701 (0.251%), neg=0, invalid=766 0134: dt=32.368000, rms=0.699 (0.263%), neg=0, invalid=766 0135: dt=32.368000, rms=0.697 (0.247%), neg=0, invalid=766 0136: dt=32.368000, rms=0.695 (0.256%), neg=0, invalid=766 0137: dt=32.368000, rms=0.694 (0.240%), neg=0, invalid=766 0138: dt=32.368000, rms=0.692 (0.222%), neg=0, invalid=766 0139: dt=32.368000, rms=0.691 (0.202%), neg=0, invalid=766 0140: dt=32.368000, rms=0.689 (0.183%), neg=0, invalid=766 0141: dt=32.368000, rms=0.688 (0.180%), neg=0, invalid=766 0142: dt=32.368000, rms=0.687 (0.174%), neg=0, invalid=766 0143: dt=32.368000, rms=0.686 (0.177%), neg=0, invalid=766 0144: dt=32.368000, rms=0.685 (0.191%), neg=0, invalid=766 0145: dt=32.368000, rms=0.683 (0.170%), neg=0, invalid=766 0146: dt=32.368000, rms=0.682 (0.186%), neg=0, invalid=766 0147: dt=32.368000, rms=0.681 (0.152%), neg=0, invalid=766 0148: dt=32.368000, rms=0.680 (0.160%), neg=0, invalid=766 0149: dt=32.368000, rms=0.679 (0.144%), neg=0, invalid=766 0150: dt=32.368000, rms=0.678 (0.122%), neg=0, invalid=766 0151: dt=32.368000, rms=0.677 (0.115%), neg=0, invalid=766 0152: dt=32.368000, rms=0.677 (0.126%), neg=0, invalid=766 0153: dt=32.368000, rms=0.676 (0.123%), neg=0, invalid=766 0154: dt=32.368000, rms=0.675 (0.125%), neg=0, invalid=766 0155: dt=32.368000, rms=0.674 (0.122%), neg=0, invalid=766 0156: dt=32.368000, rms=0.673 (0.127%), neg=0, invalid=766 0157: dt=32.368000, rms=0.672 (0.122%), neg=0, invalid=766 0158: dt=32.368000, rms=0.672 (0.122%), neg=0, invalid=766 0159: dt=32.368000, rms=0.671 (0.113%), neg=0, invalid=766 0160: dt=32.368000, rms=0.670 (0.103%), neg=0, invalid=766 0161: dt=32.368000, rms=0.669 (0.097%), neg=0, invalid=766 0162: dt=32.368000, rms=0.669 (0.092%), neg=0, invalid=766 0163: dt=32.368000, rms=0.668 (0.090%), neg=0, invalid=766 0164: dt=32.368000, rms=0.668 (0.082%), neg=0, invalid=766 0165: dt=32.368000, rms=0.667 (0.081%), neg=0, invalid=766 0166: dt=32.368000, rms=0.667 (0.085%), neg=0, invalid=766 0167: dt=32.368000, rms=0.666 (0.086%), neg=0, invalid=766 0168: dt=32.368000, rms=0.665 (0.085%), neg=0, invalid=766 0169: dt=32.368000, rms=0.665 (0.073%), neg=0, invalid=766 0170: dt=32.368000, rms=0.664 (0.071%), neg=0, invalid=766 0171: dt=32.368000, rms=0.664 (0.066%), neg=0, invalid=766 0172: dt=32.368000, rms=0.664 (0.070%), neg=0, invalid=766 0173: dt=32.368000, rms=0.663 (0.071%), neg=0, invalid=766 0174: dt=32.368000, rms=0.663 (0.070%), neg=0, invalid=766 0175: dt=32.368000, rms=0.662 (0.066%), neg=0, invalid=766 0176: dt=32.368000, rms=0.662 (0.058%), neg=0, invalid=766 0177: dt=32.368000, rms=0.661 (0.052%), neg=0, invalid=766 0178: dt=32.368000, rms=0.661 (0.056%), neg=0, invalid=766 0179: dt=32.368000, rms=0.661 (0.061%), neg=0, invalid=766 0180: dt=32.368000, rms=0.660 (0.063%), neg=0, invalid=766 0181: dt=32.368000, rms=0.660 (0.057%), neg=0, invalid=766 0182: dt=32.368000, rms=0.660 (0.052%), neg=0, invalid=766 0183: dt=32.368000, rms=0.659 (0.047%), neg=0, invalid=766 0184: dt=32.368000, rms=0.659 (0.050%), neg=0, invalid=766 0185: dt=32.368000, rms=0.659 (0.051%), neg=0, invalid=766 0186: dt=32.368000, rms=0.658 (0.052%), neg=0, invalid=766 0187: dt=32.368000, rms=0.658 (0.050%), neg=0, invalid=766 0188: dt=32.368000, rms=0.658 (0.046%), neg=0, invalid=766 0189: dt=32.368000, rms=0.657 (0.040%), neg=0, invalid=766 0190: dt=32.368000, rms=0.657 (0.036%), neg=0, invalid=766 0191: dt=32.368000, rms=0.657 (0.039%), neg=0, invalid=766 0192: dt=32.368000, rms=0.657 (0.041%), neg=0, invalid=766 0193: dt=32.368000, rms=0.656 (0.045%), neg=0, invalid=766 0194: dt=32.368000, rms=0.656 (0.046%), neg=0, invalid=766 0195: dt=32.368000, rms=0.656 (0.047%), neg=0, invalid=766 0196: dt=32.368000, rms=0.655 (0.042%), neg=0, invalid=766 0197: dt=32.368000, rms=0.655 (0.034%), neg=0, invalid=766 0198: dt=32.368000, rms=0.655 (0.028%), neg=0, invalid=766 0199: dt=32.368000, rms=0.655 (0.030%), neg=0, invalid=766 0200: dt=32.368000, rms=0.655 (0.033%), neg=0, invalid=766 0201: dt=32.368000, rms=0.654 (0.035%), neg=0, invalid=766 0202: dt=32.368000, rms=0.654 (0.033%), neg=0, invalid=766 0203: dt=32.368000, rms=0.654 (0.034%), neg=0, invalid=766 0204: dt=32.368000, rms=0.654 (0.036%), neg=0, invalid=766 0205: dt=32.368000, rms=0.653 (0.034%), neg=0, invalid=766 0206: dt=32.368000, rms=0.653 (0.028%), neg=0, invalid=766 0207: dt=32.368000, rms=0.653 (0.027%), neg=0, invalid=766 0208: dt=32.368000, rms=0.653 (0.030%), neg=0, invalid=766 0209: dt=32.368000, rms=0.653 (0.031%), neg=0, invalid=766 0210: dt=32.368000, rms=0.652 (0.029%), neg=0, invalid=766 0211: dt=32.368000, rms=0.652 (0.029%), neg=0, invalid=766 0212: dt=32.368000, rms=0.652 (0.027%), neg=0, invalid=766 0213: dt=32.368000, rms=0.652 (0.025%), neg=0, invalid=766 0214: dt=32.368000, rms=0.652 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48369.934 ms 0215: dt=1775.616000, rms=0.651 (0.089%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44517.137 ms 0216: dt=32.368000, rms=0.651 (0.025%), neg=0, invalid=766 0217: dt=32.368000, rms=0.651 (0.009%), neg=0, invalid=766 0218: dt=32.368000, rms=0.651 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46960.820 ms 0219: dt=110.976000, rms=0.651 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49171.352 ms 0220: dt=517.888000, rms=0.649 (0.258%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45738.625 ms 0221: dt=0.000000, rms=0.649 (-0.004%), neg=0, invalid=766 0222: dt=0.850000, rms=0.649 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44341.805 ms 0223: dt=103.680000, rms=0.644 (0.970%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59930.543 ms 0224: dt=36.288000, rms=0.637 (1.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44417.488 ms 0225: dt=20.736000, rms=0.636 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46196.137 ms 0226: dt=103.680000, rms=0.628 (1.288%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39541.418 ms 0227: dt=1.620000, rms=0.628 (0.004%), neg=0, invalid=766 0228: dt=0.101250, rms=0.627 (0.002%), neg=0, invalid=766 0229: dt=0.050625, rms=0.627 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28746.570 ms 0230: dt=0.035437, rms=0.627 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32536.441 ms 0231: dt=0.035437, rms=0.627 (0.000%), neg=0, invalid=766 0232: dt=0.017719, rms=0.627 (0.000%), neg=0, invalid=766 0233: dt=0.004430, rms=0.627 (0.000%), neg=0, invalid=766 0234: dt=0.002215, rms=0.627 (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=0.634, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21879.908 ms 0235: dt=0.000000, rms=0.634 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21742.174 ms 0236: dt=0.000000, rms=0.634 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21412.012 ms 0237: dt=0.000000, rms=0.634 (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=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25990.355 ms 0238: dt=0.000000, rms=0.655 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23160.225 ms 0239: dt=0.000000, rms=0.655 (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=0.697, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43921.539 ms 0240: dt=1.280000, rms=0.677 (2.909%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41247.980 ms 0241: dt=0.448000, rms=0.672 (0.701%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40426.730 ms 0242: dt=0.448000, rms=0.668 (0.617%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45498.031 ms 0243: dt=1.792000, rms=0.654 (2.175%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43485.105 ms 0244: dt=1.792000, rms=0.645 (1.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55827.000 ms 0245: dt=1.792000, rms=0.640 (0.856%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53946.336 ms 0246: dt=1.792000, rms=0.636 (0.621%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45627.012 ms 0247: dt=1.792000, rms=0.633 (0.485%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43888.008 ms 0248: dt=1.792000, rms=0.630 (0.394%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47520.051 ms 0249: dt=5.120000, rms=0.624 (0.920%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43189.840 ms 0250: dt=1.792000, rms=0.623 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48626.727 ms 0251: dt=1.792000, rms=0.622 (0.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40328.438 ms 0252: dt=1.792000, rms=0.621 (0.187%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41403.598 ms 0253: dt=1.792000, rms=0.620 (0.164%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40628.871 ms 0254: dt=5.120000, rms=0.617 (0.426%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40556.168 ms 0255: dt=1.792000, rms=0.616 (0.119%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41492.562 ms 0256: dt=1.792000, rms=0.616 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44264.352 ms 0257: dt=5.000000, rms=0.614 (0.280%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42455.559 ms 0258: dt=1.280000, rms=0.613 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44429.086 ms 0259: dt=3.500000, rms=0.612 (0.163%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43093.285 ms 0260: dt=1.792000, rms=0.612 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46662.418 ms 0261: dt=5.120000, rms=0.611 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41284.398 ms 0262: dt=0.458333, rms=0.611 (0.011%), neg=0, invalid=766 0263: dt=0.458333, rms=0.611 (0.023%), neg=0, invalid=766 0264: dt=0.458333, rms=0.611 (0.018%), neg=0, invalid=766 0265: dt=0.458333, rms=0.610 (0.029%), neg=0, invalid=766 0266: dt=0.458333, rms=0.610 (0.038%), neg=0, invalid=766 0267: dt=0.458333, rms=0.610 (0.048%), neg=0, invalid=766 0268: dt=0.458333, rms=0.609 (0.059%), neg=0, invalid=766 0269: dt=0.458333, rms=0.609 (0.063%), neg=0, invalid=766 0270: dt=0.458333, rms=0.609 (0.070%), neg=0, invalid=766 0271: dt=0.458333, rms=0.608 (0.070%), neg=0, invalid=766 0272: dt=0.458333, rms=0.608 (0.070%), neg=0, invalid=766 0273: dt=0.458333, rms=0.607 (0.072%), neg=0, invalid=766 0274: dt=0.458333, rms=0.607 (0.070%), neg=0, invalid=766 0275: dt=0.458333, rms=0.607 (0.068%), neg=0, invalid=766 0276: dt=0.458333, rms=0.606 (0.061%), neg=0, invalid=766 0277: dt=0.458333, rms=0.606 (0.057%), neg=0, invalid=766 0278: dt=0.458333, rms=0.605 (0.054%), neg=0, invalid=766 0279: dt=0.458333, rms=0.605 (0.050%), neg=0, invalid=766 0280: dt=0.458333, rms=0.605 (0.043%), neg=0, invalid=766 0281: dt=0.458333, rms=0.605 (0.042%), neg=0, invalid=766 0282: dt=0.458333, rms=0.604 (0.038%), neg=0, invalid=766 0283: dt=0.458333, rms=0.604 (0.033%), neg=0, invalid=766 0284: dt=0.458333, rms=0.604 (0.032%), neg=0, invalid=766 0285: dt=0.458333, rms=0.604 (0.032%), neg=0, invalid=766 0286: dt=0.458333, rms=0.604 (0.033%), neg=0, invalid=766 0287: dt=0.458333, rms=0.603 (0.028%), neg=0, invalid=766 0288: dt=0.458333, rms=0.603 (0.032%), neg=0, invalid=766 0289: dt=0.458333, rms=0.603 (0.032%), neg=0, invalid=766 0290: dt=0.458333, rms=0.603 (0.035%), neg=0, invalid=766 0291: dt=0.458333, rms=0.603 (0.033%), neg=0, invalid=766 0292: dt=0.458333, rms=0.602 (0.033%), neg=0, invalid=766 0293: dt=0.458333, rms=0.602 (0.034%), neg=0, invalid=766 0294: dt=0.458333, rms=0.602 (0.035%), neg=0, invalid=766 0295: dt=0.458333, rms=0.602 (0.034%), neg=0, invalid=766 0296: dt=0.458333, rms=0.602 (0.033%), neg=0, invalid=766 0297: dt=0.458333, rms=0.601 (0.032%), neg=0, invalid=766 0298: dt=0.458333, rms=0.601 (0.031%), neg=0, invalid=766 0299: dt=0.458333, rms=0.601 (0.035%), neg=0, invalid=766 0300: dt=0.458333, rms=0.601 (0.034%), neg=0, invalid=766 0301: dt=0.458333, rms=0.601 (0.032%), neg=0, invalid=766 0302: dt=0.458333, rms=0.601 (0.031%), neg=0, invalid=766 0303: dt=0.458333, rms=0.600 (0.031%), neg=0, invalid=766 0304: dt=0.458333, rms=0.600 (0.030%), neg=0, invalid=766 0305: dt=0.458333, rms=0.600 (0.030%), neg=0, invalid=766 0306: dt=0.458333, rms=0.600 (0.032%), neg=0, invalid=766 0307: dt=0.458333, rms=0.600 (0.028%), neg=0, invalid=766 0308: dt=0.458333, rms=0.599 (0.026%), neg=0, invalid=766 0309: dt=0.458333, rms=0.599 (0.029%), neg=0, invalid=766 0310: dt=0.458333, rms=0.599 (0.027%), neg=0, invalid=766 0311: dt=0.458333, rms=0.599 (0.025%), neg=0, invalid=766 0312: dt=0.458333, rms=0.599 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44890.703 ms 0313: dt=7.168000, rms=0.599 (0.018%), neg=0, invalid=766 0314: dt=1.792000, rms=0.599 (0.009%), neg=0, invalid=766 0315: dt=1.792000, rms=0.599 (0.002%), neg=0, invalid=766 0316: dt=1.792000, rms=0.599 (0.021%), neg=0, invalid=766 0317: dt=1.792000, rms=0.598 (0.011%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41481.312 ms 0318: dt=1.792000, rms=0.598 (0.155%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47523.758 ms 0319: dt=4.563380, rms=0.597 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42805.758 ms 0320: dt=0.000000, rms=0.597 (-0.009%), neg=0, invalid=766 0321: dt=0.100000, rms=0.597 (-0.001%), 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=0.581, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41172.387 ms 0322: dt=0.175373, rms=0.573 (1.500%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39410.531 ms 0323: dt=0.149332, rms=0.567 (0.920%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44273.867 ms 0324: dt=0.320000, rms=0.559 (1.532%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40227.027 ms 0325: dt=0.112000, rms=0.557 (0.311%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42075.141 ms 0326: dt=0.112000, rms=0.555 (0.271%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41304.371 ms 0327: dt=0.112000, rms=0.554 (0.242%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44588.207 ms 0328: dt=0.384000, rms=0.550 (0.737%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43895.566 ms 0329: dt=0.384000, rms=0.547 (0.497%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39871.273 ms 0330: dt=0.028000, rms=0.547 (0.029%), neg=0, invalid=766 0331: dt=0.028000, rms=0.547 (0.027%), neg=0, invalid=766 0332: dt=0.028000, rms=0.547 (0.052%), neg=0, invalid=766 0333: dt=0.028000, rms=0.546 (0.072%), neg=0, invalid=766 0334: dt=0.028000, rms=0.546 (0.089%), neg=0, invalid=766 0335: dt=0.028000, rms=0.545 (0.103%), neg=0, invalid=766 0336: dt=0.028000, rms=0.545 (0.115%), neg=0, invalid=766 0337: dt=0.028000, rms=0.544 (0.122%), neg=0, invalid=766 0338: dt=0.028000, rms=0.543 (0.128%), neg=0, invalid=766 0339: dt=0.028000, rms=0.543 (0.135%), neg=0, invalid=766 0340: dt=0.028000, rms=0.542 (0.134%), neg=0, invalid=766 0341: dt=0.028000, rms=0.541 (0.134%), neg=0, invalid=766 0342: dt=0.028000, rms=0.540 (0.131%), neg=0, invalid=766 0343: dt=0.028000, rms=0.540 (0.127%), neg=0, invalid=766 0344: dt=0.028000, rms=0.539 (0.122%), neg=0, invalid=766 0345: dt=0.028000, rms=0.538 (0.118%), neg=0, invalid=766 0346: dt=0.028000, rms=0.538 (0.112%), neg=0, invalid=766 0347: dt=0.028000, rms=0.537 (0.106%), neg=0, invalid=766 0348: dt=0.028000, rms=0.537 (0.099%), neg=0, invalid=766 0349: dt=0.028000, rms=0.536 (0.093%), neg=0, invalid=766 0350: dt=0.028000, rms=0.536 (0.085%), neg=0, invalid=766 0351: dt=0.028000, rms=0.535 (0.078%), neg=0, invalid=766 0352: dt=0.028000, rms=0.535 (0.071%), neg=0, invalid=766 0353: dt=0.028000, rms=0.535 (0.067%), neg=0, invalid=766 0354: dt=0.028000, rms=0.534 (0.062%), neg=0, invalid=766 0355: dt=0.028000, rms=0.534 (0.057%), neg=0, invalid=766 0356: dt=0.028000, rms=0.534 (0.049%), neg=0, invalid=766 0357: dt=0.028000, rms=0.533 (0.046%), neg=0, invalid=766 0358: dt=0.028000, rms=0.533 (0.042%), neg=0, invalid=766 0359: dt=0.028000, rms=0.533 (0.039%), neg=0, invalid=766 0360: dt=0.028000, rms=0.533 (0.036%), neg=0, invalid=766 0361: dt=0.028000, rms=0.533 (0.033%), neg=0, invalid=766 0362: dt=0.028000, rms=0.533 (0.030%), neg=0, invalid=766 0363: dt=0.028000, rms=0.532 (0.026%), neg=0, invalid=766 0364: dt=0.028000, rms=0.532 (0.026%), neg=0, invalid=766 0365: dt=0.028000, rms=0.532 (0.022%), neg=0, invalid=766 0366: dt=0.028000, rms=0.532 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52122.973 ms 0367: dt=0.448000, rms=0.532 (0.014%), neg=0, invalid=766 0368: dt=0.448000, rms=0.532 (0.015%), neg=0, invalid=766 0369: dt=0.448000, rms=0.532 (0.025%), neg=0, invalid=766 0370: dt=0.224000, rms=0.532 (0.008%), neg=0, invalid=766 0371: dt=0.224000, rms=0.532 (0.009%), neg=0, invalid=766 0372: dt=0.224000, rms=0.532 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42503.867 ms 0373: dt=0.112000, rms=0.532 (0.004%), neg=0, invalid=766 0374: dt=0.112000, rms=0.532 (0.004%), neg=0, invalid=766 0375: dt=0.112000, rms=0.532 (0.007%), neg=0, invalid=766 0376: dt=0.112000, rms=0.532 (0.002%), neg=0, invalid=766 0377: dt=0.112000, rms=0.531 (0.008%), neg=0, invalid=766 0378: dt=0.112000, rms=0.531 (0.011%), neg=0, invalid=766 0379: dt=0.112000, rms=0.531 (0.013%), neg=0, invalid=766 0380: dt=0.112000, rms=0.531 (0.016%), neg=0, invalid=766 0381: dt=0.112000, rms=0.531 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46287.535 ms 0382: dt=0.112000, rms=0.530 (0.247%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44080.191 ms 0383: dt=0.448000, rms=0.526 (0.689%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49534.289 ms 0384: dt=0.000000, rms=0.526 (0.000%), neg=0, invalid=766 0385: dt=0.050000, rms=0.526 (-0.004%), 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=0.523, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54744.590 ms iter 0, gcam->neg = 33 after 42 iterations, nbhd size=2, neg = 0 0386: dt=44.800000, rms=0.496 (5.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50043.555 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0387: dt=44.800000, rms=0.489 (1.483%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50916.898 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0388: dt=10.181818, rms=0.486 (0.479%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49571.961 ms 0389: dt=11.200000, rms=0.484 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50922.500 ms 0390: dt=11.200000, rms=0.484 (0.169%), neg=0, invalid=766 0391: dt=11.200000, rms=0.482 (0.253%), neg=0, invalid=766 0392: dt=11.200000, rms=0.481 (0.343%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 69 iterations, nbhd size=3, neg = 0 0393: dt=11.200000, rms=0.479 (0.378%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31762.365 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (15.282%) 0394: dt=11.200000, rms=0.477 (0.427%), neg=0, invalid=766 0395: dt=11.200000, rms=0.476 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28635.305 ms iter 1, dt=0.008000: new neg 0, old_neg 1, delta 1, rms=0.003 (6.716%) 0396: dt=11.200000, rms=0.475 (0.164%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31516.604 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (8.849%) 0397: dt=11.200000, rms=0.475 (0.075%), neg=0, invalid=766 0398: dt=11.200000, rms=0.474 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0399: dt=11.200000, rms=0.474 (0.149%), neg=0, invalid=766 0400: dt=11.200000, rms=0.473 (0.168%), neg=0, invalid=766 0401: dt=11.200000, rms=0.472 (0.230%), neg=0, invalid=766 0402: dt=11.200000, rms=0.471 (0.247%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0403: dt=11.200000, rms=0.470 (0.225%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0404: dt=11.200000, rms=0.469 (0.222%), neg=0, invalid=766 0405: dt=11.200000, rms=0.468 (0.232%), neg=0, invalid=766 0406: dt=11.200000, rms=0.466 (0.229%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0407: dt=11.200000, rms=0.465 (0.209%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0408: dt=11.200000, rms=0.465 (0.183%), neg=0, invalid=766 0409: dt=11.200000, rms=0.464 (0.189%), neg=0, invalid=766 0410: dt=11.200000, rms=0.463 (0.168%), neg=0, invalid=766 0411: dt=11.200000, rms=0.462 (0.125%), neg=0, invalid=766 0412: dt=11.200000, rms=0.462 (0.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46811.746 ms 0413: dt=11.200000, rms=0.462 (0.033%), neg=0, invalid=766 0414: dt=11.200000, rms=0.462 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48011.434 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29931.240 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (10.944%) 0415: dt=44.800000, rms=0.460 (0.420%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50035.172 ms 0416: dt=8.406780, rms=0.459 (0.196%), neg=0, invalid=766 0417: dt=8.406780, rms=0.459 (0.037%), neg=0, invalid=766 0418: dt=8.406780, rms=0.458 (0.050%), neg=0, invalid=766 0419: dt=8.406780, rms=0.458 (0.123%), neg=0, invalid=766 0420: dt=8.406780, rms=0.458 (0.083%), neg=0, invalid=766 0421: dt=8.406780, rms=0.457 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52130.734 ms 0422: dt=6.400000, rms=0.457 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52008.812 ms 0423: dt=0.252000, rms=0.470 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54567.301 ms 0424: dt=0.252000, rms=0.470 (0.001%), neg=0, invalid=766 0425: dt=0.252000, rms=0.470 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49549.633 ms 0426: dt=1.008000, rms=0.470 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49524.273 ms 0427: dt=0.720000, rms=0.470 (0.005%), neg=0, invalid=766 0428: dt=0.720000, rms=0.470 (0.002%), neg=0, invalid=766 0429: dt=0.720000, rms=0.470 (-0.013%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46875.188 ms iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0430: dt=1.380783, rms=0.490 (0.414%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55898.754 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0431: dt=0.384000, rms=0.490 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0432: dt=0.384000, rms=0.490 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47399.004 ms iter 0, gcam->neg = 20 after 25 iterations, nbhd size=4, neg = 0 0433: dt=0.910180, rms=0.489 (0.130%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49264.910 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0434: dt=0.448000, rms=0.489 (0.026%), neg=0, invalid=766 0435: dt=0.448000, rms=0.489 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0436: dt=0.448000, rms=0.489 (-0.036%), 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=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57778.688 ms iter 0, gcam->neg = 916 after 19 iterations, nbhd size=2, neg = 0 0437: dt=2.188172, rms=0.425 (9.246%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61725.801 ms 0438: dt=0.000438, rms=0.425 (-0.000%), neg=0, invalid=766 0439: dt=0.000438, rms=0.425 (0.001%), neg=0, invalid=766 0440: dt=0.000438, rms=0.425 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58789.309 ms 0441: dt=0.001750, rms=0.425 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50681.090 ms 0442: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0443: dt=0.050000, rms=0.425 (-0.113%), 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=0.404, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51773.555 ms iter 0, gcam->neg = 477 after 13 iterations, nbhd size=1, neg = 0 0444: dt=0.676471, rms=0.393 (2.836%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51069.473 ms 0445: dt=0.000438, rms=0.393 (-0.003%), neg=0, invalid=766 0446: dt=0.000438, rms=0.393 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0447: dt=0.000438, rms=0.393 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49680.844 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0448: dt=0.000438, rms=0.393 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48882.316 ms 0449: dt=0.001750, rms=0.393 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51228.617 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0450: dt=0.007000, rms=0.393 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63095.301 ms iter 0, gcam->neg = 10 after 15 iterations, nbhd size=2, neg = 0 0451: dt=0.112000, rms=0.392 (0.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59263.281 ms 0452: dt=0.000438, rms=0.392 (0.006%), neg=0, invalid=766 0453: dt=0.000438, rms=0.392 (0.000%), neg=0, invalid=766 0454: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0455: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0456: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0457: dt=0.000438, rms=0.392 (0.002%), neg=0, invalid=766 0458: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0459: dt=0.000438, rms=0.392 (0.002%), neg=0, invalid=766 0460: dt=0.000438, rms=0.392 (0.003%), neg=0, invalid=766 0461: dt=0.000438, rms=0.392 (0.003%), 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=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53937.613 ms iter 0, gcam->neg = 174 after 17 iterations, nbhd size=2, neg = 0 0462: dt=0.227872, rms=0.387 (0.976%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49557.051 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0463: dt=0.001750, rms=0.387 (-0.000%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0464: dt=0.001750, rms=0.387 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0465: dt=0.001750, rms=0.387 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0466: dt=0.001750, rms=0.387 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0467: dt=0.001750, rms=0.387 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=0.001750, rms=0.387 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0469: dt=0.001750, rms=0.387 (0.018%), neg=0, invalid=766 0470: dt=0.001750, rms=0.387 (0.020%), neg=0, invalid=766 0471: dt=0.001750, rms=0.387 (0.021%), neg=0, invalid=766 0472: dt=0.001750, rms=0.387 (0.024%), neg=0, invalid=766 0473: dt=0.001750, rms=0.387 (0.025%), neg=0, invalid=766 0474: dt=0.001750, rms=0.387 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0475: dt=0.001750, rms=0.387 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0476: dt=0.001750, rms=0.386 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0477: dt=0.001750, rms=0.386 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0478: dt=0.001750, rms=0.386 (0.029%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53174.926 ms iter 0, gcam->neg = 150 after 16 iterations, nbhd size=2, neg = 0 0479: dt=0.260700, rms=0.383 (0.863%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54478.023 ms 0480: dt=0.003000, rms=0.383 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0481: dt=0.003000, rms=0.383 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0482: dt=0.003000, rms=0.383 (0.010%), neg=0, invalid=766 0483: dt=0.003000, rms=0.383 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0484: dt=0.003000, rms=0.383 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0485: dt=0.003000, rms=0.383 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0486: dt=0.003000, rms=0.382 (0.023%), neg=0, invalid=766 0487: dt=0.003000, rms=0.382 (0.026%), neg=0, invalid=766 0488: dt=0.003000, rms=0.382 (0.028%), neg=0, invalid=766 0489: dt=0.003000, rms=0.382 (0.028%), neg=0, invalid=766 0490: dt=0.003000, rms=0.382 (0.031%), neg=0, invalid=766 0491: dt=0.003000, rms=0.382 (0.030%), neg=0, invalid=766 0492: dt=0.003000, rms=0.382 (0.033%), neg=0, invalid=766 0493: dt=0.003000, rms=0.382 (0.033%), neg=0, invalid=766 0494: dt=0.003000, rms=0.382 (0.034%), neg=0, invalid=766 0495: dt=0.003000, rms=0.381 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52402.449 ms iter 0, gcam->neg = 42 after 16 iterations, nbhd size=2, neg = 0 0496: dt=0.096000, rms=0.381 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53226.469 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=0.004000, rms=0.381 (0.006%), 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=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51726.527 ms iter 0, gcam->neg = 51 after 61 iterations, nbhd size=2, neg = 0 0498: dt=11.200000, rms=0.380 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48240.867 ms iter 0, gcam->neg = 85 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 37058.094 ms iter 1, dt=0.000080: new neg 0, old_neg 5, delta 5, rms=0.001 (66.649%) 0499: dt=8.000000, rms=0.380 (0.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60628.879 ms iter 0, gcam->neg = 68 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 34479.977 ms iter 1, dt=0.000100: new neg 1, old_neg 9, delta 8, rms=0.002 (78.285%) gcamFindOptimalTimeStep: Complete in 27431.150 ms iter 2, dt=0.000492: new neg 0, old_neg 1, delta 1, rms=0.001 (38.753%) 0500: dt=11.200000, rms=0.380 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 200 iterations, nbhd size=4, neg = 19 starting rms=0.009, neg=19, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 35093.051 ms iter 1, dt=0.000039: new neg 0, old_neg 19, delta 19, rms=0.002 (80.064%) 0501: dt=11.200000, rms=0.380 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 51 after 200 iterations, nbhd size=2, neg = 18 starting rms=0.010, neg=18, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 33738.629 ms iter 1, dt=0.000039: new neg 1, old_neg 18, delta 17, rms=0.002 (75.822%) gcamFindOptimalTimeStep: Complete in 31657.713 ms iter 2, dt=0.000147: new neg 0, old_neg 1, delta 1, rms=0.002 (33.379%) 0502: dt=11.200000, rms=0.380 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 200 iterations, nbhd size=1, neg = 29 starting rms=0.012, neg=29, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31362.740 ms iter 1, dt=0.000039: new neg 1, old_neg 29, delta 28, rms=0.002 (80.780%) gcamFindOptimalTimeStep: Complete in 30608.059 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (30.218%) 0503: dt=11.200000, rms=0.380 (-0.052%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52934.734 ms iter 0, gcam->neg = 96 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.009, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 39011.109 ms iter 1, dt=0.000080: new neg 0, old_neg 11, delta 11, rms=0.001 (82.801%) 0504: dt=25.600000, rms=0.378 (0.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65820.320 ms iter 0, gcam->neg = 82 after 200 iterations, nbhd size=1, neg = 14 starting rms=0.009, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29656.904 ms iter 1, dt=0.000023: new neg 1, old_neg 14, delta 13, rms=0.003 (67.479%) gcamFindOptimalTimeStep: Complete in 29748.238 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.002 (22.324%) 0505: dt=38.400000, rms=0.378 (0.214%), neg=0, invalid=766 iter 0, gcam->neg = 184 after 200 iterations, nbhd size=4, neg = 27 starting rms=0.011, neg=27, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31134.328 ms iter 1, dt=0.000031: new neg 1, old_neg 27, delta 26, rms=0.003 (67.967%) gcamFindOptimalTimeStep: Complete in 30026.637 ms iter 2, dt=0.000573: new neg 1, old_neg 1, delta 0, rms=0.001 (70.941%) gcamFindOptimalTimeStep: Complete in 28902.654 ms iter 3, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.001 (3.522%) gcamFindOptimalTimeStep: Complete in 29774.980 ms iter 4, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.001 (0.897%) gcamFindOptimalTimeStep: Complete in 30334.256 ms iter 5, dt=0.000026: new neg 1, old_neg 1, delta 0, rms=0.001 (0.434%) gcamFindOptimalTimeStep: Complete in 31154.449 ms iter 6, dt=0.000001: new neg 1, old_neg 1, delta 0, rms=0.001 (0.007%) ---------- unfolding failed - restoring original position -------------------- 0506: dt=38.400000, rms=0.378 (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=0.378, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57980.133 ms iter 0, gcam->neg = 99 after 200 iterations, nbhd size=3, neg = 20 starting rms=0.009, neg=20, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 38384.324 ms iter 1, dt=0.000082: new neg 0, old_neg 20, delta 20, rms=0.002 (81.920%) 0507: dt=2.300000, rms=0.377 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53451.609 ms iter 0, gcam->neg = 93 after 200 iterations, nbhd size=4, neg = 16 starting rms=0.009, neg=16, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26858.004 ms iter 1, dt=0.000031: new neg 1, old_neg 16, delta 15, rms=0.002 (77.085%) gcamFindOptimalTimeStep: Complete in 29758.330 ms iter 2, dt=0.000149: new neg 0, old_neg 1, delta 1, rms=0.001 (35.366%) 0508: dt=2.967033, rms=0.377 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59454.812 ms iter 0, gcam->neg = 49 after 200 iterations, nbhd size=2, neg = 16 starting rms=0.009, neg=16, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30595.230 ms iter 1, dt=0.000031: new neg 1, old_neg 16, delta 15, rms=0.002 (78.879%) gcamFindOptimalTimeStep: Complete in 32717.273 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (34.891%) 0509: dt=2.123457, rms=0.376 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=4, neg = 20 starting rms=0.010, neg=20, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29350.688 ms iter 1, dt=0.000125: new neg 0, old_neg 20, delta 20, rms=0.001 (86.023%) 0510: dt=2.123457, rms=0.376 (0.084%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 200 iterations, nbhd size=1, neg = 15 starting rms=0.009, neg=15, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25628.580 ms iter 1, dt=0.000023: new neg 3, old_neg 15, delta 12, rms=0.002 (73.631%) gcamFindOptimalTimeStep: Complete in 28529.732 ms iter 2, dt=0.000009: new neg 0, old_neg 3, delta 3, rms=0.002 (19.282%) 0511: dt=2.123457, rms=0.376 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 97 after 200 iterations, nbhd size=3, neg = 15 starting rms=0.009, neg=15, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27143.879 ms iter 1, dt=0.000031: new neg 1, old_neg 15, delta 14, rms=0.002 (76.214%) gcamFindOptimalTimeStep: Complete in 27872.564 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (33.252%) 0512: dt=2.123457, rms=0.375 (0.089%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=2, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27387.707 ms iter 1, dt=0.000023: new neg 0, old_neg 12, delta 12, rms=0.002 (78.154%) 0513: dt=2.123457, rms=0.375 (0.078%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52938.312 ms iter 0, gcam->neg = 59 after 200 iterations, nbhd size=4, neg = 17 starting rms=0.008, neg=17, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26733.141 ms iter 1, dt=0.000023: new neg 0, old_neg 17, delta 17, rms=0.001 (81.421%) 0514: dt=2.533333, rms=0.374 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54158.887 ms iter 0, gcam->neg = 40 after 200 iterations, nbhd size=2, neg = 7 starting rms=0.005, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25878.598 ms iter 1, dt=0.000125: new neg 0, old_neg 7, delta 7, rms=0.001 (79.015%) 0515: dt=1.932203, rms=0.374 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.005, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25586.547 ms iter 1, dt=0.000023: new neg 0, old_neg 7, delta 7, rms=0.001 (71.669%) 0516: dt=1.932203, rms=0.374 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=2, neg = 8 starting rms=0.006, neg=8, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26971.246 ms iter 1, dt=0.000023: new neg 1, old_neg 8, delta 7, rms=0.002 (71.978%) gcamFindOptimalTimeStep: Complete in 28379.342 ms iter 2, dt=0.000410: new neg 1, old_neg 1, delta 0, rms=0.001 (34.785%) gcamFindOptimalTimeStep: Complete in 27520.703 ms iter 3, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (6.807%) 0517: dt=1.932203, rms=0.373 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.006, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29431.486 ms iter 1, dt=0.000023: new neg 0, old_neg 11, delta 11, rms=0.001 (79.595%) 0518: dt=1.932203, rms=0.373 (0.086%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 45545.488 ms iter 1, dt=0.000080: new neg 0, old_neg 6, delta 6, rms=0.001 (78.359%) 0519: dt=1.932203, rms=0.373 (0.080%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65675.602 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.002, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27956.996 ms iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.001 (67.313%) 0520: dt=0.112000, rms=0.374 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57940.004 ms iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30431.123 ms iter 1, dt=0.000023: new neg 0, old_neg 4, delta 4, rms=0.001 (71.974%) 0521: dt=0.263636, rms=0.374 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52654.027 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0522: dt=0.112000, rms=0.374 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27251.303 ms iter 1, dt=0.000023: new neg 1, old_neg 3, delta 2, rms=0.001 (65.878%) gcamFindOptimalTimeStep: Complete in 27550.412 ms iter 2, dt=0.000102: new neg 0, old_neg 1, delta 1, rms=0.001 (33.528%) 0523: dt=0.112000, rms=0.374 (-0.001%), 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 50964.148 ms iter 0, gcam->neg = 24 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27928.506 ms iter 1, dt=0.000023: new neg 1, old_neg 6, delta 5, rms=0.003 (45.649%) gcamFindOptimalTimeStep: Complete in 25506.211 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.001 (68.645%) 0524: dt=0.448000, rms=0.374 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55894.922 ms iter 0, gcam->neg = 13 after 50 iterations, nbhd size=3, neg = 0 0525: dt=0.286765, rms=0.374 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.002, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28749.418 ms iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0526: dt=0.286765, rms=0.374 (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=0.372, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49632.594 ms iter 0, gcam->neg = 35 after 63 iterations, nbhd size=1, neg = 0 0527: dt=0.064000, rms=0.371 (0.243%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50898.426 ms iter 0, gcam->neg = 27 after 26 iterations, nbhd size=3, neg = 0 0528: dt=0.048000, rms=0.370 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 10 iterations, nbhd size=1, neg = 0 0529: dt=0.048000, rms=0.370 (0.128%), neg=0, invalid=766 iter 0, gcam->neg = 82 after 36 iterations, nbhd size=4, neg = 0 0530: dt=0.048000, rms=0.369 (0.222%), neg=0, invalid=766 iter 0, gcam->neg = 138 after 32 iterations, nbhd size=4, neg = 0 0531: dt=0.048000, rms=0.368 (0.263%), neg=0, invalid=766 iter 0, gcam->neg = 218 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28025.447 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0532: dt=0.048000, rms=0.368 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50119.648 ms 0533: dt=0.000438, rms=0.368 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53281.723 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0534: dt=0.003000, rms=0.368 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55469.000 ms 0535: dt=0.007000, rms=0.368 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52437.164 ms 0536: dt=0.000438, rms=0.368 (0.001%), 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 58280.164 ms iter 0, gcam->neg = 53 after 29 iterations, nbhd size=3, neg = 0 0537: dt=0.096000, rms=0.367 (0.290%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49792.504 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0538: dt=0.005000, rms=0.367 (0.012%), neg=0, invalid=766 0539: dt=0.005000, rms=0.367 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0540: dt=0.005000, rms=0.367 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0541: dt=0.005000, rms=0.366 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=2, neg = 0 0542: dt=0.005000, rms=0.366 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.007, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 27760.432 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0543: dt=0.005000, rms=0.366 (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=0.366, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56960.781 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0544: dt=0.001250, rms=0.366 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58431.270 ms iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0545: dt=0.020000, rms=0.366 (0.074%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71595.156 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0546: dt=0.003000, rms=0.366 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0547: dt=0.003000, rms=0.366 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0548: dt=0.003000, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0549: dt=0.003000, rms=0.365 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0550: dt=0.003000, rms=0.365 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0551: dt=0.003000, rms=0.365 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0552: dt=0.003000, rms=0.365 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0553: dt=0.003000, rms=0.365 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0554: dt=0.003000, rms=0.365 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0555: dt=0.003000, rms=0.364 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0556: dt=0.003000, rms=0.364 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0557: dt=0.003000, rms=0.364 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0558: dt=0.003000, rms=0.364 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0559: dt=0.003000, rms=0.364 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0560: dt=0.003000, rms=0.363 (0.060%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.363, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58133.020 ms iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0561: dt=0.016000, rms=0.363 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58769.652 ms 0562: dt=0.001750, rms=0.363 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0563: dt=0.001750, rms=0.363 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0564: dt=0.001750, rms=0.363 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0565: dt=0.001750, rms=0.363 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0566: dt=0.001750, rms=0.363 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0567: dt=0.001750, rms=0.363 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0568: dt=0.001750, rms=0.363 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0569: dt=0.001750, rms=0.363 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0570: dt=0.001750, rms=0.363 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0571: dt=0.001750, rms=0.362 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0572: dt=0.001750, rms=0.362 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0573: dt=0.001750, rms=0.362 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 27 iterations, nbhd size=4, neg = 0 0574: dt=0.001750, rms=0.362 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0575: dt=0.001750, rms=0.362 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 10 iterations, nbhd size=1, neg = 0 0576: dt=0.001750, rms=0.362 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0577: dt=0.001750, rms=0.362 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 13 iterations, nbhd size=2, neg = 0 0578: dt=0.001750, rms=0.362 (0.039%), 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 49830.246 ms iter 0, gcam->neg = 13 after 15 iterations, nbhd size=2, neg = 0 0579: dt=0.019802, rms=0.361 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54793.094 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0580: dt=0.007000, rms=0.361 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 16 iterations, nbhd size=2, neg = 0 0581: dt=0.007000, rms=0.361 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0582: dt=0.007000, rms=0.361 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0583: dt=0.007000, rms=0.361 (0.059%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 7 iterations, nbhd size=1, neg = 0 0584: dt=0.007000, rms=0.360 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 30 iterations, nbhd size=3, neg = 0 0585: dt=0.007000, rms=0.360 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 16 iterations, nbhd size=2, neg = 0 0586: dt=0.007000, rms=0.360 (0.087%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 17 iterations, nbhd size=2, neg = 0 0587: dt=0.007000, rms=0.359 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 16 iterations, nbhd size=2, neg = 0 0588: dt=0.007000, rms=0.359 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 42 after 15 iterations, nbhd size=2, neg = 0 0589: dt=0.007000, rms=0.359 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 45 after 12 iterations, nbhd size=1, neg = 0 0590: dt=0.007000, rms=0.358 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 29 iterations, nbhd size=4, neg = 0 0591: dt=0.007000, rms=0.358 (0.070%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.358, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50655.379 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0592: dt=0.001750, rms=0.358 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73462.773 ms iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0593: dt=0.016000, rms=0.358 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60765.492 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0594: dt=0.001750, rms=0.358 (0.005%), neg=0, invalid=766 0595: dt=0.001750, rms=0.358 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0596: dt=0.001750, rms=0.358 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0597: dt=0.001750, rms=0.358 (0.013%), neg=0, invalid=766 0598: dt=0.001750, rms=0.358 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0599: dt=0.001750, rms=0.358 (0.020%), neg=0, invalid=766 0600: dt=0.001750, rms=0.358 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0601: dt=0.001750, rms=0.357 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0602: dt=0.001750, rms=0.357 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0603: dt=0.001750, rms=0.357 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0604: dt=0.001750, rms=0.357 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=2, neg = 0 0605: dt=0.001750, rms=0.357 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0606: dt=0.001750, rms=0.357 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0607: dt=0.001750, rms=0.357 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0608: dt=0.001750, rms=0.357 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0609: dt=0.001750, rms=0.357 (0.031%), 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 8 hours, 17 minutes and 22 seconds. #-------------------------------------- #@# CA Reg Inv Thu May 7 21:08:45 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Thu May 7 21:10:06 EDT 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/autofs/space/plato_002/users/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... 11143983 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 34 seconds. #-------------------------------------- #@# SkullLTA Thu May 7 21:11:40 EDT 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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=17.0 skull bounding box = (49, 27, 19) --> (212, 211, 234) using (103, 88, 127) as brain centroid... mean wm in atlas = 126, using box (83,65,100) --> (123, 110,153) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10338.0, old_max_log_p =-10356.5 (thresh=-10346.1) 1.077 0.010 0.035 -18.223; -0.019 1.256 0.341 -46.795; -0.018 -0.241 0.879 43.000; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10334.6, old_max_log_p =-10338.0 (thresh=-10327.6) 1.077 0.010 0.035 -18.223; -0.017 1.277 0.224 -37.131; -0.020 -0.075 0.916 21.623; 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=-10326.3, old_max_log_p =-10334.6 (thresh=-10324.3) 1.050 -0.155 -0.026 7.557; 0.129 1.340 0.237 -64.289; 0.014 -0.079 0.932 12.067; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10323.6, old_max_log_p =-10326.3 (thresh=-10316.0) 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 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 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 004: -log(p) = 10323.4 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) 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: 006: -log(p) = 10323.4 tol 0.000010 Resulting transform: 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10323.6 (old=-10356.5) transform before final EM align: 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 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 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1145759.8 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) dfp_em_step_func: 008: -log(p) = 1145748.8 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) dfp_em_step_func: 009: -log(p) = 1145747.9 after pass:transform: ( 1.06, -0.13, -0.00, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.01, -0.06, 0.93, 12.15) 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) = 1145745.4 after pass:transform: ( 1.06, -0.13, -0.00, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.01, -0.06, 0.93, 12.15) 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... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 1145745.4 tol 0.000000 final transform: 1.056 -0.130 -0.004 2.994; 0.110 1.342 0.221 -59.591; -0.008 -0.060 0.930 12.154; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 20 minutes and 26 seconds. #-------------------------------------- #@# SubCort Seg Thu May 7 21:32:07 EDT 2015 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 = 0.12744 (21) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (9907 voxels, overlap=0.289) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (9907 voxels, peak = 20), gca=20.2 gca peak = 0.14982 (20) mri peak = 0.12685 (22) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (8880 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (8880 voxels, peak = 18), gca=18.0 gca peak = 0.28003 (97) mri peak = 0.12997 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.12261 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (410 voxels, overlap=0.820) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (410 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.09091 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (986 voxels, overlap=0.240) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (986 voxels, peak = 71), gca=71.3 gca peak = 0.32745 (63) mri peak = 0.07676 (72) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (947 voxels, overlap=0.634) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (947 voxels, peak = 68), gca=67.7 gca peak = 0.08597 (105) mri peak = 0.09584 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, peak = 105), gca=105.0 gca peak = 0.09209 (106) mri peak = 0.08532 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (25445 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (25445 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.03871 (73) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (30832 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (30832 voxels, peak = 72), gca=72.4 gca peak = 0.08598 (64) mri peak = 0.03788 (75) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (34464 voxels, overlap=0.330) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (34464 voxels, peak = 77), gca=76.8 gca peak = 0.24164 (71) mri peak = 0.12527 (86) Right_Caudate (50): linear fit = 1.17 x + 0.0 (718 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.17 x + 0.0 (718 voxels, peak = 83), gca=83.4 gca peak = 0.18227 (75) mri peak = 0.13480 (83) Left_Caudate (11): linear fit = 1.08 x + 0.0 (638 voxels, overlap=0.516) Left_Caudate (11): linear fit = 1.08 x + 0.0 (638 voxels, peak = 81), gca=80.6 gca peak = 0.10629 (62) mri peak = 0.06011 (68) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (22772 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (22772 voxels, peak = 71), gca=71.3 gca peak = 0.11668 (59) mri peak = 0.05980 (68) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25748 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25748 voxels, peak = 66), gca=66.4 gca peak = 0.17849 (88) mri peak = 0.14498 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5310 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5310 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.14210 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5270 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5270 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.10247 (77) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (281 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (281 voxels, peak = 74), gca=73.6 gca peak = 0.42394 (62) mri peak = 0.09695 (79) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (277 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (277 voxels, peak = 74), gca=74.4 gca peak = 0.10041 (96) mri peak = 0.06372 (99) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3330 voxels, overlap=0.861) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3330 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.07220 (96) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3412 voxels, overlap=0.654) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3412 voxels, peak = 95), gca=94.6 gca peak = 0.08514 (81) mri peak = 0.07251 (93) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2035 voxels, overlap=0.545) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2035 voxels, peak = 89), gca=89.1 gca peak = 0.09624 (82) mri peak = 0.08383 (90) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1503 voxels, overlap=0.585) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1503 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.08155 (93) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12416 voxels, overlap=0.733) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12416 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.11040 (103) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1017 voxels, overlap=0.184) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1017 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09052 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1131 voxels, overlap=0.410) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1131 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.15452 (26) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (341 voxels, overlap=0.038) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (341 voxels, peak = 23), gca=23.4 gca peak = 0.26069 (23) mri peak = 0.11477 (23) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (529 voxels, overlap=0.696) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (529 voxels, peak = 22), gca=21.9 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 1.15 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.87 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16292 (21) mri peak = 0.12744 (21) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (9907 voxels, overlap=0.915) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (9907 voxels, peak = 21), gca=21.0 gca peak = 0.15073 (19) mri peak = 0.12685 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (8880 voxels, overlap=0.808) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (8880 voxels, peak = 19), gca=19.5 gca peak = 0.25294 (100) mri peak = 0.12997 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, peak = 102), gca=102.5 gca peak = 0.18507 (101) mri peak = 0.12261 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (410 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (410 voxels, peak = 101), gca=101.0 gca peak = 0.24928 (71) mri peak = 0.09091 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (986 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (986 voxels, peak = 71), gca=71.0 gca peak = 0.31225 (68) mri peak = 0.07676 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (947 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (947 voxels, peak = 68), gca=68.0 gca peak = 0.08621 (105) mri peak = 0.09584 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, peak = 105), gca=105.0 gca peak = 0.08536 (108) mri peak = 0.08532 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (25445 voxels, overlap=0.763) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (25445 voxels, peak = 108), gca=108.0 gca peak = 0.06954 (72) mri peak = 0.03871 (73) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (30832 voxels, overlap=0.877) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (30832 voxels, peak = 72), gca=72.0 gca peak = 0.07345 (76) mri peak = 0.03788 (75) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34464 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34464 voxels, peak = 76), gca=76.0 gca peak = 0.21504 (83) mri peak = 0.12527 (86) Right_Caudate (50): linear fit = 1.00 x + 0.0 (718 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (718 voxels, peak = 83), gca=83.0 gca peak = 0.16044 (80) mri peak = 0.13480 (83) Left_Caudate (11): linear fit = 1.00 x + 0.0 (638 voxels, overlap=0.866) Left_Caudate (11): linear fit = 1.00 x + 0.0 (638 voxels, peak = 80), gca=80.0 gca peak = 0.09118 (70) mri peak = 0.06011 (68) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22772 voxels, overlap=0.969) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22772 voxels, peak = 68), gca=68.2 gca peak = 0.11770 (67) mri peak = 0.05980 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25748 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25748 voxels, peak = 67), gca=67.0 gca peak = 0.16848 (92) mri peak = 0.14498 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5310 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5310 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.14210 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5270 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5270 voxels, peak = 91), gca=91.0 gca peak = 0.32099 (73) mri peak = 0.10247 (77) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (281 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (281 voxels, peak = 75), gca=74.8 gca peak = 0.34937 (75) mri peak = 0.09695 (79) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (277 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (277 voxels, peak = 77), gca=76.9 gca peak = 0.10167 (99) mri peak = 0.06372 (99) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, overlap=0.968) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, peak = 99), gca=99.0 gca peak = 0.09750 (94) mri peak = 0.07220 (96) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3412 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3412 voxels, peak = 94), gca=94.0 gca peak = 0.08039 (91) mri peak = 0.07251 (93) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2035 voxels, overlap=0.903) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2035 voxels, peak = 91), gca=91.0 gca peak = 0.09054 (83) mri peak = 0.08383 (90) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1503 voxels, overlap=0.888) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1503 voxels, peak = 83), gca=83.0 gca peak = 0.07244 (90) mri peak = 0.08155 (93) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12416 voxels, overlap=0.833) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12416 voxels, peak = 90), gca=90.0 gca peak = 0.12058 (104) mri peak = 0.11040 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1017 voxels, overlap=0.778) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1017 voxels, peak = 104), gca=104.0 gca peak = 0.15598 (99) mri peak = 0.09052 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1131 voxels, overlap=0.873) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1131 voxels, peak = 99), gca=99.0 gca peak = 0.21185 (31) mri peak = 0.15452 (26) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (341 voxels, overlap=0.380) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (341 voxels, peak = 23), gca=23.2 gca peak = 0.20373 (22) mri peak = 0.11477 (23) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (529 voxels, overlap=0.776) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (529 voxels, peak = 21), gca=21.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26811 (38) gca peak CSF = 0.18566 (33) gca peak Left_Accumbens_area = 0.57937 (75) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.25693 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (37) gca peak WM_hypointensities = 0.15176 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34486 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 Right_Pallidum too bright - rescaling by 1.008 (from 1.025) to 103.3 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 26382 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 362 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 80783 changed. image ll: -2.243, PF=1.000 pass 2: 11402 changed. image ll: -2.241, PF=1.000 pass 3: 3810 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 25 minutes and 34 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/cc_up.lta R01L019_MD_12m will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/norm.mgz 7726 voxels in left wm, 18659 in right wm, xrange [126, 132] searching rotation angles z=[-9 5], y=[-5 9] searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 global minimum found at slice 130.0, rotations (1.85, -1.36) final transformation (x=130.0, yr=1.848, zr=-1.364): 0.999 0.024 0.032 -7.564; -0.024 1.000 -0.001 27.199; -0.032 0.000 0.999 33.245; 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 128 132 125 eigenvectors: 0.000 -0.002 1.000; -0.094 -0.996 -0.002; 0.996 -0.094 -0.000; writing aseg with callosum to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Thu May 7 21:58:27 EDT 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu May 7 21:58:27 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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... 1612 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 4 minutes and 7 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 108 gm peak at 76 (76), valley at 57 (57) csf peak at 21, setting threshold to 57 white matter peak found at 111 white matter peak found at 109 gm peak at 77 (77), valley at 44 (44) csf peak at 21, setting threshold to 58 #-------------------------------------------- #@# Mask BFS Thu May 7 22:02:41 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1647048 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu May 7 22:02:46 EDT 2015 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.5 +- 5.7 [80.0 --> 125.0] GM (73.0) : 69.9 +- 11.8 [30.0 --> 96.0] setting bottom of white matter range to 81.7 setting top of gray matter range to 93.5 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... 5164 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4482 filled 2957 bright non-wm voxels segmented. 3418 diagonally connected voxels added... white matter segmentation took 2.0 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.70 minutes reading wm segmentation from wm.seg.mgz... 116 voxels added to wm to prevent paths from MTL structures to cortex 3099 additional wm voxels added 0 additional wm voxels added SEG EDIT: 88266 voxels turned on, 51981 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 13 found - 13 modified | TOTAL: 31 pass 2 (xy-): 0 found - 13 modified | TOTAL: 31 pass 1 (yz+): 12 found - 12 modified | TOTAL: 43 pass 2 (yz+): 0 found - 12 modified | TOTAL: 43 pass 1 (yz-): 15 found - 15 modified | TOTAL: 58 pass 2 (yz-): 0 found - 15 modified | TOTAL: 58 pass 1 (xz+): 18 found - 18 modified | TOTAL: 76 pass 2 (xz+): 0 found - 18 modified | TOTAL: 76 pass 1 (xz-): 23 found - 23 modified | TOTAL: 99 pass 2 (xz-): 0 found - 23 modified | TOTAL: 99 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 10 found - 10 modified | TOTAL: 22 pass 2 (+++): 0 found - 10 modified | TOTAL: 22 pass 1 (+++): 4 found - 4 modified | TOTAL: 26 pass 2 (+++): 0 found - 4 modified | TOTAL: 26 Iteration Number : 1 pass 1 (++): 58 found - 58 modified | TOTAL: 58 pass 2 (++): 0 found - 58 modified | TOTAL: 58 pass 1 (+-): 77 found - 77 modified | TOTAL: 135 pass 2 (+-): 0 found - 77 modified | TOTAL: 135 pass 1 (--): 78 found - 78 modified | TOTAL: 213 pass 2 (--): 1 found - 79 modified | TOTAL: 214 pass 3 (--): 0 found - 79 modified | TOTAL: 214 pass 1 (-+): 74 found - 74 modified | TOTAL: 288 pass 2 (-+): 0 found - 74 modified | TOTAL: 288 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 4 found - 4 modified | TOTAL: 11 pass 2 (xz+): 0 found - 4 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 4 found - 4 modified | TOTAL: 5 pass 2 (+-): 0 found - 4 modified | TOTAL: 5 pass 1 (--): 1 found - 1 modified | TOTAL: 6 pass 2 (--): 0 found - 1 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 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 = 435 (out of 532129: 0.081747) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu May 7 22:05:34 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1144 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 118, 155), TAL = (2.0, 27.0, 10.0) talairach voxel to voxel transform 0.997 -0.014 -0.029 8.418; 0.009 0.796 -0.266 41.493; 0.023 0.218 0.979 -19.794; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 118, 155) --> (2.0, 27.0, 10.0) done. writing output to filled.mgz... filling took 1.3 minutes talairach cc position changed to (2.00, 27.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 10.00) SRC: (109.95, 95.12, 160.15) search lh wm seed point around talairach space (-16.00, 27.00, 10.00), SRC: (145.85, 95.44, 160.97) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu May 7 22:06:50 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 2 found - 2 modified | TOTAL: 2 pass 2 (yz-): 0 found - 2 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 252263: 0.001586) 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 40: 348 vertices, 419 faces slice 50: 5821 vertices, 6092 faces slice 60: 14572 vertices, 14949 faces slice 70: 25713 vertices, 26063 faces slice 80: 36483 vertices, 36877 faces slice 90: 46541 vertices, 46922 faces slice 100: 57575 vertices, 57972 faces slice 110: 69154 vertices, 69565 faces slice 120: 79819 vertices, 80224 faces slice 130: 90149 vertices, 90529 faces slice 140: 99669 vertices, 100052 faces slice 150: 108587 vertices, 108946 faces slice 160: 115924 vertices, 116213 faces slice 170: 122652 vertices, 122944 faces slice 180: 128635 vertices, 128877 faces slice 190: 133000 vertices, 133183 faces slice 200: 135668 vertices, 135755 faces slice 210: 135874 vertices, 135922 faces slice 220: 135874 vertices, 135922 faces slice 230: 135874 vertices, 135922 faces slice 240: 135874 vertices, 135922 faces slice 250: 135874 vertices, 135922 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... 135874 voxel in cpt #1: X=-48 [v=135874,e=407766,f=271844] located at (-30.328466, -17.472305, 25.969604) For the whole surface: X=-48 [v=135874,e=407766,f=271844] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu May 7 22:07:07 EDT 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu May 7 22:07:13 EDT 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts avg radius = 47.8 mm, total surface area = 71982 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.042 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.034 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu May 7 22:08:09 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 0.98 +- 0.59 (0.00-->6.69) (max @ vno 78117 --> 79307) face area 0.03 +- 0.03 (-0.07-->0.55) scaling brain by 0.310... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.682, avgs=0 005/300: dt: 0.9000, rms radial error=176.422, avgs=0 010/300: dt: 0.9000, rms radial error=175.864, avgs=0 015/300: dt: 0.9000, rms radial error=175.129, avgs=0 020/300: dt: 0.9000, rms radial error=174.292, avgs=0 025/300: dt: 0.9000, rms radial error=173.396, avgs=0 030/300: dt: 0.9000, rms radial error=172.466, avgs=0 035/300: dt: 0.9000, rms radial error=171.527, avgs=0 040/300: dt: 0.9000, rms radial error=170.581, avgs=0 045/300: dt: 0.9000, rms radial error=169.641, avgs=0 050/300: dt: 0.9000, rms radial error=168.703, avgs=0 055/300: dt: 0.9000, rms radial error=167.766, avgs=0 060/300: dt: 0.9000, rms radial error=166.834, avgs=0 065/300: dt: 0.9000, rms radial error=165.905, avgs=0 070/300: dt: 0.9000, rms radial error=164.981, avgs=0 075/300: dt: 0.9000, rms radial error=164.061, avgs=0 080/300: dt: 0.9000, rms radial error=163.146, avgs=0 085/300: dt: 0.9000, rms radial error=162.236, avgs=0 090/300: dt: 0.9000, rms radial error=161.330, avgs=0 095/300: dt: 0.9000, rms radial error=160.430, avgs=0 100/300: dt: 0.9000, rms radial error=159.534, avgs=0 105/300: dt: 0.9000, rms radial error=158.643, avgs=0 110/300: dt: 0.9000, rms radial error=157.757, avgs=0 115/300: dt: 0.9000, rms radial error=156.875, avgs=0 120/300: dt: 0.9000, rms radial error=155.998, avgs=0 125/300: dt: 0.9000, rms radial error=155.126, avgs=0 130/300: dt: 0.9000, rms radial error=154.258, avgs=0 135/300: dt: 0.9000, rms radial error=153.396, avgs=0 140/300: dt: 0.9000, rms radial error=152.538, avgs=0 145/300: dt: 0.9000, rms radial error=151.684, avgs=0 150/300: dt: 0.9000, rms radial error=150.835, avgs=0 155/300: dt: 0.9000, rms radial error=149.990, avgs=0 160/300: dt: 0.9000, rms radial error=149.150, avgs=0 165/300: dt: 0.9000, rms radial error=148.315, avgs=0 170/300: dt: 0.9000, rms radial error=147.483, avgs=0 175/300: dt: 0.9000, rms radial error=146.657, avgs=0 180/300: dt: 0.9000, rms radial error=145.834, avgs=0 185/300: dt: 0.9000, rms radial error=145.016, avgs=0 190/300: dt: 0.9000, rms radial error=144.202, avgs=0 195/300: dt: 0.9000, rms radial error=143.393, avgs=0 200/300: dt: 0.9000, rms radial error=142.588, avgs=0 205/300: dt: 0.9000, rms radial error=141.788, avgs=0 210/300: dt: 0.9000, rms radial error=140.992, avgs=0 215/300: dt: 0.9000, rms radial error=140.200, avgs=0 220/300: dt: 0.9000, rms radial error=139.412, avgs=0 225/300: dt: 0.9000, rms radial error=138.628, avgs=0 230/300: dt: 0.9000, rms radial error=137.849, avgs=0 235/300: dt: 0.9000, rms radial error=137.074, avgs=0 240/300: dt: 0.9000, rms radial error=136.303, avgs=0 245/300: dt: 0.9000, rms radial error=135.537, avgs=0 250/300: dt: 0.9000, rms radial error=134.775, avgs=0 255/300: dt: 0.9000, rms radial error=134.016, avgs=0 260/300: dt: 0.9000, rms radial error=133.262, avgs=0 265/300: dt: 0.9000, rms radial error=132.513, avgs=0 270/300: dt: 0.9000, rms radial error=131.767, avgs=0 275/300: dt: 0.9000, rms radial error=131.025, avgs=0 280/300: dt: 0.9000, rms radial error=130.288, avgs=0 285/300: dt: 0.9000, rms radial error=129.554, avgs=0 290/300: dt: 0.9000, rms radial error=128.825, avgs=0 295/300: dt: 0.9000, rms radial error=128.099, avgs=0 300/300: dt: 0.9000, rms radial error=127.378, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15920.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2696.67 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 3 (K=160.0), pass 1, starting sse = 296.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00902 epoch 4 (K=640.0), pass 1, starting sse = 19.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/14 = 0.01069 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.14 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu May 7 22:16:20 EDT 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 R01L019_MD_12m 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=-48 (nv=135874, nf=271844, ne=407766, g=25) 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... 4017 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 34 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3770 (-4.6885) -vertex loglikelihood: -6.2361 (-3.1180) -normal dot loglikelihood: -3.5754 (-3.5754) -quad curv loglikelihood: -6.4282 (-3.2141) Total Loglikelihood : -25.6167 CORRECTING DEFECT 0 (vertices=36, convex hull=62) After retessellation of defect 0, euler #=-31 (133500,399664,266133) : difference with theory (-31) = 0 CORRECTING DEFECT 1 (vertices=36, convex hull=73) After retessellation of defect 1, euler #=-30 (133519,399749,266200) : difference with theory (-30) = 0 CORRECTING DEFECT 2 (vertices=20, convex hull=57) After retessellation of defect 2, euler #=-29 (133529,399802,266244) : difference with theory (-29) = 0 CORRECTING DEFECT 3 (vertices=108, convex hull=110) After retessellation of defect 3, euler #=-28 (133570,399975,266377) : difference with theory (-28) = 0 CORRECTING DEFECT 4 (vertices=44, convex hull=75) After retessellation of defect 4, euler #=-27 (133586,400055,266442) : difference with theory (-27) = 0 CORRECTING DEFECT 5 (vertices=10, convex hull=29) After retessellation of defect 5, euler #=-26 (133589,400073,266458) : difference with theory (-26) = 0 CORRECTING DEFECT 6 (vertices=22, convex hull=65) After retessellation of defect 6, euler #=-25 (133602,400137,266510) : difference with theory (-25) = 0 CORRECTING DEFECT 7 (vertices=31, convex hull=66) After retessellation of defect 7, euler #=-24 (133612,400192,266556) : difference with theory (-24) = 0 CORRECTING DEFECT 8 (vertices=47, convex hull=34) After retessellation of defect 8, euler #=-23 (133615,400209,266571) : difference with theory (-23) = 0 CORRECTING DEFECT 9 (vertices=57, convex hull=24) After retessellation of defect 9, euler #=-22 (133620,400236,266594) : difference with theory (-22) = 0 CORRECTING DEFECT 10 (vertices=33, convex hull=67) After retessellation of defect 10, euler #=-21 (133632,400299,266646) : difference with theory (-21) = 0 CORRECTING DEFECT 11 (vertices=34, convex hull=76) After retessellation of defect 11, euler #=-20 (133654,400398,266724) : difference with theory (-20) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=66) After retessellation of defect 12, euler #=-19 (133670,400470,266781) : difference with theory (-19) = 0 CORRECTING DEFECT 13 (vertices=9, convex hull=12) After retessellation of defect 13, euler #=-18 (133671,400476,266787) : difference with theory (-18) = 0 CORRECTING DEFECT 14 (vertices=91, convex hull=102) After retessellation of defect 14, euler #=-17 (133714,400652,266921) : difference with theory (-17) = 0 CORRECTING DEFECT 15 (vertices=19, convex hull=41) After retessellation of defect 15, euler #=-16 (133722,400690,266952) : difference with theory (-16) = 0 CORRECTING DEFECT 16 (vertices=32, convex hull=28) After retessellation of defect 16, euler #=-15 (133727,400717,266975) : difference with theory (-15) = 0 CORRECTING DEFECT 17 (vertices=16, convex hull=20) After retessellation of defect 17, euler #=-14 (133729,400728,266985) : difference with theory (-14) = 0 CORRECTING DEFECT 18 (vertices=684, convex hull=176) After retessellation of defect 18, euler #=-13 (133738,400844,267093) : difference with theory (-13) = 0 CORRECTING DEFECT 19 (vertices=34, convex hull=26) After retessellation of defect 19, euler #=-12 (133742,400862,267108) : difference with theory (-12) = 0 CORRECTING DEFECT 20 (vertices=7, convex hull=23) After retessellation of defect 20, euler #=-11 (133743,400873,267119) : difference with theory (-11) = 0 CORRECTING DEFECT 21 (vertices=6, convex hull=20) After retessellation of defect 21, euler #=-10 (133745,400885,267130) : difference with theory (-10) = 0 CORRECTING DEFECT 22 (vertices=43, convex hull=46) After retessellation of defect 22, euler #=-9 (133754,400936,267173) : difference with theory (-9) = 0 CORRECTING DEFECT 23 (vertices=30, convex hull=32) After retessellation of defect 23, euler #=-8 (133761,400969,267200) : difference with theory (-8) = 0 CORRECTING DEFECT 24 (vertices=24, convex hull=53) After retessellation of defect 24, euler #=-7 (133776,401036,267253) : difference with theory (-7) = 0 CORRECTING DEFECT 25 (vertices=294, convex hull=43) After retessellation of defect 25, euler #=-6 (133785,401081,267290) : difference with theory (-6) = 0 CORRECTING DEFECT 26 (vertices=199, convex hull=172) After retessellation of defect 26, euler #=-5 (133817,401255,267433) : difference with theory (-5) = 0 CORRECTING DEFECT 27 (vertices=28, convex hull=65) After retessellation of defect 27, euler #=-4 (133834,401331,267493) : difference with theory (-4) = 0 CORRECTING DEFECT 28 (vertices=95, convex hull=50) After retessellation of defect 28, euler #=-3 (133848,401392,267541) : difference with theory (-3) = 0 CORRECTING DEFECT 29 (vertices=40, convex hull=38) After retessellation of defect 29, euler #=-2 (133857,401434,267575) : difference with theory (-2) = 0 CORRECTING DEFECT 30 (vertices=38, convex hull=46) After retessellation of defect 30, euler #=-1 (133863,401467,267603) : difference with theory (-1) = 0 CORRECTING DEFECT 31 (vertices=95, convex hull=111) After retessellation of defect 31, euler #=0 (133895,401617,267722) : difference with theory (0) = 0 CORRECTING DEFECT 32 (vertices=59, convex hull=76) After retessellation of defect 32, euler #=1 (133908,401686,267779) : difference with theory (1) = 0 CORRECTING DEFECT 33 (vertices=43, convex hull=79) After retessellation of defect 33, euler #=2 (133920,401754,267836) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->6.30) (max @ vno 121757 --> 124521) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->6.30) (max @ vno 121757 --> 124521) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 131 mutations (37.3%), 220 crossovers (62.7%), 241 vertices were eliminated building final representation... 1954 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133920, nf=267836, ne=401754, g=0) writing corrected surface to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.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: 164 intersecting 001: 4 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133920 - 401754 + 267836 = 2 --> 0 holes F =2V-4: 267836 = 267840-4 (0) 2E=3F: 803508 = 803508 (0) total defect index = 0 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting 001: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu May 7 22:50:22 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 9996 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.orig... computing class statistics... border white: 263133 voxels (1.57%) border gray 285814 voxels (1.70%) WM (93.0): 94.5 +- 7.5 [70.0 --> 110.0] GM (83.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.2 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.81) (max @ vno 121757 --> 124521) face area 0.28 +- 0.12 (0.00-->1.91) mean absolute distance = 0.89 +- 1.09 3978 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=72 using class modes intead of means.... mean inside = 93.3, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.3, 394 (394) missing vertices, mean dist 0.3 [0.9 (%33.4)->0.9 (%66.6))] %31 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.06-->3.75) (max @ vno 100672 --> 99830) face area 0.28 +- 0.13 (0.00-->2.07) mean absolute distance = 0.45 +- 0.84 4393 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4860794.5, rms=9.84 001: dt: 0.5000, sse=5454707.0, rms=7.01 002: dt: 0.5000, sse=5751984.0, rms=5.25 003: dt: 0.5000, sse=6074107.5, rms=4.18 004: dt: 0.5000, sse=6275254.5, rms=3.55 005: dt: 0.5000, sse=6434900.5, rms=3.20 006: dt: 0.5000, sse=6516387.5, rms=3.01 007: dt: 0.5000, sse=6584589.5, rms=2.92 008: dt: 0.5000, sse=6605145.0, rms=2.86 rms = 2.83, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6630874.5, rms=2.83 010: dt: 0.2500, sse=4068937.5, rms=1.94 011: dt: 0.2500, sse=3782270.2, rms=1.75 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3662489.8, rms=1.71 rms = 1.68, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3599748.2, rms=1.68 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... mean border=83.6, 297 (182) missing vertices, mean dist -0.3 [0.6 (%63.7)->0.3 (%36.3))] %43 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.09-->3.87) (max @ vno 53481 --> 54544) face area 0.35 +- 0.16 (0.00-->2.55) mean absolute distance = 0.36 +- 0.51 3649 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4067286.0, rms=4.02 014: dt: 0.5000, sse=4425814.0, rms=2.65 015: dt: 0.5000, sse=5035989.0, rms=2.43 016: dt: 0.5000, sse=5270408.5, rms=2.30 rms = 2.51, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4327496.0, rms=1.75 018: dt: 0.2500, sse=4016774.8, rms=1.51 019: dt: 0.2500, sse=3896499.0, rms=1.45 rms = 1.44, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3851171.2, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3807579.0, rms=1.42 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.2, 250 (142) missing vertices, mean dist -0.2 [0.4 (%69.1)->0.2 (%30.9))] %64 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 53481 --> 54544) face area 0.34 +- 0.16 (0.00-->2.56) mean absolute distance = 0.27 +- 0.39 2786 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4091090.8, rms=3.71 022: dt: 0.5000, sse=4367550.5, rms=2.14 rms = 2.18, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4152905.5, rms=1.69 024: dt: 0.2500, sse=4078198.0, rms=1.38 025: dt: 0.2500, sse=4022475.2, rms=1.31 rms = 1.30, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3999576.0, rms=1.30 rms = 1.28, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3968094.5, rms=1.28 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.5, 244 (129) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.2 (%40.1))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4008492.5, rms=1.96 028: dt: 0.5000, sse=4993594.0, rms=1.56 rms = 1.94, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4571938.5, rms=1.16 030: dt: 0.2500, sse=4375760.0, rms=1.07 rms = 1.04, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4431807.5, rms=1.04 rms = 1.03, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4427412.5, rms=1.03 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 7 non-cortical segments detected only using segment with 1823 vertices erasing segment 1 (vno[0] = 79967) erasing segment 2 (vno[0] = 97202) erasing segment 3 (vno[0] = 101440) erasing segment 4 (vno[0] = 106337) erasing segment 5 (vno[0] = 107121) erasing segment 6 (vno[0] = 107151) writing cortex label to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.cortex.label writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->3.94) (max @ vno 53481 --> 54544) face area 0.34 +- 0.16 (0.00-->2.64) refinement took 6.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu May 7 22:57:07 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu May 7 22:57:13 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.0 mm, total surface area = 81475 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 1.1 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 302 vertices thresholded to be in k1 ~ [-0.25 0.37], k2 ~ [-0.11 0.08] total integrated curvature = 0.517*4pi (6.494) --> 0 handles ICI = 1.5, FI = 10.6, variation=175.741 157 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 164 vertices thresholded to be in [-0.14 0.18] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu May 7 23:00:00 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm R01L019_MD_12m 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 [ R01L019_MD_12m/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 [ 241 ] Gb_filter = 0 WARN: S lookup min: -0.477153 WARN: S explicit min: 0.000000 vertex = 970 #-------------------------------------------- #@# Sphere lh Thu May 7 23:00:06 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.28 hours scaling brain by 0.290... pass 1: epoch 1 of 3 starting distance error %18.87 pass 1: epoch 2 of 3 starting distance error %18.83 unfolding complete - removing small folds... starting distance error %18.80 removing remaining folds... final distance error %18.82 #-------------------------------------------- #@# Surf Reg lh Fri May 8 00:17:11 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.609 curvature mean = 0.028, std = 0.939 curvature mean = 0.022, std = 0.872 curvature mean = 0.016, std = 0.966 curvature mean = 0.010, std = 0.946 curvature mean = 0.015, std = 0.979 curvature mean = 0.004, std = 0.975 curvature mean = 0.014, std = 0.982 curvature mean = 0.001, std = 0.989 curvature mean = -0.027, std = 0.349 curvature mean = 0.003, std = 0.068 curvature mean = 0.050, std = 0.288 curvature mean = 0.003, std = 0.080 curvature mean = 0.020, std = 0.448 curvature mean = 0.003, std = 0.086 curvature mean = 0.011, std = 0.561 curvature mean = 0.004, std = 0.089 curvature mean = 0.002, std = 0.650 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri May 8 01:03:40 EDT 2015 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 May 8 01:03:44 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri May 8 01:03:47 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 1309 labels changed using aseg relabeling using gibbs priors... 000: 2835 changed, 133920 examined... 001: 629 changed, 12304 examined... 002: 161 changed, 3602 examined... 003: 46 changed, 958 examined... 004: 15 changed, 264 examined... 005: 7 changed, 101 examined... 006: 4 changed, 51 examined... 007: 4 changed, 23 examined... 008: 2 changed, 22 examined... 009: 2 changed, 11 examined... 010: 2 changed, 10 examined... 011: 1 changed, 17 examined... 012: 0 changed, 6 examined... 220 labels changed using aseg 000: 113 total segments, 71 labels (203 vertices) changed 001: 43 total segments, 1 labels (1 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1612 vertices marked for relabeling... 1612 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri May 8 01:04:58 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 9996 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.orig... computing class statistics... border white: 263133 voxels (1.57%) border gray 285814 voxels (1.70%) WM (93.0): 94.5 +- 7.5 [70.0 --> 110.0] GM (83.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.2 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=72 using class modes intead of means.... mean inside = 93.3, mean outside = 77.1 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->2.81) (max @ vno 121757 --> 124521) face area 0.28 +- 0.12 (0.00-->1.91) mean absolute distance = 0.89 +- 1.11 4125 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 635 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown mean border=81.3, 394 (394) missing vertices, mean dist 0.3 [0.9 (%33.4)->0.9 (%66.6))] %31 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.06-->3.75) (max @ vno 100672 --> 99830) face area 0.28 +- 0.13 (0.00-->2.07) mean absolute distance = 0.45 +- 0.85 4476 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4874588.5, rms=9.83 001: dt: 0.5000, sse=5473083.5, rms=7.00 002: dt: 0.5000, sse=5771055.5, rms=5.24 003: dt: 0.5000, sse=6095718.0, rms=4.18 004: dt: 0.5000, sse=6297909.5, rms=3.54 005: dt: 0.5000, sse=6457905.0, rms=3.19 006: dt: 0.5000, sse=6539625.5, rms=3.01 007: dt: 0.5000, sse=6609874.0, rms=2.91 008: dt: 0.5000, sse=6631123.5, rms=2.86 rms = 2.83, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6657133.5, rms=2.83 010: dt: 0.2500, sse=4085309.8, rms=1.94 011: dt: 0.2500, sse=3796931.5, rms=1.75 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3678252.2, rms=1.71 rms = 1.68, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3614670.2, rms=1.68 positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 360 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown deleting segment 4 with 70 points - only 28.57% unknown deleting segment 5 with 5 points - only 0.00% unknown mean border=83.6, 304 (182) missing vertices, mean dist -0.3 [0.6 (%63.7)->0.3 (%36.3))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.09-->3.88) (max @ vno 100672 --> 99830) face area 0.35 +- 0.16 (0.00-->2.55) mean absolute distance = 0.36 +- 0.51 3708 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4089949.0, rms=4.02 014: dt: 0.5000, sse=4453195.0, rms=2.66 015: dt: 0.5000, sse=5067204.0, rms=2.43 016: dt: 0.5000, sse=5303320.0, rms=2.30 rms = 2.51, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4354031.0, rms=1.75 018: dt: 0.2500, sse=4041992.2, rms=1.51 019: dt: 0.2500, sse=3920005.2, rms=1.45 rms = 1.44, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3874152.8, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3831249.0, rms=1.42 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 543 points - only 0.00% unknown deleting segment 4 with 70 points - only 28.57% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=86.2, 256 (141) missing vertices, mean dist -0.2 [0.4 (%69.0)->0.2 (%31.0))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 53481 --> 54544) face area 0.34 +- 0.16 (0.00-->2.45) mean absolute distance = 0.27 +- 0.39 2855 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4115526.0, rms=3.71 022: dt: 0.5000, sse=4394393.5, rms=2.13 rms = 2.18, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4178724.0, rms=1.69 024: dt: 0.2500, sse=4106913.2, rms=1.38 025: dt: 0.2500, sse=4049645.5, rms=1.31 rms = 1.30, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4026307.5, rms=1.30 rms = 1.29, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3994311.8, rms=1.29 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 595 points - only 0.00% unknown deleting segment 2 with 70 points - only 28.57% unknown deleting segment 3 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=87.5, 257 (128) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.2 (%40.1))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4034813.8, rms=1.96 028: dt: 0.5000, sse=5027091.5, rms=1.56 rms = 1.93, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4603559.0, rms=1.16 030: dt: 0.2500, sse=4407188.5, rms=1.07 rms = 1.04, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4465087.0, rms=1.04 rms = 1.03, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4459584.5, rms=1.03 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 284 (284) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.2 (%100.0))] %43 local maxima, %43 large gradients and % 9 min vals, 475 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21977076.0, rms=27.55 001: dt: 0.5000, sse=17343194.0, rms=24.05 002: dt: 0.5000, sse=13766925.0, rms=20.96 003: dt: 0.5000, sse=11353767.0, rms=18.38 004: dt: 0.5000, sse=9930012.0, rms=16.17 005: dt: 0.5000, sse=8878990.0, rms=14.25 006: dt: 0.5000, sse=8092687.5, rms=12.56 007: dt: 0.5000, sse=7483448.5, rms=11.02 008: dt: 0.5000, sse=7078872.5, rms=9.59 009: dt: 0.5000, sse=6794013.0, rms=8.28 010: dt: 0.5000, sse=6653829.0, rms=7.14 011: dt: 0.5000, sse=6545143.5, rms=6.21 012: dt: 0.5000, sse=6600215.5, rms=5.55 013: dt: 0.5000, sse=6617156.0, rms=5.08 014: dt: 0.5000, sse=6713612.0, rms=4.78 015: dt: 0.5000, sse=6702366.5, rms=4.55 016: dt: 0.5000, sse=6745808.5, rms=4.41 017: dt: 0.5000, sse=6756191.5, rms=4.29 018: dt: 0.5000, sse=6735244.5, rms=4.22 019: dt: 0.5000, sse=6754499.5, rms=4.15 rms = 4.12, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6777590.5, rms=4.12 021: dt: 0.2500, sse=4283047.5, rms=3.02 022: dt: 0.2500, sse=3971046.2, rms=2.71 023: dt: 0.2500, sse=3807428.5, rms=2.64 rms = 2.60, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3770194.2, rms=2.60 025: dt: 0.1250, sse=3622595.8, rms=2.49 rms = 2.47, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3595186.8, rms=2.47 positioning took 3.0 minutes mean border=56.2, 314 (24) missing vertices, mean dist 0.2 [0.2 (%35.2)->0.5 (%64.8))] %62 local maxima, %28 large gradients and % 6 min vals, 190 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4658059.5, rms=6.23 027: dt: 0.5000, sse=4702376.5, rms=4.37 028: dt: 0.5000, sse=5825497.0, rms=4.27 rms = 4.34, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4729452.0, rms=3.31 030: dt: 0.2500, sse=4346066.5, rms=2.88 031: dt: 0.2500, sse=4277346.0, rms=2.73 032: dt: 0.2500, sse=4226947.5, rms=2.67 rms = 2.63, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4226379.0, rms=2.63 034: dt: 0.1250, sse=4092287.5, rms=2.49 rms = 2.47, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4072919.0, rms=2.47 positioning took 1.1 minutes mean border=53.9, 490 (15) missing vertices, mean dist 0.1 [0.2 (%35.1)->0.3 (%64.9))] %72 local maxima, %18 large gradients and % 5 min vals, 223 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4305745.0, rms=3.77 rms = 3.98, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4127555.8, rms=3.01 037: dt: 0.2500, sse=4133533.0, rms=2.59 038: dt: 0.2500, sse=4227870.0, rms=2.45 rms = 2.41, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4262360.0, rms=2.41 040: dt: 0.1250, sse=4140711.0, rms=2.30 rms = 2.28, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4127218.5, rms=2.28 positioning took 0.8 minutes mean border=52.8, 848 (12) missing vertices, mean dist 0.1 [0.2 (%42.8)->0.3 (%57.2))] %76 local maxima, %14 large gradients and % 5 min vals, 197 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4169924.8, rms=2.64 rms = 3.35, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=4086209.5, rms=2.30 043: dt: 0.2500, sse=4179736.5, rms=2.21 044: dt: 0.2500, sse=4211404.0, rms=2.16 rms = 2.13, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=4290806.0, rms=2.13 046: dt: 0.1250, sse=4200897.5, rms=2.05 rms = 2.03, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=4187674.2, rms=2.03 positioning took 0.7 minutes writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.area.pial vertex spacing 1.01 +- 0.41 (0.11-->7.57) (max @ vno 101694 --> 101695) face area 0.41 +- 0.29 (0.00-->11.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133920 vertices processed 25000 of 133920 vertices processed 50000 of 133920 vertices processed 75000 of 133920 vertices processed 100000 of 133920 vertices processed 125000 of 133920 vertices processed 0 of 133920 vertices processed 25000 of 133920 vertices processed 50000 of 133920 vertices processed 75000 of 133920 vertices processed 100000 of 133920 vertices processed 125000 of 133920 vertices processed thickness calculation complete, 664:1309 truncations. 65764 vertices at 0 distance 86174 vertices at 1 distance 64405 vertices at 2 distance 25701 vertices at 3 distance 8816 vertices at 4 distance 2882 vertices at 5 distance 1210 vertices at 6 distance 528 vertices at 7 distance 296 vertices at 8 distance 160 vertices at 9 distance 88 vertices at 10 distance 69 vertices at 11 distance 48 vertices at 12 distance 28 vertices at 13 distance 31 vertices at 14 distance 27 vertices at 15 distance 19 vertices at 16 distance 14 vertices at 17 distance 6 vertices at 18 distance 15 vertices at 19 distance 21 vertices at 20 distance writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.thickness positioning took 13.0 minutes #-------------------------------------------- #@# Surf Volume lh Fri May 8 01:17:57 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 May 8 01:17:57 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1367 979 2214 2.287 0.562 0.121 0.032 11 1.8 bankssts 986 683 1929 2.853 0.805 0.141 0.038 18 1.5 caudalanteriorcingulate 2762 1847 4965 2.391 0.612 0.128 0.043 32 5.0 caudalmiddlefrontal 2214 1360 2632 1.714 0.465 0.153 0.060 37 5.5 cuneus 454 327 1428 2.947 0.970 0.173 0.077 9 1.5 entorhinal 4078 2742 8359 2.599 0.872 0.163 0.081 90 12.1 fusiform 7413 4924 13172 2.366 0.606 0.143 0.050 111 15.0 inferiorparietal 4596 3115 10135 2.702 0.768 0.163 0.069 87 13.3 inferiortemporal 2118 1391 3186 2.139 0.760 0.144 0.061 40 5.1 isthmuscingulate 6849 4346 10348 2.036 0.657 0.150 0.055 159 15.8 lateraloccipital 3842 2585 6865 2.332 0.725 0.159 0.072 68 11.3 lateralorbitofrontal 4260 2744 5172 1.725 0.511 0.155 0.058 66 10.7 lingual 2812 1879 4973 2.307 0.829 0.159 0.117 111 15.2 medialorbitofrontal 4308 2934 9931 2.743 0.691 0.156 0.080 238 14.4 middletemporal 980 695 2356 2.650 0.880 0.124 0.051 11 1.8 parahippocampal 2142 1285 3052 2.196 0.571 0.127 0.105 52 4.5 paracentral 2803 1842 5268 2.487 0.587 0.129 0.042 32 5.1 parsopercularis 874 597 1802 2.459 0.620 0.196 0.096 23 3.0 parsorbitalis 1928 1307 3496 2.292 0.606 0.157 0.058 32 4.6 parstriangularis 1806 1239 1537 1.327 0.315 0.131 0.040 17 3.1 pericalcarine 6592 4208 8805 1.852 0.592 0.129 0.043 78 12.1 postcentral 1712 1192 3246 2.472 0.728 0.171 0.087 41 6.4 posteriorcingulate 7606 4752 12038 2.382 0.620 0.129 0.062 93 21.4 precentral 6260 4177 9353 2.077 0.592 0.148 0.057 97 14.5 precuneus 1473 967 3179 2.772 1.001 0.153 0.065 32 3.8 rostralanteriorcingulate 7857 5468 14132 2.150 0.659 0.161 0.081 168 22.4 rostralmiddlefrontal 9873 6784 20447 2.564 0.673 0.162 0.634 2867 32.9 superiorfrontal 8783 5793 14178 2.149 0.573 0.138 0.049 121 16.3 superiorparietal 6133 4117 11538 2.454 0.706 0.121 0.040 67 9.9 superiortemporal 5832 4000 10879 2.461 0.594 0.162 0.078 128 15.4 supramarginal 304 213 861 2.764 0.656 0.212 0.110 9 1.4 frontalpole 607 449 2897 3.605 0.767 0.185 0.085 14 2.0 temporalpole 873 440 1141 2.421 0.424 0.128 0.063 14 2.5 transversetemporal 3557 2378 6714 2.819 1.030 0.116 0.049 37 7.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri May 8 01:18:15 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 14 labels changed using aseg relabeling using gibbs priors... 000: 9160 changed, 133920 examined... 001: 2218 changed, 34851 examined... 002: 669 changed, 11509 examined... 003: 288 changed, 3721 examined... 004: 141 changed, 1588 examined... 005: 85 changed, 841 examined... 006: 57 changed, 470 examined... 007: 26 changed, 312 examined... 008: 23 changed, 166 examined... 009: 11 changed, 121 examined... 010: 6 changed, 55 examined... 011: 0 changed, 36 examined... 4 labels changed using aseg 000: 267 total segments, 186 labels (1969 vertices) changed 001: 91 total segments, 11 labels (121 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 973 vertices marked for relabeling... 973 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 7 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri May 8 01:19:23 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1199 825 2136 2.100 0.720 0.182 0.080 27 3.8 G_and_S_frontomargin 1581 1044 3157 2.324 0.870 0.153 0.056 22 3.7 G_and_S_occipital_inf 1667 924 2462 2.260 0.525 0.131 0.060 33 4.2 G_and_S_paracentral 1556 1017 2630 2.285 0.643 0.142 0.049 20 2.9 G_and_S_subcentral 572 395 1399 2.509 0.627 0.217 0.286 33 3.1 G_and_S_transv_frontopol 2568 1774 5054 2.530 0.827 0.145 0.060 49 5.7 G_and_S_cingul-Ant 1630 1141 2867 2.372 0.653 0.144 0.042 21 2.9 G_and_S_cingul-Mid-Ant 1278 909 2454 2.496 0.643 0.136 0.046 14 2.6 G_and_S_cingul-Mid-Post 616 429 1407 2.507 0.646 0.184 0.092 16 2.0 G_cingul-Post-dorsal 553 363 853 2.065 0.950 0.145 0.077 11 1.5 G_cingul-Post-ventral 1812 1104 2363 1.762 0.550 0.159 0.063 32 4.9 G_cuneus 1858 1176 3784 2.628 0.567 0.147 0.055 28 4.4 G_front_inf-Opercular 293 195 472 2.178 0.503 0.194 0.089 8 1.1 G_front_inf-Orbital 1167 783 2465 2.469 0.554 0.167 0.069 23 3.5 G_front_inf-Triangul 3790 2621 8532 2.470 0.657 0.179 0.084 100 12.9 G_front_middle 6342 4269 14578 2.714 0.672 0.180 0.980 2843 27.2 G_front_sup 451 286 1023 3.232 0.619 0.134 0.057 7 1.1 G_Ins_lg_and_S_cent_ins 727 468 2020 3.616 0.822 0.157 0.098 15 3.1 G_insular_short 2199 1379 4431 2.501 0.609 0.157 0.064 98 5.7 G_occipital_middle 2044 1221 2844 2.017 0.543 0.140 0.047 29 3.9 G_occipital_sup 1403 897 3214 2.789 0.707 0.164 0.080 39 3.9 G_oc-temp_lat-fusifor 3029 1873 3933 1.741 0.540 0.154 0.056 48 7.4 G_oc-temp_med-Lingual 1154 791 3382 3.022 0.897 0.162 0.085 23 4.1 G_oc-temp_med-Parahip 2511 1705 5435 2.500 0.702 0.183 0.089 61 8.6 G_orbital 2608 1715 5633 2.566 0.544 0.158 0.056 48 6.3 G_pariet_inf-Angular 3127 2146 6881 2.666 0.534 0.179 0.081 72 8.8 G_pariet_inf-Supramar 3411 2263 6657 2.379 0.566 0.155 0.060 63 7.3 G_parietal_sup 2409 1486 3634 1.965 0.530 0.135 0.050 36 5.2 G_postcentral 2867 1609 5315 2.623 0.517 0.126 0.091 46 12.1 G_precentral 3106 2064 5697 2.270 0.510 0.166 0.070 63 8.7 G_precuneus 1090 722 2510 2.616 0.745 0.185 0.116 38 5.9 G_rectus 294 188 364 1.862 0.827 0.194 0.482 51 6.7 G_subcallosal 622 327 881 2.310 0.394 0.124 0.065 11 1.9 G_temp_sup-G_T_transv 2362 1523 5433 2.607 0.646 0.143 0.057 41 5.2 G_temp_sup-Lateral 812 542 1877 3.047 0.687 0.100 0.029 5 0.9 G_temp_sup-Plan_polar 890 632 1752 2.455 0.595 0.099 0.025 6 0.9 G_temp_sup-Plan_tempo 2869 1886 6952 2.755 0.810 0.173 0.076 60 9.6 G_temporal_inf 2694 1812 7099 2.941 0.578 0.177 0.104 223 11.5 G_temporal_middle 351 237 584 2.244 0.549 0.141 0.034 5 0.5 Lat_Fis-ant-Horizont 302 201 425 2.201 0.611 0.124 0.036 2 0.4 Lat_Fis-ant-Vertical 1407 931 1737 2.113 0.626 0.121 0.040 11 2.4 Lat_Fis-post 2338 1473 2921 1.772 0.529 0.160 0.057 39 5.7 Pole_occipital 1514 1088 6127 3.299 0.928 0.192 0.128 48 6.9 Pole_temporal 2696 1826 2583 1.633 0.567 0.143 0.053 36 6.4 S_calcarine 3171 2153 3337 1.676 0.556 0.126 0.040 29 5.7 S_central 1186 792 1767 2.247 0.765 0.126 0.041 13 2.1 S_cingul-Marginalis 631 412 937 2.362 0.795 0.104 0.031 3 0.9 S_circular_insula_ant 1599 1048 2475 2.671 0.968 0.094 0.025 10 1.6 S_circular_insula_inf 1918 1348 2679 2.206 0.585 0.099 0.028 10 2.3 S_circular_insula_sup 907 651 1580 2.930 0.871 0.161 0.062 14 2.3 S_collat_transv_ant 420 268 409 1.693 0.360 0.145 0.047 4 0.8 S_collat_transv_post 2682 1818 4151 2.124 0.574 0.128 0.038 27 4.5 S_front_inf 1208 835 1767 1.933 0.611 0.138 0.059 18 2.7 S_front_middle 2321 1589 3604 2.232 0.587 0.107 0.032 14 3.0 S_front_sup 187 131 226 1.752 0.425 0.150 0.041 2 0.4 S_interm_prim-Jensen 3236 2217 4303 2.019 0.444 0.128 0.042 33 5.9 S_intrapariet_and_P_trans 935 610 1161 1.879 0.514 0.135 0.044 10 1.7 S_oc_middle_and_Lunatus 1487 993 1956 2.034 0.453 0.128 0.039 14 2.3 S_oc_sup_and_transversal 607 414 791 1.867 0.637 0.107 0.039 6 1.1 S_occipital_ant 908 640 1437 2.367 0.620 0.142 0.046 10 1.6 S_oc-temp_lat 1627 1186 2120 1.927 0.521 0.126 0.035 14 2.3 S_oc-temp_med_and_Lingual 468 339 751 1.983 0.578 0.169 0.061 8 1.2 S_orbital_lateral 849 570 1024 1.941 0.732 0.116 0.035 7 1.2 S_orbital_med-olfact 1208 841 2063 2.241 0.740 0.165 0.079 22 4.0 S_orbital-H_Shaped 2077 1361 2251 1.674 0.482 0.118 0.038 20 3.1 S_parieto_occipital 1613 1023 1977 2.369 1.011 0.157 0.080 45 5.5 S_pericallosal 3226 2164 4108 1.898 0.555 0.132 0.061 57 6.1 S_postcentral 1487 1005 2083 2.227 0.563 0.126 0.038 13 2.5 S_precentral-inf-part 1297 887 1942 2.401 0.663 0.123 0.038 10 2.0 S_precentral-sup-part 624 432 1119 2.487 0.824 0.161 0.055 11 1.4 S_suborbital 1348 913 1770 1.926 0.499 0.131 0.042 13 2.3 S_subparietal 1074 750 1674 2.428 0.665 0.134 0.042 13 1.7 S_temporal_inf 5629 3884 8393 2.262 0.602 0.121 0.038 52 8.7 S_temporal_sup 355 226 416 1.980 0.567 0.136 0.040 4 0.6 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Fri May 8 01:19:45 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 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 261312: 0.000765) 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 40: 345 vertices, 391 faces slice 50: 4714 vertices, 4908 faces slice 60: 12904 vertices, 13267 faces slice 70: 23231 vertices, 23599 faces slice 80: 34986 vertices, 35384 faces slice 90: 46023 vertices, 46389 faces slice 100: 57606 vertices, 57994 faces slice 110: 69215 vertices, 69662 faces slice 120: 80642 vertices, 81043 faces slice 130: 91594 vertices, 92013 faces slice 140: 102231 vertices, 102658 faces slice 150: 111634 vertices, 111972 faces slice 160: 119379 vertices, 119699 faces slice 170: 126704 vertices, 127001 faces slice 180: 132903 vertices, 133157 faces slice 190: 137887 vertices, 138115 faces slice 200: 140546 vertices, 140674 faces slice 210: 140862 vertices, 140930 faces slice 220: 140862 vertices, 140930 faces slice 230: 140862 vertices, 140930 faces slice 240: 140862 vertices, 140930 faces slice 250: 140862 vertices, 140930 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... 140862 voxel in cpt #1: X=-68 [v=140862,e=422790,f=281860] located at (26.897993, -15.740867, 27.394770) For the whole surface: X=-68 [v=140862,e=422790,f=281860] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri May 8 01:20:00 EDT 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 May 8 01:20:06 EDT 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts avg radius = 47.2 mm, total surface area = 74312 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.1 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.042 (target=0.015) step 025: RMS=0.038 (target=0.015) step 030: RMS=0.035 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri May 8 01:21:14 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 0.98 +- 0.58 (0.00-->5.74) (max @ vno 107810 --> 107828) face area 0.02 +- 0.03 (-0.09-->0.51) scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.821, avgs=0 005/300: dt: 0.9000, rms radial error=176.562, avgs=0 010/300: dt: 0.9000, rms radial error=176.007, avgs=0 015/300: dt: 0.9000, rms radial error=175.279, avgs=0 020/300: dt: 0.9000, rms radial error=174.450, avgs=0 025/300: dt: 0.9000, rms radial error=173.562, avgs=0 030/300: dt: 0.9000, rms radial error=172.643, avgs=0 035/300: dt: 0.9000, rms radial error=171.708, avgs=0 040/300: dt: 0.9000, rms radial error=170.764, avgs=0 045/300: dt: 0.9000, rms radial error=169.819, avgs=0 050/300: dt: 0.9000, rms radial error=168.874, avgs=0 055/300: dt: 0.9000, rms radial error=167.932, avgs=0 060/300: dt: 0.9000, rms radial error=166.993, avgs=0 065/300: dt: 0.9000, rms radial error=166.059, avgs=0 070/300: dt: 0.9000, rms radial error=165.129, avgs=0 075/300: dt: 0.9000, rms radial error=164.204, avgs=0 080/300: dt: 0.9000, rms radial error=163.283, avgs=0 085/300: dt: 0.9000, rms radial error=162.368, avgs=0 090/300: dt: 0.9000, rms radial error=161.457, avgs=0 095/300: dt: 0.9000, rms radial error=160.551, avgs=0 100/300: dt: 0.9000, rms radial error=159.650, avgs=0 105/300: dt: 0.9000, rms radial error=158.754, avgs=0 110/300: dt: 0.9000, rms radial error=157.864, avgs=0 115/300: dt: 0.9000, rms radial error=156.978, avgs=0 120/300: dt: 0.9000, rms radial error=156.097, avgs=0 125/300: dt: 0.9000, rms radial error=155.221, avgs=0 130/300: dt: 0.9000, rms radial error=154.350, avgs=0 135/300: dt: 0.9000, rms radial error=153.483, avgs=0 140/300: dt: 0.9000, rms radial error=152.621, avgs=0 145/300: dt: 0.9000, rms radial error=151.763, avgs=0 150/300: dt: 0.9000, rms radial error=150.910, avgs=0 155/300: dt: 0.9000, rms radial error=150.062, avgs=0 160/300: dt: 0.9000, rms radial error=149.218, avgs=0 165/300: dt: 0.9000, rms radial error=148.379, avgs=0 170/300: dt: 0.9000, rms radial error=147.545, avgs=0 175/300: dt: 0.9000, rms radial error=146.715, avgs=0 180/300: dt: 0.9000, rms radial error=145.889, avgs=0 185/300: dt: 0.9000, rms radial error=145.069, avgs=0 190/300: dt: 0.9000, rms radial error=144.254, avgs=0 195/300: dt: 0.9000, rms radial error=143.443, avgs=0 200/300: dt: 0.9000, rms radial error=142.636, avgs=0 205/300: dt: 0.9000, rms radial error=141.834, avgs=0 210/300: dt: 0.9000, rms radial error=141.037, avgs=0 215/300: dt: 0.9000, rms radial error=140.243, avgs=0 220/300: dt: 0.9000, rms radial error=139.455, avgs=0 225/300: dt: 0.9000, rms radial error=138.670, avgs=0 230/300: dt: 0.9000, rms radial error=137.891, avgs=0 235/300: dt: 0.9000, rms radial error=137.115, avgs=0 240/300: dt: 0.9000, rms radial error=136.343, avgs=0 245/300: dt: 0.9000, rms radial error=135.576, avgs=0 250/300: dt: 0.9000, rms radial error=134.813, avgs=0 255/300: dt: 0.9000, rms radial error=134.055, avgs=0 260/300: dt: 0.9000, rms radial error=133.300, avgs=0 265/300: dt: 0.9000, rms radial error=132.550, avgs=0 270/300: dt: 0.9000, rms radial error=131.804, avgs=0 275/300: dt: 0.9000, rms radial error=131.062, avgs=0 280/300: dt: 0.9000, rms radial error=130.324, avgs=0 285/300: dt: 0.9000, rms radial error=129.590, avgs=0 290/300: dt: 0.9000, rms radial error=128.861, avgs=0 295/300: dt: 0.9000, rms radial error=128.135, avgs=0 300/300: dt: 0.9000, rms radial error=127.413, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16571.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2816.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 306.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00788 epoch 4 (K=640.0), pass 1, starting sse = 20.67 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/14 = 0.01046 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri May 8 01:28:36 EDT 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 R01L019_MD_12m 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=-68 (nv=140862, nf=281860, ne=422790, g=35) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 4610 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 15 -merging segment 24 into 15 -merging segment 26 into 15 36 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4587 (-4.7293) -vertex loglikelihood: -6.1844 (-3.0922) -normal dot loglikelihood: -3.6445 (-3.6445) -quad curv loglikelihood: -6.5205 (-3.2603) Total Loglikelihood : -25.8081 CORRECTING DEFECT 0 (vertices=52, convex hull=93) After retessellation of defect 0, euler #=-35 (138107,413257,275115) : difference with theory (-33) = 2 CORRECTING DEFECT 1 (vertices=28, convex hull=59) After retessellation of defect 1, euler #=-34 (138118,413310,275158) : difference with theory (-32) = 2 CORRECTING DEFECT 2 (vertices=37, convex hull=92) After retessellation of defect 2, euler #=-33 (138139,413412,275240) : difference with theory (-31) = 2 CORRECTING DEFECT 3 (vertices=82, convex hull=127) After retessellation of defect 3, euler #=-32 (138189,413616,275395) : difference with theory (-30) = 2 CORRECTING DEFECT 4 (vertices=18, convex hull=54) After retessellation of defect 4, euler #=-31 (138197,413663,275435) : difference with theory (-29) = 2 CORRECTING DEFECT 5 (vertices=145, convex hull=109) After retessellation of defect 5, euler #=-30 (138239,413836,275567) : difference with theory (-28) = 2 CORRECTING DEFECT 6 (vertices=22, convex hull=36) After retessellation of defect 6, euler #=-29 (138241,413861,275591) : difference with theory (-27) = 2 CORRECTING DEFECT 7 (vertices=44, convex hull=59) After retessellation of defect 7, euler #=-28 (138250,413912,275634) : difference with theory (-26) = 2 CORRECTING DEFECT 8 (vertices=17, convex hull=29) After retessellation of defect 8, euler #=-27 (138252,413927,275648) : difference with theory (-25) = 2 CORRECTING DEFECT 9 (vertices=7, convex hull=18) After retessellation of defect 9, euler #=-26 (138255,413939,275658) : difference with theory (-24) = 2 CORRECTING DEFECT 10 (vertices=32, convex hull=50) After retessellation of defect 10, euler #=-25 (138271,414007,275711) : difference with theory (-23) = 2 CORRECTING DEFECT 11 (vertices=47, convex hull=41) After retessellation of defect 11, euler #=-24 (138281,414053,275748) : difference with theory (-22) = 2 CORRECTING DEFECT 12 (vertices=18, convex hull=19) After retessellation of defect 12, euler #=-23 (138282,414061,275756) : difference with theory (-21) = 2 CORRECTING DEFECT 13 (vertices=7, convex hull=20) After retessellation of defect 13, euler #=-22 (138283,414070,275765) : difference with theory (-20) = 2 CORRECTING DEFECT 14 (vertices=6, convex hull=26) After retessellation of defect 14, euler #=-21 (138286,414085,275778) : difference with theory (-19) = 2 CORRECTING DEFECT 15 (vertices=1533, convex hull=637) After retessellation of defect 15, euler #=-17 (138750,415852,277085) : difference with theory (-18) = -1 CORRECTING DEFECT 16 (vertices=32, convex hull=33) Warning - incorrect dp selected!!!!(-82.862072 >= -82.862072 ) After retessellation of defect 16, euler #=-16 (138752,415869,277101) : difference with theory (-17) = -1 CORRECTING DEFECT 17 (vertices=35, convex hull=37) After retessellation of defect 17, euler #=-15 (138760,415906,277131) : difference with theory (-16) = -1 CORRECTING DEFECT 18 (vertices=29, convex hull=71) After retessellation of defect 18, euler #=-14 (138777,415984,277193) : difference with theory (-15) = -1 CORRECTING DEFECT 19 (vertices=8, convex hull=37) After retessellation of defect 19, euler #=-13 (138779,416002,277210) : difference with theory (-14) = -1 CORRECTING DEFECT 20 (vertices=52, convex hull=40) After retessellation of defect 20, euler #=-12 (138785,416035,277238) : difference with theory (-13) = -1 CORRECTING DEFECT 21 (vertices=8, convex hull=13) After retessellation of defect 21, euler #=-11 (138787,416045,277247) : difference with theory (-12) = -1 CORRECTING DEFECT 22 (vertices=21, convex hull=25) After retessellation of defect 22, euler #=-11 (138790,416063,277262) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=17, convex hull=40) After retessellation of defect 23, euler #=-10 (138802,416112,277300) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=178, convex hull=51) After retessellation of defect 24, euler #=-9 (138811,416163,277343) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=8, convex hull=24) After retessellation of defect 25, euler #=-8 (138812,416173,277353) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=10, convex hull=31) After retessellation of defect 26, euler #=-7 (138815,416193,277371) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=23, convex hull=62) After retessellation of defect 27, euler #=-6 (138828,416257,277423) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=26, convex hull=58) After retessellation of defect 28, euler #=-5 (138847,416340,277488) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=61, convex hull=94) After retessellation of defect 29, euler #=-4 (138856,416407,277547) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=18, convex hull=39) After retessellation of defect 30, euler #=-3 (138863,416441,277575) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=43, convex hull=76) After retessellation of defect 31, euler #=-2 (138889,416549,277658) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=20, convex hull=52) After retessellation of defect 32, euler #=-1 (138898,416597,277698) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=57, convex hull=121) After retessellation of defect 33, euler #=0 (138941,416777,277836) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=20, convex hull=53) After retessellation of defect 34, euler #=1 (138951,416830,277880) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=20, convex hull=46) After retessellation of defect 35, euler #=2 (138959,416871,277914) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->6.04) (max @ vno 40989 --> 138309) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->6.04) (max @ vno 40989 --> 138309) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 157 mutations (34.7%), 295 crossovers (65.3%), 33 vertices were eliminated building final representation... 1903 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138959, nf=277914, ne=416871, g=0) writing corrected surface to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 25.5 minutes 0 defective edges removing intersecting faces 000: 276 intersecting 001: 15 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 138959 - 416871 + 277914 = 2 --> 0 holes F =2V-4: 277914 = 277918-4 (0) 2E=3F: 833742 = 833742 (0) total defect index = 0 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 144 intersecting 001: 15 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri May 8 01:54:11 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 10683 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... computing class statistics... border white: 263133 voxels (1.57%) border gray 285814 voxels (1.70%) WM (93.0): 94.4 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.1 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.2 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.3 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->4.04) (max @ vno 40989 --> 138209) face area 0.28 +- 0.12 (0.00-->1.88) mean absolute distance = 0.87 +- 1.10 4321 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=74 using class modes intead of means.... mean inside = 93.3, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.1, 348 (348) missing vertices, mean dist 0.2 [0.9 (%38.0)->0.9 (%62.0))] %33 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.12-->4.73) (max @ vno 100360 --> 138660) face area 0.28 +- 0.13 (0.00-->1.95) mean absolute distance = 0.45 +- 0.85 4643 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4889994.0, rms=9.32 001: dt: 0.5000, sse=5628997.5, rms=6.50 002: dt: 0.5000, sse=5937940.0, rms=4.82 003: dt: 0.5000, sse=6271614.0, rms=3.91 004: dt: 0.5000, sse=6470655.0, rms=3.38 005: dt: 0.5000, sse=6616358.0, rms=3.08 006: dt: 0.5000, sse=6662063.0, rms=2.91 007: dt: 0.5000, sse=6711137.5, rms=2.81 008: dt: 0.5000, sse=6709863.5, rms=2.75 rms = 2.71, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6736783.5, rms=2.71 010: dt: 0.2500, sse=4270585.5, rms=1.90 011: dt: 0.2500, sse=3990179.0, rms=1.74 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3874310.0, rms=1.71 rms = 1.67, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3811859.8, rms=1.67 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 mean border=85.1, 334 (173) missing vertices, mean dist -0.3 [0.6 (%61.9)->0.3 (%38.1))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 +- 0.25 (0.09-->5.19) (max @ vno 100360 --> 138660) face area 0.35 +- 0.16 (0.00-->2.96) mean absolute distance = 0.37 +- 0.53 4031 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4214650.5, rms=3.65 014: dt: 0.5000, sse=4599709.0, rms=2.42 015: dt: 0.5000, sse=5152344.5, rms=2.21 016: dt: 0.5000, sse=5369297.0, rms=2.13 rms = 2.31, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4500642.0, rms=1.67 018: dt: 0.2500, sse=4201490.5, rms=1.48 rms = 1.44, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4094942.8, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4041488.2, rms=1.42 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.7, 300 (141) missing vertices, mean dist -0.2 [0.4 (%69.0)->0.2 (%31.0))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 +- 0.25 (0.06-->5.37) (max @ vno 100360 --> 138660) face area 0.34 +- 0.16 (0.00-->3.27) mean absolute distance = 0.28 +- 0.38 3970 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4323636.0, rms=3.64 021: dt: 0.5000, sse=4527674.5, rms=2.09 022: dt: 0.5000, sse=5012846.0, rms=2.02 rms = 2.05, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4488024.0, rms=1.57 024: dt: 0.2500, sse=4283407.0, rms=1.33 rms = 1.30, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4223276.0, rms=1.30 rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4181113.5, rms=1.28 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.9, 286 (119) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.2 (%39.7))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4215968.0, rms=1.92 027: dt: 0.5000, sse=5129668.0, rms=1.45 rms = 1.79, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4727356.0, rms=1.13 029: dt: 0.2500, sse=4551352.0, rms=1.06 rms = 1.03, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4606946.5, rms=1.03 rms = 1.03, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4597002.5, rms=1.03 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 18 non-cortical segments detected only using segment with 1905 vertices erasing segment 1 (vno[0] = 57934) erasing segment 2 (vno[0] = 60175) erasing segment 3 (vno[0] = 68356) erasing segment 4 (vno[0] = 76555) erasing segment 5 (vno[0] = 90304) erasing segment 6 (vno[0] = 98154) erasing segment 7 (vno[0] = 101064) erasing segment 8 (vno[0] = 101866) erasing segment 9 (vno[0] = 102729) erasing segment 10 (vno[0] = 102751) erasing segment 11 (vno[0] = 104557) erasing segment 12 (vno[0] = 104564) erasing segment 13 (vno[0] = 106318) erasing segment 14 (vno[0] = 106334) erasing segment 15 (vno[0] = 107250) erasing segment 16 (vno[0] = 110467) erasing segment 17 (vno[0] = 138530) writing cortex label to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.cortex.label writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.area vertex spacing 0.89 +- 0.25 (0.09-->5.30) (max @ vno 100360 --> 138660) face area 0.33 +- 0.16 (0.00-->3.29) refinement took 6.5 minutes #-------------------------------------------- #@# Smooth2 rh Fri May 8 02:00:39 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 May 8 02:00:47 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.5 mm, total surface area = 83273 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (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=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: 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 347 vertices thresholded to be in k1 ~ [-0.26 0.42], k2 ~ [-0.11 0.07] total integrated curvature = 0.511*4pi (6.424) --> 0 handles ICI = 1.5, FI = 10.9, variation=178.512 183 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 = 0.001 144 vertices thresholded to be in [-0.15 0.19] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Fri May 8 02:03:42 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm R01L019_MD_12m 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 [ R01L019_MD_12m/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 [ 248 ] Gb_filter = 0 WARN: S lookup min: -0.814063 WARN: S explicit min: 0.000000 vertex = 524 #-------------------------------------------- #@# Sphere rh Fri May 8 02:03:48 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.35 hours scaling brain by 0.287... pass 1: epoch 1 of 3 starting distance error %19.70 pass 1: epoch 2 of 3 starting distance error %19.64 unfolding complete - removing small folds... starting distance error %19.61 removing remaining folds... final distance error %19.63 #-------------------------------------------- #@# Surf Reg rh Fri May 8 03:24:54 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.602 curvature mean = 0.019, std = 0.938 curvature mean = 0.026, std = 0.867 curvature mean = 0.002, std = 0.961 curvature mean = 0.010, std = 0.945 curvature mean = -0.002, std = 0.973 curvature mean = 0.004, std = 0.976 curvature mean = -0.004, std = 0.974 curvature mean = 0.001, std = 0.990 curvature mean = -0.029, std = 0.329 curvature mean = 0.004, std = 0.071 curvature mean = 0.058, std = 0.308 curvature mean = 0.004, std = 0.084 curvature mean = 0.023, std = 0.480 curvature mean = 0.004, std = 0.091 curvature mean = 0.012, std = 0.607 curvature mean = 0.005, std = 0.093 curvature mean = 0.003, std = 0.722 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri May 8 04:15:41 EDT 2015 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 May 8 04:15:44 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri May 8 04:15:46 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 1470 labels changed using aseg relabeling using gibbs priors... 000: 3039 changed, 138959 examined... 001: 681 changed, 12940 examined... 002: 150 changed, 3782 examined... 003: 61 changed, 942 examined... 004: 22 changed, 386 examined... 005: 5 changed, 136 examined... 006: 3 changed, 35 examined... 007: 0 changed, 16 examined... 176 labels changed using aseg 000: 110 total segments, 71 labels (343 vertices) changed 001: 42 total segments, 3 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2022 vertices marked for relabeling... 2022 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri May 8 04:16:37 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 10683 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... computing class statistics... border white: 263133 voxels (1.57%) border gray 285814 voxels (1.70%) WM (93.0): 94.4 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.1 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.2 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.3 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=74 using class modes intead of means.... mean inside = 93.3, mean outside = 77.5 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->4.04) (max @ vno 40989 --> 138209) face area 0.28 +- 0.12 (0.00-->1.88) mean absolute distance = 0.87 +- 1.11 4405 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 109 points - only 0.00% unknown deleting segment 4 with 59 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 62 points - only 0.00% unknown mean border=83.1, 348 (348) missing vertices, mean dist 0.2 [0.9 (%38.1)->0.9 (%61.9))] %33 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.12-->4.73) (max @ vno 100360 --> 138660) face area 0.28 +- 0.13 (0.00-->1.95) mean absolute distance = 0.46 +- 0.85 4508 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4894987.5, rms=9.32 001: dt: 0.5000, sse=5634812.5, rms=6.50 002: dt: 0.5000, sse=5944886.0, rms=4.82 003: dt: 0.5000, sse=6276165.0, rms=3.91 004: dt: 0.5000, sse=6475228.5, rms=3.38 005: dt: 0.5000, sse=6620905.0, rms=3.08 006: dt: 0.5000, sse=6668351.0, rms=2.91 007: dt: 0.5000, sse=6713869.5, rms=2.81 008: dt: 0.5000, sse=6717670.5, rms=2.75 rms = 2.71, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6739434.5, rms=2.71 010: dt: 0.2500, sse=4272618.5, rms=1.90 011: dt: 0.2500, sse=3991048.2, rms=1.74 rms = 1.70, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3875582.8, rms=1.70 rms = 1.67, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3813574.0, rms=1.67 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 2 with 254 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 31 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown mean border=85.1, 334 (173) missing vertices, mean dist -0.3 [0.6 (%61.8)->0.3 (%38.2))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 +- 0.25 (0.09-->5.19) (max @ vno 100360 --> 138660) face area 0.35 +- 0.16 (0.00-->2.96) mean absolute distance = 0.37 +- 0.53 4085 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4227163.5, rms=3.65 014: dt: 0.5000, sse=4621729.0, rms=2.42 015: dt: 0.5000, sse=5172983.5, rms=2.21 016: dt: 0.5000, sse=5391670.5, rms=2.14 rms = 2.32, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4518407.5, rms=1.68 018: dt: 0.2500, sse=4217013.5, rms=1.48 rms = 1.44, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4110304.8, rms=1.44 rms = 1.42, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4058040.0, rms=1.42 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 275 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 31 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown mean border=87.7, 303 (141) missing vertices, mean dist -0.2 [0.4 (%69.0)->0.2 (%31.0))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 +- 0.25 (0.06-->5.37) (max @ vno 100360 --> 138660) face area 0.34 +- 0.16 (0.00-->3.27) mean absolute distance = 0.28 +- 0.39 3168 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4341451.0, rms=3.64 021: dt: 0.5000, sse=4547422.5, rms=2.09 022: dt: 0.5000, sse=5033693.5, rms=2.02 rms = 2.05, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4507016.0, rms=1.57 024: dt: 0.2500, sse=4302064.5, rms=1.33 rms = 1.30, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4240968.5, rms=1.30 rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4198167.5, rms=1.28 positioning took 0.7 minutes 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 262 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 103 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 50.00% unknown deleting segment 8 with 31 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=88.9, 289 (119) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.2 (%39.7))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4233532.5, rms=1.92 027: dt: 0.5000, sse=5151260.0, rms=1.45 rms = 1.79, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4747758.0, rms=1.13 029: dt: 0.2500, sse=4571764.5, rms=1.06 rms = 1.03, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4625347.0, rms=1.03 rms = 1.03, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4616355.0, rms=1.03 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... mean border=62.4, 376 (376) missing vertices, mean dist 1.9 [0.3 (%0.0)->2.1 (%100.0))] %40 local maxima, %43 large gradients and %13 min vals, 566 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21637566.0, rms=26.72 001: dt: 0.5000, sse=17263118.0, rms=23.42 002: dt: 0.5000, sse=13852728.0, rms=20.52 003: dt: 0.5000, sse=11562840.0, rms=18.06 004: dt: 0.5000, sse=10141387.0, rms=15.93 005: dt: 0.5000, sse=9054421.0, rms=14.04 006: dt: 0.5000, sse=8269468.0, rms=12.38 007: dt: 0.5000, sse=7671583.0, rms=10.86 008: dt: 0.5000, sse=7226411.0, rms=9.45 009: dt: 0.5000, sse=6945213.5, rms=8.16 010: dt: 0.5000, sse=6777941.5, rms=7.04 011: dt: 0.5000, sse=6723453.5, rms=6.11 012: dt: 0.5000, sse=6744284.5, rms=5.42 013: dt: 0.5000, sse=6822483.0, rms=4.94 014: dt: 0.5000, sse=6870290.5, rms=4.64 015: dt: 0.5000, sse=6919963.0, rms=4.44 016: dt: 0.5000, sse=6937075.0, rms=4.31 017: dt: 0.5000, sse=6966858.0, rms=4.22 018: dt: 0.5000, sse=6978432.0, rms=4.16 rms = 4.12, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7008213.5, rms=4.12 020: dt: 0.2500, sse=4463374.0, rms=3.08 021: dt: 0.2500, sse=4152519.8, rms=2.78 022: dt: 0.2500, sse=3973257.5, rms=2.71 rms = 2.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3941957.8, rms=2.69 024: dt: 0.1250, sse=3752192.0, rms=2.57 rms = 2.55, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3725044.5, rms=2.55 positioning took 2.7 minutes mean border=59.0, 488 (25) missing vertices, mean dist 0.2 [0.2 (%37.0)->0.5 (%63.0))] %60 local maxima, %28 large gradients and % 8 min vals, 213 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4682368.0, rms=5.83 026: dt: 0.5000, sse=4825856.0, rms=4.35 027: dt: 0.5000, sse=6025884.5, rms=4.26 rms = 4.30, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4896220.0, rms=3.34 029: dt: 0.2500, sse=4483324.0, rms=2.93 030: dt: 0.2500, sse=4396072.0, rms=2.80 031: dt: 0.2500, sse=4361487.5, rms=2.74 rms = 2.70, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4345185.5, rms=2.70 033: dt: 0.1250, sse=4204927.0, rms=2.57 rms = 2.55, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4184371.0, rms=2.55 positioning took 1.0 minutes mean border=56.9, 648 (21) missing vertices, mean dist 0.1 [0.2 (%36.2)->0.3 (%63.8))] %71 local maxima, %17 large gradients and % 8 min vals, 196 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4399026.0, rms=3.70 rms = 3.94, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4221654.0, rms=2.99 036: dt: 0.2500, sse=4209555.0, rms=2.63 037: dt: 0.2500, sse=4314646.0, rms=2.50 rms = 2.46, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4325151.0, rms=2.46 039: dt: 0.1250, sse=4223916.0, rms=2.37 rms = 2.35, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4217207.0, rms=2.35 positioning took 0.7 minutes mean border=55.8, 1132 (21) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %75 local maxima, %13 large gradients and % 7 min vals, 169 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4255162.0, rms=2.65 rms = 3.30, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4172056.8, rms=2.34 042: dt: 0.2500, sse=4256508.0, rms=2.25 rms = 2.20, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4302631.0, rms=2.20 044: dt: 0.1250, sse=4254360.5, rms=2.12 rms = 2.11, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4245523.5, rms=2.11 positioning took 0.6 minutes writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.area.pial vertex spacing 0.99 +- 0.40 (0.10-->7.32) (max @ vno 104805 --> 103896) face area 0.40 +- 0.28 (0.00-->5.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138959 vertices processed 25000 of 138959 vertices processed 50000 of 138959 vertices processed 75000 of 138959 vertices processed 100000 of 138959 vertices processed 125000 of 138959 vertices processed 0 of 138959 vertices processed 25000 of 138959 vertices processed 50000 of 138959 vertices processed 75000 of 138959 vertices processed 100000 of 138959 vertices processed 125000 of 138959 vertices processed thickness calculation complete, 380:611 truncations. 71065 vertices at 0 distance 86059 vertices at 1 distance 66774 vertices at 2 distance 27383 vertices at 3 distance 9407 vertices at 4 distance 3145 vertices at 5 distance 1176 vertices at 6 distance 478 vertices at 7 distance 285 vertices at 8 distance 166 vertices at 9 distance 123 vertices at 10 distance 86 vertices at 11 distance 60 vertices at 12 distance 39 vertices at 13 distance 29 vertices at 14 distance 29 vertices at 15 distance 29 vertices at 16 distance 16 vertices at 17 distance 16 vertices at 18 distance 7 vertices at 19 distance 10 vertices at 20 distance writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.thickness positioning took 11.4 minutes #-------------------------------------------- #@# Surf Volume rh Fri May 8 04:28:00 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 May 8 04:28:00 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1402 969 2179 2.256 0.444 0.111 0.030 13 1.7 bankssts 1472 1000 2675 2.485 0.899 0.167 0.077 37 4.8 caudalanteriorcingulate 3176 2128 5582 2.275 0.594 0.143 0.055 43 7.1 caudalmiddlefrontal 2266 1390 2593 1.650 0.415 0.154 0.058 38 5.1 cuneus 461 311 1085 2.627 0.853 0.174 0.102 11 1.9 entorhinal 3901 2588 6689 2.411 0.714 0.155 0.069 65 11.8 fusiform 7899 5222 13292 2.326 0.618 0.153 0.055 137 18.1 inferiorparietal 4964 3291 10160 2.627 0.717 0.166 0.095 130 16.9 inferiortemporal 1632 1038 2514 2.079 0.760 0.162 0.120 87 7.6 isthmuscingulate 6120 3864 8934 2.080 0.610 0.156 0.062 98 15.8 lateraloccipital 3784 2497 6362 2.262 0.751 0.162 0.077 71 12.3 lateralorbitofrontal 4225 2747 5500 1.808 0.584 0.158 0.068 75 13.0 lingual 3197 2134 5569 2.163 0.809 0.143 0.070 72 8.8 medialorbitofrontal 5465 3744 12118 2.706 0.683 0.148 0.063 102 13.5 middletemporal 923 638 1871 2.455 0.870 0.120 0.044 12 1.6 parahippocampal 2611 1557 3591 2.181 0.528 0.125 0.049 31 5.6 paracentral 2283 1570 4583 2.502 0.596 0.148 0.045 35 4.3 parsopercularis 1088 715 2215 2.532 0.648 0.161 0.085 24 3.2 parsorbitalis 2001 1360 3596 2.230 0.633 0.148 0.053 29 4.3 parstriangularis 1880 1227 1646 1.369 0.318 0.150 0.057 28 4.5 pericalcarine 6617 4118 8495 1.888 0.598 0.124 0.041 80 11.5 postcentral 1863 1283 3339 2.282 0.772 0.170 0.124 142 6.0 posteriorcingulate 7743 4818 12132 2.354 0.589 0.129 0.057 101 20.1 precentral 6723 4402 9619 2.002 0.575 0.142 0.051 99 14.3 precuneus 1358 886 2577 2.601 0.838 0.160 0.075 30 4.0 rostralanteriorcingulate 7832 5290 13526 2.088 0.692 0.165 0.074 186 23.9 rostralmiddlefrontal 9399 6323 18598 2.442 0.701 0.155 0.095 243 30.6 superiorfrontal 9595 6212 15123 2.136 0.575 0.140 0.050 143 18.1 superiorparietal 6622 4332 11761 2.418 0.616 0.127 0.050 169 15.4 superiortemporal 6957 4566 12087 2.436 0.621 0.143 0.054 107 16.7 supramarginal 470 307 1223 2.657 0.755 0.206 0.113 16 2.1 frontalpole 639 451 1883 3.060 0.651 0.167 0.184 22 1.7 temporalpole 642 345 744 1.953 0.501 0.128 0.048 7 1.2 transversetemporal 3555 2345 6743 2.807 0.982 0.138 0.148 163 14.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri May 8 04:28:16 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 2 labels changed using aseg relabeling using gibbs priors... 000: 9329 changed, 138959 examined... 001: 2271 changed, 36030 examined... 002: 742 changed, 11688 examined... 003: 317 changed, 4073 examined... 004: 146 changed, 1766 examined... 005: 74 changed, 846 examined... 006: 42 changed, 431 examined... 007: 20 changed, 238 examined... 008: 6 changed, 129 examined... 009: 4 changed, 30 examined... 010: 3 changed, 27 examined... 011: 1 changed, 19 examined... 012: 0 changed, 7 examined... 1 labels changed using aseg 000: 262 total segments, 181 labels (2122 vertices) changed 001: 87 total segments, 8 labels (156 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 162 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1214 vertices marked for relabeling... 1214 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri May 8 04:29:15 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 969 634 1681 2.158 0.772 0.170 0.075 22 3.2 G_and_S_frontomargin 1402 939 2323 2.186 0.624 0.149 0.049 20 2.9 G_and_S_occipital_inf 1423 777 1911 2.110 0.486 0.135 0.060 22 3.4 G_and_S_paracentral 1427 913 2509 2.416 0.495 0.147 0.049 22 2.9 G_and_S_subcentral 1112 742 2693 2.494 0.766 0.214 0.123 44 5.5 G_and_S_transv_frontopol 2979 2025 5236 2.260 0.698 0.146 0.064 57 7.3 G_and_S_cingul-Ant 1592 1098 2912 2.431 0.751 0.155 0.068 28 4.6 G_and_S_cingul-Mid-Ant 1610 1098 2877 2.385 0.627 0.136 0.054 21 3.4 G_and_S_cingul-Mid-Post 673 425 1657 2.839 0.510 0.201 0.123 26 3.3 G_cingul-Post-dorsal 269 179 472 2.250 0.703 0.230 0.339 28 3.4 G_cingul-Post-ventral 2102 1270 2538 1.718 0.467 0.159 0.063 40 5.3 G_cuneus 1482 1009 3560 2.725 0.563 0.164 0.058 31 3.6 G_front_inf-Opercular 364 238 848 2.715 0.503 0.179 0.091 9 1.5 G_front_inf-Orbital 1022 688 2224 2.490 0.517 0.168 0.067 20 2.7 G_front_inf-Triangul 3437 2332 7645 2.464 0.625 0.182 0.089 94 12.4 G_front_middle 6315 4049 13959 2.615 0.688 0.168 0.116 198 26.0 G_front_sup 455 305 1148 3.449 0.735 0.198 0.243 35 3.0 G_Ins_lg_and_S_cent_ins 674 399 1846 3.459 0.869 0.144 0.070 12 2.0 G_insular_short 1788 1163 4081 2.788 0.553 0.174 0.070 40 5.1 G_occipital_middle 2159 1282 3228 2.103 0.473 0.145 0.058 38 5.2 G_occipital_sup 1467 918 2946 2.518 0.654 0.153 0.090 28 5.7 G_oc-temp_lat-fusifor 2930 1816 4142 1.903 0.639 0.168 0.080 62 10.6 G_oc-temp_med-Lingual 1357 848 2828 2.680 0.801 0.182 0.330 131 9.2 G_oc-temp_med-Parahip 2737 1761 5640 2.493 0.716 0.179 0.095 69 9.9 G_orbital 3294 2152 6359 2.480 0.576 0.172 0.070 74 9.4 G_pariet_inf-Angular 3642 2385 7481 2.659 0.614 0.152 0.056 60 8.1 G_pariet_inf-Supramar 2870 1858 5667 2.423 0.548 0.153 0.069 57 6.6 G_parietal_sup 2451 1384 3256 1.958 0.515 0.132 0.047 39 5.0 G_postcentral 3046 1593 5247 2.586 0.524 0.129 0.082 59 11.9 G_precentral 3279 2113 6290 2.317 0.558 0.162 0.067 70 8.4 G_precuneus 775 505 1561 2.284 0.555 0.151 0.071 18 2.5 G_rectus 504 315 882 2.621 0.960 0.154 0.133 19 2.4 G_subcallosal 539 277 674 2.034 0.462 0.135 0.048 7 1.0 G_temp_sup-G_T_transv 2203 1373 5033 2.726 0.563 0.145 0.078 130 9.2 G_temp_sup-Lateral 811 553 1659 2.739 0.589 0.112 0.033 6 1.0 G_temp_sup-Plan_polar 1094 686 1727 2.229 0.472 0.115 0.034 11 1.5 G_temp_sup-Plan_tempo 2868 1864 6445 2.673 0.751 0.175 0.109 92 12.1 G_temporal_inf 3388 2237 8682 2.932 0.615 0.161 0.078 77 10.2 G_temporal_middle 360 250 407 1.769 0.504 0.120 0.025 2 0.5 Lat_Fis-ant-Horizont 142 104 234 2.373 0.567 0.120 0.042 1 0.2 Lat_Fis-ant-Vertical 1676 1119 2098 2.141 0.642 0.123 0.067 26 5.9 Lat_Fis-post 3058 1859 3753 1.801 0.504 0.157 0.062 49 7.9 Pole_occipital 1847 1246 4732 2.756 0.694 0.158 0.091 40 5.6 Pole_temporal 2355 1582 2263 1.570 0.527 0.142 0.049 28 4.9 S_calcarine 3250 2267 3426 1.649 0.552 0.116 0.033 20 4.7 S_central 1358 952 1834 1.993 0.546 0.118 0.039 13 2.5 S_cingul-Marginalis 607 412 985 2.557 0.490 0.127 0.048 5 1.4 S_circular_insula_ant 1493 1035 2276 2.463 0.956 0.100 0.025 9 1.5 S_circular_insula_inf 1530 1092 2310 2.375 0.555 0.107 0.029 8 2.0 S_circular_insula_sup 677 473 1237 2.861 1.063 0.169 0.057 11 1.6 S_collat_transv_ant 453 296 430 1.582 0.429 0.164 0.063 6 1.1 S_collat_transv_post 2023 1369 2795 1.959 0.513 0.138 0.041 23 3.3 S_front_inf 2426 1657 3758 1.865 0.706 0.152 0.066 52 6.2 S_front_middle 2700 1845 3996 2.171 0.604 0.125 0.054 43 4.8 S_front_sup 548 355 632 1.964 0.448 0.134 0.042 6 0.9 S_interm_prim-Jensen 3852 2584 4664 1.863 0.465 0.125 0.038 39 6.0 S_intrapariet_and_P_trans 475 318 730 2.394 0.579 0.158 0.060 7 1.1 S_oc_middle_and_Lunatus 1630 1094 2068 1.999 0.509 0.134 0.036 17 2.4 S_oc_sup_and_transversal 344 224 533 2.105 0.513 0.118 0.041 3 0.5 S_occipital_ant 785 548 1272 2.437 0.587 0.150 0.050 9 1.7 S_oc-temp_lat 1550 1156 2002 1.979 0.466 0.119 0.030 13 2.0 S_oc-temp_med_and_Lingual 292 201 391 1.826 0.482 0.137 0.039 4 0.5 S_orbital_lateral 1006 674 1112 1.773 0.864 0.118 0.046 12 1.6 S_orbital_med-olfact 1209 808 1821 2.066 0.642 0.153 0.068 19 3.5 S_orbital-H_Shaped 2214 1427 2253 1.645 0.522 0.117 0.030 19 2.8 S_parieto_occipital 2234 1439 2576 1.929 0.886 0.162 0.110 183 6.7 S_pericallosal 2779 1879 3596 2.030 0.535 0.127 0.040 28 4.6 S_postcentral 1377 959 2050 2.169 0.575 0.125 0.034 11 2.0 S_precentral-inf-part 1383 936 1924 2.182 0.500 0.126 0.036 11 2.2 S_precentral-sup-part 520 354 509 1.635 0.600 0.093 0.021 3 0.5 S_suborbital 1547 1051 1900 1.863 0.496 0.145 0.052 17 3.4 S_subparietal 1685 1200 2332 2.286 0.477 0.138 0.044 18 2.9 S_temporal_inf 6498 4454 9421 2.226 0.565 0.125 0.038 74 10.4 S_temporal_sup 373 248 418 1.765 0.470 0.107 0.029 2 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Fri May 8 04:29:32 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon R01L019_MD_12m SUBJECTS_DIR is /autofs/cluster/hab/FreeSurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 4 writing volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri May 8 04:43:57 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m 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 /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject R01L019_MD_12m $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 /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject R01L019_MD_12m sysname Linux hostname compute-0-107 machine x86_64 user mlapoint atlas_icv (eTIV) = 1619216 mm^3 (det: 1.203117 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 211185 rh white matter volume 216986 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 245810.682364, pTot = 463684.781897 c = 217874.099533 rh surface-based volumes (mm3): wTot = 247013.319495, pTot = 462257.158231 c = 215243.838735 Computing SupraTentVolCor SupraTentVolCor = 57629.000 SupraTentVol = 983570.940 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 22183 22183 4 5 Left-Inf-Lat-Vent 959 959 5 7 Left-Cerebellum-White-Matter 12689 12689 6 8 Left-Cerebellum-Cortex 46359 46359 7 10 Left-Thalamus-Proper 5420 5420 8 11 Left-Caudate 3162 3162 9 12 Left-Putamen 5263 5263 10 13 Left-Pallidum 1517 1517 11 14 3rd-Ventricle 2052 2052 12 15 4th-Ventricle 3195 3195 13 16 Brain-Stem 20634 20634 14 17 Left-Hippocampus 3506 3506 15 18 Left-Amygdala 1095 1095 16 24 CSF 1962 1962 17 26 Left-Accumbens-area 472 472 18 28 Left-VentralDC 3426 3426 19 30 Left-vessel 127 127 20 31 Left-choroid-plexus 2857 2857 23 43 Right-Lateral-Ventricle 19592 19592 24 44 Right-Inf-Lat-Vent 1168 1168 25 46 Right-Cerebellum-White-Matter 12888 12888 26 47 Right-Cerebellum-Cortex 49752 49752 27 49 Right-Thalamus-Proper 5548 5548 28 50 Right-Caudate 3205 3205 29 51 Right-Putamen 4584 4584 30 52 Right-Pallidum 1370 1370 31 53 Right-Hippocampus 3440 3440 32 54 Right-Amygdala 1057 1057 33 58 Right-Accumbens-area 502 502 34 60 Right-VentralDC 3255 3255 35 62 Right-vessel 121 121 36 63 Right-choroid-plexus 3279 3279 37 72 5th-Ventricle 36 36 38 77 WM-hypointensities 5932 5932 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 51 51 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 375 375 45 251 CC_Posterior 720 720 46 252 CC_Mid_Posterior 261 261 47 253 CC_Central 359 359 48 254 CC_Mid_Anterior 336 336 49 255 CC_Anterior 603 603 Reporting on 45 segmentations SubCortGrayVol = 163567 #----------------------------------------- #@# AParc-to-ASeg Fri May 8 04:53:01 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --volmask SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 427190 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --volmask --a2009s SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 427190 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri May 8 04:56:07 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/ribbon.mgz Loading filled from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7866 vertices from left hemi Ripped 8194 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 831013 Used brute-force search on 26 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1479.000000 1 k 6.000000 2 k 4.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 1459.000000 1 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m 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 R01L019_MD_12m --surf-wm-vol --ctab /autofs/space/plato_002/users/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 R01L019_MD_12m --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-107 machine x86_64 user mlapoint atlas_icv (eTIV) = 1619216 mm^3 (det: 1.203117 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 211185 rh white matter volume 216986 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1650567 # brainmaskvolume 1650567.0 # nbrainsegvoxels 246938 # brainsegvolume 246938.0 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 2746 2746 2 3002 wm-lh-caudalanteriorcingulate 2951 2951 3 3003 wm-lh-caudalmiddlefrontal 5139 5139 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2155 2155 6 3006 wm-lh-entorhinal 628 628 7 3007 wm-lh-fusiform 5344 5344 8 3008 wm-lh-inferiorparietal 10461 10461 9 3009 wm-lh-inferiortemporal 5838 5838 10 3010 wm-lh-isthmuscingulate 4665 4665 11 3011 wm-lh-lateraloccipital 7558 7558 12 3012 wm-lh-lateralorbitofrontal 6559 6559 13 3013 wm-lh-lingual 4533 4533 14 3014 wm-lh-medialorbitofrontal 3731 3731 15 3015 wm-lh-middletemporal 4597 4597 16 3016 wm-lh-parahippocampal 1708 1708 17 3017 wm-lh-paracentral 3106 3106 18 3018 wm-lh-parsopercularis 3565 3565 19 3019 wm-lh-parsorbitalis 871 871 20 3020 wm-lh-parstriangularis 2739 2739 21 3021 wm-lh-pericalcarine 3008 3008 22 3022 wm-lh-postcentral 6587 6587 23 3023 wm-lh-posteriorcingulate 4015 4015 24 3024 wm-lh-precentral 12862 12862 25 3025 wm-lh-precuneus 9562 9562 26 3026 wm-lh-rostralanteriorcingulate 2792 2792 27 3027 wm-lh-rostralmiddlefrontal 11694 11694 28 3028 wm-lh-superiorfrontal 15170 15170 29 3029 wm-lh-superiorparietal 12530 12530 30 3030 wm-lh-superiortemporal 7937 7937 31 3031 wm-lh-supramarginal 9111 9111 32 3032 wm-lh-frontalpole 263 263 33 3033 wm-lh-temporalpole 645 645 34 3034 wm-lh-transversetemporal 1027 1027 35 3035 wm-lh-insula 9761 9761 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 2639 2639 120 4002 wm-rh-caudalanteriorcingulate 3201 3201 121 4003 wm-rh-caudalmiddlefrontal 5393 5393 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 2207 2207 124 4006 wm-rh-entorhinal 568 568 125 4007 wm-rh-fusiform 5107 5107 126 4008 wm-rh-inferiorparietal 10963 10963 127 4009 wm-rh-inferiortemporal 5779 5779 128 4010 wm-rh-isthmuscingulate 3279 3279 129 4011 wm-rh-lateraloccipital 7795 7795 130 4012 wm-rh-lateralorbitofrontal 5933 5933 131 4013 wm-rh-lingual 4700 4700 132 4014 wm-rh-medialorbitofrontal 3659 3659 133 4015 wm-rh-middletemporal 5643 5643 134 4016 wm-rh-parahippocampal 1651 1651 135 4017 wm-rh-paracentral 4298 4298 136 4018 wm-rh-parsopercularis 3218 3218 137 4019 wm-rh-parsorbitalis 1086 1086 138 4020 wm-rh-parstriangularis 2966 2966 139 4021 wm-rh-pericalcarine 2606 2606 140 4022 wm-rh-postcentral 7155 7155 141 4023 wm-rh-posteriorcingulate 4163 4163 142 4024 wm-rh-precentral 12966 12966 143 4025 wm-rh-precuneus 10563 10563 144 4026 wm-rh-rostralanteriorcingulate 2926 2926 145 4027 wm-rh-rostralmiddlefrontal 10806 10806 146 4028 wm-rh-superiorfrontal 14325 14325 147 4029 wm-rh-superiorparietal 12428 12428 148 4030 wm-rh-superiortemporal 7601 7601 149 4031 wm-rh-supramarginal 10348 10348 150 4032 wm-rh-frontalpole 380 380 151 4033 wm-rh-temporalpole 665 665 152 4034 wm-rh-transversetemporal 672 672 153 4035 wm-rh-insula 9704 9704 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 17170 17170 237 5002 Right-UnsegmentedWhiteMatter 19330 19330 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label #-------------------------------------------- #@# BA Labels lh Fri May 8 05:16:53 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA1.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 332 Checking for and removing duplicates Writing label file ./lh.BA1.label 4461 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA2.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 523 Checking for and removing duplicates Writing label file ./lh.BA2.label 8432 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3a.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 169 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4246 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3b.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 354 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6337 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4a.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 495 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6279 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4p.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 368 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4438 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA6.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1225 Checking for and removing duplicates Writing label file ./lh.BA6.label 14814 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA44.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 541 Checking for and removing duplicates Writing label file ./lh.BA44.label 4722 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA45.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1073 Checking for and removing duplicates Writing label file ./lh.BA45.label 4495 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V1.label --trgsubject R01L019_MD_12m --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1157 Checking for and removing duplicates Writing label file ./lh.V1.label 5798 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V2.label --trgsubject R01L019_MD_12m --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 2785 Checking for and removing duplicates Writing label file ./lh.V2.label 10899 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.MT.label --trgsubject R01L019_MD_12m --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 338 Checking for and removing duplicates Writing label file ./lh.MT.label 2356 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s R01L019_MD_12m --hemi lh --ctab /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label cmdline mris_label2annot --s R01L019_MD_12m --hemi lh --ctab /autofs/space/plato_002/users/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 compute-0-107 machine x86_64 user mlapoint subject R01L019_MD_12m hemi lh SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer ColorTable /autofs/space/plato_002/users/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 93604 unhit vertices Writing annot to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab R01L019_MD_12m lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /autofs/space/plato_002/users/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 1192 672 1700 1.953 0.416 0.153 0.064 25 3.5 BA1 4001 2687 5782 1.993 0.579 0.132 0.063 71 7.7 BA2 991 689 791 1.406 0.354 0.148 0.045 12 1.9 BA3a 2355 1543 2948 1.719 0.652 0.126 0.041 25 4.1 BA3b 1768 963 2742 2.481 0.501 0.128 0.126 47 4.5 BA4a 1425 910 2003 2.228 0.511 0.125 0.049 15 3.2 BA4p 9035 5873 17483 2.580 0.647 0.148 0.687 2826 32.4 BA6 2563 1674 4793 2.517 0.571 0.143 0.050 34 5.4 BA44 3513 2384 6122 2.195 0.611 0.145 0.051 51 7.6 BA45 3304 2146 3416 1.505 0.466 0.134 0.045 40 6.2 V1 8375 5228 10340 1.820 0.538 0.159 0.062 137 22.4 V2 1794 1187 2869 2.077 0.684 0.131 0.045 23 3.4 MT #-------------------------------------------- #@# BA Labels rh Fri May 8 05:19:06 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA1.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 417 Checking for and removing duplicates Writing label file ./rh.BA1.label 4379 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA2.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 609 Checking for and removing duplicates Writing label file ./rh.BA2.label 7296 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3a.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 163 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4143 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3b.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 290 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4812 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4a.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 569 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6316 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4p.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 188 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4661 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA6.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1279 Checking for and removing duplicates Writing label file ./rh.BA6.label 13535 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA44.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 815 Checking for and removing duplicates Writing label file ./rh.BA44.label 7727 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA45.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 900 Checking for and removing duplicates Writing label file ./rh.BA45.label 6255 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V1.label --trgsubject R01L019_MD_12m --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1318 Checking for and removing duplicates Writing label file ./rh.V1.label 6045 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V2.label --trgsubject R01L019_MD_12m --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 2696 Checking for and removing duplicates Writing label file ./rh.V2.label 10712 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.MT.label --trgsubject R01L019_MD_12m --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 338 Checking for and removing duplicates Writing label file ./rh.MT.label 2270 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s R01L019_MD_12m --hemi rh --ctab /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label cmdline mris_label2annot --s R01L019_MD_12m --hemi rh --ctab /autofs/space/plato_002/users/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 compute-0-107 machine x86_64 user mlapoint subject R01L019_MD_12m hemi rh SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer ColorTable /autofs/space/plato_002/users/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 98967 unhit vertices Writing annot to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab R01L019_MD_12m rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /autofs/space/plato_002/users/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 1080 542 1435 2.152 0.423 0.147 0.060 21 2.9 BA1 3576 2344 5109 2.092 0.546 0.127 0.042 42 6.1 BA2 995 697 818 1.431 0.334 0.137 0.043 9 1.8 BA3a 2174 1373 2248 1.473 0.414 0.113 0.035 22 3.4 BA3b 1647 926 2421 2.310 0.454 0.117 0.039 17 2.8 BA4a 1280 860 1878 2.233 0.485 0.125 0.046 12 2.6 BA4p 8188 4991 14833 2.497 0.637 0.148 0.102 224 32.4 BA6 3748 2569 6987 2.408 0.604 0.144 0.046 51 7.1 BA44 3910 2650 6976 2.263 0.669 0.156 0.063 69 9.5 BA45 3593 2285 3892 1.546 0.451 0.157 0.060 60 9.1 V1 7975 4973 9638 1.803 0.531 0.156 0.065 136 22.2 V2 1826 1232 3079 2.322 0.632 0.129 0.041 20 3.1 MT /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri May 8 05:21:14 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o R01L019_MD_12m label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject R01L019_MD_12m. processing subject lh.EC_average... reading output surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 880 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 R01L019_MD_12m lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 323 209 1016 3.047 0.803 0.160 0.064 6 1.1 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri May 8 05:21:32 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o R01L019_MD_12m label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject R01L019_MD_12m. processing subject rh.EC_average... reading output surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 729 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 R01L019_MD_12m rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 234 153 690 2.850 0.697 0.144 0.062 4 0.7 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s R01L019_MD_12m finished without error at Fri May 8 05:21:51 EDT 2015 New invocation of recon-all Mon May 11 17:04:02 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon2 -autorecon3 -no-isrunning -subjid R01L019_MD_12m subjid R01L019_MD_12m setenv SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-65 2.6.32-504.8.1.el6.x86_64 #1 SMP Wed Jan 28 21:11:36 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 256658 total used free shared buffers cached Mem: 32877376 6976020 25901356 168 213548 3997892 -/+ buffers/cache: 2764580 30112796 Swap: 67108860 91308 67017552 ######################################## 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: 2015/05/11-21:04:03-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/11-21:04:03-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/11-21:04:04-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:04-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:05-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:05-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:05-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:06-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:06-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:07-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:07-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:07-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:08-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:08-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:09-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:09-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:09-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:10-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:10-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:10-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:11-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:11-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:12-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:12-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:12-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:13-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:13-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:14-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:14-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:14-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:15-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:15-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/11-21:04:16-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 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: 2015/05/11-21:04:16-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:17-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:17-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:17-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/05/11-21:04:18-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: mlapoint Machine: compute-0-65 Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Mon May 11 17:04:18 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/autofs/space/plato_002/users/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 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (60, 47, 28) --> (199, 186, 201) using (106, 93, 115) as brain centroid... mean wm in atlas = 107, using box (89,76,94) --> (123, 110,136) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -7440.6 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-6.3, 7.4, -9.7): log p = -7262.037 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7171.5, old_max_log_p =-7262.0 (thresh=-7254.8) 1.000 0.000 0.000 -6.250; 0.000 1.135 0.169 -27.108; 0.000 -0.112 0.997 3.184; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7171.5, old_max_log_p =-7171.5 (thresh=-7164.3) 1.000 0.000 0.000 -6.250; 0.000 1.135 0.169 -27.108; 0.000 -0.112 0.997 3.184; 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=-7074.9, old_max_log_p =-7171.5 (thresh=-7164.3) 1.017 0.036 0.015 -12.500; -0.034 1.175 0.310 -39.218; 0.005 -0.249 0.949 25.451; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7068.7, old_max_log_p =-7074.9 (thresh=-7067.8) 0.998 0.035 0.014 -9.888; -0.034 1.175 0.310 -39.218; 0.005 -0.249 0.949 25.451; 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=-7045.8, old_max_log_p =-7068.7 (thresh=-7061.7) 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.260 0.949 29.870; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7044.5, old_max_log_p =-7045.8 (thresh=-7038.7) 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7044.5 tol 0.000010 Resulting transform: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7044.5 (old=-7440.6) transform before final EM align: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00189 0.00915 0.03215 -8.17728; -0.01774 1.16867 0.31751 -42.05781; -0.01933 -0.26064 0.94997 29.78112; 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: 010: -log(p) = 840374.6 tol 0.000000 final transform: 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 45 seconds. #-------------------------------------- #@# CA Normalize Mon May 11 17:26:03 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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 nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (60, 47, 28) --> (199, 186, 201) using (106, 93, 115) as brain centroid... mean wm in atlas = 107, using box (89,76,94) --> (123, 110,136) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 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 (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 220.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 220.0 0 of 80 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 100.0 --> 220.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 220.0 0 of 22 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 98.0 --> 220.0 0 of 18 (0.0%) samples deleted using 179 total control points for intensity normalization... bias field = 0.953 +- 0.094 0 of 179 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 205.0 0 of 102 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 205.0 0 of 136 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 205.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 205.0 5 of 50 (10.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 82.0 --> 205.0 0 of 86 (0.0%) samples deleted using 424 total control points for intensity normalization... bias field = 0.974 +- 0.055 0 of 419 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 54, 36) --> (195, 154, 201) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 199.0 0 of 181 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 53, 35) --> (130, 146, 201) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 199.0 0 of 205 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 130, 65) --> (179, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 199.0 0 of 67 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 130, 62) --> (130, 167, 119) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 199.0 0 of 80 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 119, 99) --> (145, 177, 129) Brain_Stem: limiting intensities to 76.0 --> 199.0 0 of 177 (0.0%) samples deleted using 710 total control points for intensity normalization... bias field = 0.995 +- 0.042 0 of 710 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 56 seconds. #-------------------------------------- #@# CA Reg Mon May 11 17:28:00 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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) = 1.20 (predicted orig area = 6.7) 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=0.888, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45575.086 ms 0001: dt=129.472000, rms=0.833 (6.189%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46214.992 ms 0002: dt=92.480000, rms=0.822 (1.342%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49435.105 ms 0003: dt=369.920000, rms=0.800 (2.710%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40865.453 ms 0004: dt=55.488000, rms=0.792 (0.971%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51004.902 ms 0005: dt=73.984000, rms=0.790 (0.212%), neg=0, invalid=766 0006: dt=73.984000, rms=0.787 (0.373%), neg=0, invalid=766 0007: dt=73.984000, rms=0.782 (0.602%), neg=0, invalid=766 0008: dt=73.984000, rms=0.777 (0.700%), neg=0, invalid=766 0009: dt=73.984000, rms=0.771 (0.720%), neg=0, invalid=766 0010: dt=73.984000, rms=0.766 (0.752%), neg=0, invalid=766 0011: dt=73.984000, rms=0.759 (0.834%), neg=0, invalid=766 0012: dt=73.984000, rms=0.753 (0.834%), neg=0, invalid=766 0013: dt=73.984000, rms=0.747 (0.787%), neg=0, invalid=766 0014: dt=73.984000, rms=0.742 (0.681%), neg=0, invalid=766 0015: dt=73.984000, rms=0.738 (0.576%), neg=0, invalid=766 0016: dt=73.984000, rms=0.733 (0.570%), neg=0, invalid=766 0017: dt=73.984000, rms=0.729 (0.547%), neg=0, invalid=766 0018: dt=73.984000, rms=0.726 (0.476%), neg=0, invalid=766 0019: dt=73.984000, rms=0.723 (0.420%), neg=0, invalid=766 0020: dt=73.984000, rms=0.720 (0.390%), neg=0, invalid=766 0021: dt=73.984000, rms=0.717 (0.417%), neg=0, invalid=766 0022: dt=73.984000, rms=0.714 (0.428%), neg=0, invalid=766 0023: dt=73.984000, rms=0.711 (0.389%), neg=0, invalid=766 0024: dt=73.984000, rms=0.709 (0.328%), neg=0, invalid=766 0025: dt=73.984000, rms=0.707 (0.286%), neg=0, invalid=766 0026: dt=73.984000, rms=0.705 (0.282%), neg=0, invalid=766 0027: dt=73.984000, rms=0.703 (0.284%), neg=0, invalid=766 0028: dt=73.984000, rms=0.701 (0.263%), neg=0, invalid=766 0029: dt=73.984000, rms=0.699 (0.250%), neg=0, invalid=766 0030: dt=73.984000, rms=0.698 (0.222%), neg=0, invalid=766 0031: dt=73.984000, rms=0.696 (0.223%), neg=0, invalid=766 0032: dt=73.984000, rms=0.695 (0.193%), neg=0, invalid=766 0033: dt=73.984000, rms=0.693 (0.174%), neg=0, invalid=766 0034: dt=73.984000, rms=0.692 (0.191%), neg=0, invalid=766 0035: dt=73.984000, rms=0.691 (0.185%), neg=0, invalid=766 0036: dt=73.984000, rms=0.690 (0.129%), neg=0, invalid=766 0037: dt=73.984000, rms=0.689 (0.109%), neg=0, invalid=766 0038: dt=73.984000, rms=0.688 (0.134%), neg=0, invalid=766 0039: dt=73.984000, rms=0.687 (0.136%), neg=0, invalid=766 0040: dt=73.984000, rms=0.687 (0.113%), neg=0, invalid=766 0041: dt=73.984000, rms=0.686 (0.117%), neg=0, invalid=766 0042: dt=73.984000, rms=0.685 (0.120%), neg=0, invalid=766 0043: dt=73.984000, rms=0.684 (0.124%), neg=0, invalid=766 0044: dt=73.984000, rms=0.683 (0.102%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54096.348 ms 0045: dt=443.904000, rms=0.683 (0.041%), neg=0, invalid=766 0046: dt=443.904000, rms=0.683 (-0.168%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57861.547 ms 0047: dt=92.480000, rms=0.683 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51737.047 ms 0048: dt=517.888000, rms=0.682 (0.197%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58720.480 ms 0049: dt=0.000000, rms=0.682 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.690, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50320.836 ms 0050: dt=145.152000, rms=0.681 (1.277%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43569.832 ms 0051: dt=82.944000, rms=0.672 (1.418%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52402.047 ms 0052: dt=15.552000, rms=0.669 (0.401%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42049.660 ms 0053: dt=9.072000, rms=0.668 (0.097%), neg=0, invalid=766 0054: dt=9.072000, rms=0.668 (0.051%), neg=0, invalid=766 0055: dt=9.072000, rms=0.667 (0.084%), neg=0, invalid=766 0056: dt=9.072000, rms=0.667 (0.138%), neg=0, invalid=766 0057: dt=9.072000, rms=0.665 (0.205%), neg=0, invalid=766 0058: dt=9.072000, rms=0.663 (0.300%), neg=0, invalid=766 0059: dt=9.072000, rms=0.661 (0.365%), neg=0, invalid=766 0060: dt=9.072000, rms=0.658 (0.381%), neg=0, invalid=766 0061: dt=9.072000, rms=0.656 (0.377%), neg=0, invalid=766 0062: dt=9.072000, rms=0.653 (0.363%), neg=0, invalid=766 0063: dt=9.072000, rms=0.651 (0.336%), neg=0, invalid=766 0064: dt=9.072000, rms=0.649 (0.325%), neg=0, invalid=766 0065: dt=9.072000, rms=0.647 (0.318%), neg=0, invalid=766 0066: dt=9.072000, rms=0.645 (0.333%), neg=0, invalid=766 0067: dt=9.072000, rms=0.643 (0.342%), neg=0, invalid=766 0068: dt=9.072000, rms=0.640 (0.331%), neg=0, invalid=766 0069: dt=9.072000, rms=0.639 (0.303%), neg=0, invalid=766 0070: dt=9.072000, rms=0.637 (0.278%), neg=0, invalid=766 0071: dt=9.072000, rms=0.635 (0.248%), neg=0, invalid=766 0072: dt=9.072000, rms=0.634 (0.224%), neg=0, invalid=766 0073: dt=9.072000, rms=0.632 (0.207%), neg=0, invalid=766 0074: dt=9.072000, rms=0.631 (0.207%), neg=0, invalid=766 0075: dt=9.072000, rms=0.630 (0.213%), neg=0, invalid=766 0076: dt=9.072000, rms=0.628 (0.216%), neg=0, invalid=766 0077: dt=9.072000, rms=0.627 (0.210%), neg=0, invalid=766 0078: dt=9.072000, rms=0.626 (0.192%), neg=0, invalid=766 0079: dt=9.072000, rms=0.625 (0.165%), neg=0, invalid=766 0080: dt=9.072000, rms=0.624 (0.146%), neg=0, invalid=766 0081: dt=9.072000, rms=0.623 (0.137%), neg=0, invalid=766 0082: dt=9.072000, rms=0.622 (0.131%), neg=0, invalid=766 0083: dt=9.072000, rms=0.621 (0.133%), neg=0, invalid=766 0084: dt=9.072000, rms=0.621 (0.127%), neg=0, invalid=766 0085: dt=9.072000, rms=0.620 (0.124%), neg=0, invalid=766 0086: dt=9.072000, rms=0.619 (0.115%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52295.660 ms 0087: dt=145.152000, rms=0.619 (0.079%), neg=0, invalid=766 0088: dt=145.152000, rms=0.619 (-0.859%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43750.008 ms 0089: dt=31.104000, rms=0.618 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45070.375 ms 0090: dt=9.072000, rms=0.618 (0.010%), neg=0, invalid=766 0091: dt=9.072000, rms=0.618 (0.005%), neg=0, invalid=766 0092: dt=9.072000, rms=0.618 (0.008%), neg=0, invalid=766 0093: dt=9.072000, rms=0.618 (0.001%), neg=0, invalid=766 0094: dt=9.072000, rms=0.618 (0.005%), neg=0, invalid=766 0095: dt=9.072000, rms=0.618 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50662.613 ms 0096: dt=2.800000, rms=0.644 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55496.469 ms 0097: dt=1.200000, rms=0.644 (0.004%), neg=0, invalid=766 0098: dt=1.200000, rms=0.644 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50582.895 ms 0099: dt=0.000000, rms=0.644 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50700.621 ms 0100: dt=4.924471, rms=0.704 (2.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50346.988 ms 0101: dt=1.500000, rms=0.704 (0.034%), neg=0, invalid=766 0102: dt=1.500000, rms=0.704 (-0.033%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52873.340 ms 0103: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.792, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48156.141 ms 0104: dt=1.067485, rms=0.788 (0.547%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43396.176 ms 0105: dt=0.448000, rms=0.785 (0.284%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49841.832 ms 0106: dt=1.944444, rms=0.781 (0.524%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47960.277 ms 0107: dt=1.024000, rms=0.781 (0.083%), neg=0, invalid=766 0108: dt=1.024000, rms=0.780 (0.081%), neg=0, invalid=766 0109: dt=1.024000, rms=0.780 (-0.024%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.780, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39740.012 ms 0110: dt=1.055118, rms=0.779 (0.124%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37793.234 ms 0111: dt=0.000000, rms=0.779 (0.003%), neg=0, invalid=766 0112: dt=0.100000, rms=0.779 (-0.006%), 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=0.715, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37993.531 ms 0113: dt=0.448000, rms=0.696 (2.770%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33689.488 ms 0114: dt=0.000000, rms=0.696 (0.004%), neg=0, invalid=766 0115: dt=0.050000, rms=0.696 (-0.356%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.696, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40157.059 ms 0116: dt=0.000000, rms=0.696 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13333 (21) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2829 voxels, overlap=0.355) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2829 voxels, peak = 18), gca=18.0 gca peak = 0.14022 (22) mri peak = 0.13267 (22) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2037 voxels, overlap=0.666) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2037 voxels, peak = 19), gca=19.2 gca peak = 0.24234 (100) mri peak = 0.09976 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (414 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (414 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.10552 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (414 voxels, overlap=0.516) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (414 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.06384 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (829 voxels, overlap=0.039) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (829 voxels, peak = 72), gca=72.4 gca peak = 0.29892 (64) mri peak = 0.05544 (74) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (733 voxels, overlap=0.177) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (733 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.08450 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68273 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68273 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.07787 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (65634 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (65634 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03394 (67) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (25796 voxels, overlap=0.726) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (25796 voxels, peak = 69), gca=69.3 gca peak = 0.13270 (63) mri peak = 0.03150 (79) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (26474 voxels, overlap=0.251) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (26474 voxels, peak = 76), gca=75.6 gca peak = 0.15182 (70) mri peak = 0.13176 (79) Right_Caudate (50): linear fit = 1.12 x + 0.0 (490 voxels, overlap=0.203) Right_Caudate (50): linear fit = 1.12 x + 0.0 (490 voxels, peak = 79), gca=78.8 gca peak = 0.14251 (76) mri peak = 0.11433 (86) Left_Caudate (11): linear fit = 1.05 x + 0.0 (618 voxels, overlap=0.614) Left_Caudate (11): linear fit = 1.05 x + 0.0 (618 voxels, peak = 80), gca=79.8 gca peak = 0.12116 (60) mri peak = 0.04418 (68) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20345 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20345 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04208 (68) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (26188 voxels, overlap=0.511) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (26188 voxels, peak = 69), gca=68.6 gca peak = 0.22684 (88) mri peak = 0.08690 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9996 voxels, overlap=0.769) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9996 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.09166 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9090 voxels, overlap=0.730) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9090 voxels, peak = 91), gca=91.3 gca peak = 0.25455 (62) mri peak = 0.08278 (76) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (302 voxels, overlap=0.402) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (302 voxels, peak = 71), gca=71.3 gca peak = 0.39668 (62) mri peak = 0.09286 (79) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (281 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (281 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.06250 (103) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4632 voxels, overlap=0.868) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4632 voxels, peak = 98), gca=97.6 gca peak = 0.12071 (89) mri peak = 0.06557 (100) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3814 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3814 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.05669 (88) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2791 voxels, overlap=0.780) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2791 voxels, peak = 90), gca=90.2 gca peak = 0.15214 (84) mri peak = 0.07075 (88) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2669 voxels, overlap=0.675) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2669 voxels, peak = 90), gca=90.3 gca peak = 0.08983 (85) mri peak = 0.08257 (93) Brain_Stem (16): linear fit = 1.08 x + 0.0 (11867 voxels, overlap=0.741) Brain_Stem (16): linear fit = 1.08 x + 0.0 (11867 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.10567 (99) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1055 voxels, overlap=0.237) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1055 voxels, peak = 101), gca=101.2 gca peak = 0.12914 (94) mri peak = 0.08736 (102) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1148 voxels, overlap=0.513) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1148 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) mri peak = 0.10485 (23) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (68 voxels, overlap=0.192) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (68 voxels, peak = 25), gca=25.2 gca peak = 0.13542 (27) mri peak = 0.10496 (23) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (548 voxels, overlap=0.558) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (548 voxels, peak = 22), gca=22.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) 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 1.16 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.79 x + 0.0 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=0.735, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42017.969 ms 0117: dt=92.480000, rms=0.726 (1.254%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46040.359 ms 0118: dt=92.480000, rms=0.724 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43567.410 ms 0119: dt=129.472000, rms=0.719 (0.768%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42859.645 ms 0120: dt=32.368000, rms=0.718 (0.049%), neg=0, invalid=766 0121: dt=32.368000, rms=0.718 (0.069%), neg=0, invalid=766 0122: dt=32.368000, rms=0.717 (0.109%), neg=0, invalid=766 0123: dt=32.368000, rms=0.716 (0.163%), neg=0, invalid=766 0124: dt=32.368000, rms=0.714 (0.226%), neg=0, invalid=766 0125: dt=32.368000, rms=0.713 (0.252%), neg=0, invalid=766 0126: dt=32.368000, rms=0.711 (0.234%), neg=0, invalid=766 0127: dt=32.368000, rms=0.710 (0.199%), neg=0, invalid=766 0128: dt=32.368000, rms=0.708 (0.185%), neg=0, invalid=766 0129: dt=32.368000, rms=0.707 (0.178%), neg=0, invalid=766 0130: dt=32.368000, rms=0.706 (0.186%), neg=0, invalid=766 0131: dt=32.368000, rms=0.704 (0.206%), neg=0, invalid=766 0132: dt=32.368000, rms=0.702 (0.241%), neg=0, invalid=766 0133: dt=32.368000, rms=0.701 (0.251%), neg=0, invalid=766 0134: dt=32.368000, rms=0.699 (0.263%), neg=0, invalid=766 0135: dt=32.368000, rms=0.697 (0.247%), neg=0, invalid=766 0136: dt=32.368000, rms=0.695 (0.256%), neg=0, invalid=766 0137: dt=32.368000, rms=0.694 (0.240%), neg=0, invalid=766 0138: dt=32.368000, rms=0.692 (0.222%), neg=0, invalid=766 0139: dt=32.368000, rms=0.691 (0.202%), neg=0, invalid=766 0140: dt=32.368000, rms=0.689 (0.183%), neg=0, invalid=766 0141: dt=32.368000, rms=0.688 (0.180%), neg=0, invalid=766 0142: dt=32.368000, rms=0.687 (0.174%), neg=0, invalid=766 0143: dt=32.368000, rms=0.686 (0.177%), neg=0, invalid=766 0144: dt=32.368000, rms=0.685 (0.191%), neg=0, invalid=766 0145: dt=32.368000, rms=0.683 (0.170%), neg=0, invalid=766 0146: dt=32.368000, rms=0.682 (0.186%), neg=0, invalid=766 0147: dt=32.368000, rms=0.681 (0.152%), neg=0, invalid=766 0148: dt=32.368000, rms=0.680 (0.160%), neg=0, invalid=766 0149: dt=32.368000, rms=0.679 (0.144%), neg=0, invalid=766 0150: dt=32.368000, rms=0.678 (0.122%), neg=0, invalid=766 0151: dt=32.368000, rms=0.677 (0.115%), neg=0, invalid=766 0152: dt=32.368000, rms=0.677 (0.126%), neg=0, invalid=766 0153: dt=32.368000, rms=0.676 (0.123%), neg=0, invalid=766 0154: dt=32.368000, rms=0.675 (0.125%), neg=0, invalid=766 0155: dt=32.368000, rms=0.674 (0.122%), neg=0, invalid=766 0156: dt=32.368000, rms=0.673 (0.127%), neg=0, invalid=766 0157: dt=32.368000, rms=0.672 (0.122%), neg=0, invalid=766 0158: dt=32.368000, rms=0.672 (0.122%), neg=0, invalid=766 0159: dt=32.368000, rms=0.671 (0.113%), neg=0, invalid=766 0160: dt=32.368000, rms=0.670 (0.103%), neg=0, invalid=766 0161: dt=32.368000, rms=0.669 (0.097%), neg=0, invalid=766 0162: dt=32.368000, rms=0.669 (0.092%), neg=0, invalid=766 0163: dt=32.368000, rms=0.668 (0.090%), neg=0, invalid=766 0164: dt=32.368000, rms=0.668 (0.082%), neg=0, invalid=766 0165: dt=32.368000, rms=0.667 (0.081%), neg=0, invalid=766 0166: dt=32.368000, rms=0.667 (0.085%), neg=0, invalid=766 0167: dt=32.368000, rms=0.666 (0.086%), neg=0, invalid=766 0168: dt=32.368000, rms=0.665 (0.085%), neg=0, invalid=766 0169: dt=32.368000, rms=0.665 (0.073%), neg=0, invalid=766 0170: dt=32.368000, rms=0.664 (0.071%), neg=0, invalid=766 0171: dt=32.368000, rms=0.664 (0.066%), neg=0, invalid=766 0172: dt=32.368000, rms=0.664 (0.070%), neg=0, invalid=766 0173: dt=32.368000, rms=0.663 (0.071%), neg=0, invalid=766 0174: dt=32.368000, rms=0.663 (0.070%), neg=0, invalid=766 0175: dt=32.368000, rms=0.662 (0.066%), neg=0, invalid=766 0176: dt=32.368000, rms=0.662 (0.058%), neg=0, invalid=766 0177: dt=32.368000, rms=0.661 (0.052%), neg=0, invalid=766 0178: dt=32.368000, rms=0.661 (0.056%), neg=0, invalid=766 0179: dt=32.368000, rms=0.661 (0.061%), neg=0, invalid=766 0180: dt=32.368000, rms=0.660 (0.063%), neg=0, invalid=766 0181: dt=32.368000, rms=0.660 (0.057%), neg=0, invalid=766 0182: dt=32.368000, rms=0.660 (0.052%), neg=0, invalid=766 0183: dt=32.368000, rms=0.659 (0.047%), neg=0, invalid=766 0184: dt=32.368000, rms=0.659 (0.050%), neg=0, invalid=766 0185: dt=32.368000, rms=0.659 (0.051%), neg=0, invalid=766 0186: dt=32.368000, rms=0.658 (0.052%), neg=0, invalid=766 0187: dt=32.368000, rms=0.658 (0.050%), neg=0, invalid=766 0188: dt=32.368000, rms=0.658 (0.046%), neg=0, invalid=766 0189: dt=32.368000, rms=0.657 (0.040%), neg=0, invalid=766 0190: dt=32.368000, rms=0.657 (0.036%), neg=0, invalid=766 0191: dt=32.368000, rms=0.657 (0.039%), neg=0, invalid=766 0192: dt=32.368000, rms=0.657 (0.041%), neg=0, invalid=766 0193: dt=32.368000, rms=0.656 (0.045%), neg=0, invalid=766 0194: dt=32.368000, rms=0.656 (0.046%), neg=0, invalid=766 0195: dt=32.368000, rms=0.656 (0.047%), neg=0, invalid=766 0196: dt=32.368000, rms=0.655 (0.042%), neg=0, invalid=766 0197: dt=32.368000, rms=0.655 (0.034%), neg=0, invalid=766 0198: dt=32.368000, rms=0.655 (0.028%), neg=0, invalid=766 0199: dt=32.368000, rms=0.655 (0.030%), neg=0, invalid=766 0200: dt=32.368000, rms=0.655 (0.033%), neg=0, invalid=766 0201: dt=32.368000, rms=0.654 (0.035%), neg=0, invalid=766 0202: dt=32.368000, rms=0.654 (0.033%), neg=0, invalid=766 0203: dt=32.368000, rms=0.654 (0.034%), neg=0, invalid=766 0204: dt=32.368000, rms=0.654 (0.036%), neg=0, invalid=766 0205: dt=32.368000, rms=0.653 (0.034%), neg=0, invalid=766 0206: dt=32.368000, rms=0.653 (0.028%), neg=0, invalid=766 0207: dt=32.368000, rms=0.653 (0.027%), neg=0, invalid=766 0208: dt=32.368000, rms=0.653 (0.030%), neg=0, invalid=766 0209: dt=32.368000, rms=0.653 (0.031%), neg=0, invalid=766 0210: dt=32.368000, rms=0.652 (0.029%), neg=0, invalid=766 0211: dt=32.368000, rms=0.652 (0.029%), neg=0, invalid=766 0212: dt=32.368000, rms=0.652 (0.027%), neg=0, invalid=766 0213: dt=32.368000, rms=0.652 (0.025%), neg=0, invalid=766 0214: dt=32.368000, rms=0.652 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41771.004 ms 0215: dt=1775.616000, rms=0.651 (0.089%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39322.590 ms 0216: dt=32.368000, rms=0.651 (0.025%), neg=0, invalid=766 0217: dt=32.368000, rms=0.651 (0.009%), neg=0, invalid=766 0218: dt=32.368000, rms=0.651 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42047.043 ms 0219: dt=110.976000, rms=0.651 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41763.488 ms 0220: dt=517.888000, rms=0.649 (0.258%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36897.508 ms 0221: dt=0.000000, rms=0.649 (-0.004%), neg=0, invalid=766 0222: dt=0.850000, rms=0.649 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36876.805 ms 0223: dt=103.680000, rms=0.644 (0.970%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36893.621 ms 0224: dt=36.288000, rms=0.637 (1.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34461.000 ms 0225: dt=20.736000, rms=0.636 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36974.812 ms 0226: dt=103.680000, rms=0.628 (1.288%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32017.148 ms 0227: dt=1.620000, rms=0.628 (0.004%), neg=0, invalid=766 0228: dt=0.101250, rms=0.627 (0.002%), neg=0, invalid=766 0229: dt=0.050625, rms=0.627 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24688.982 ms 0230: dt=0.035437, rms=0.627 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24672.762 ms 0231: dt=0.035437, rms=0.627 (0.000%), neg=0, invalid=766 0232: dt=0.017719, rms=0.627 (0.000%), neg=0, invalid=766 0233: dt=0.004430, rms=0.627 (0.000%), neg=0, invalid=766 0234: dt=0.002215, rms=0.627 (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=0.634, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17371.809 ms 0235: dt=0.000000, rms=0.634 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17415.154 ms 0236: dt=0.000000, rms=0.634 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17366.582 ms 0237: dt=0.000000, rms=0.634 (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=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17401.482 ms 0238: dt=0.000000, rms=0.655 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17380.756 ms 0239: dt=0.000000, rms=0.655 (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=0.697, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36923.664 ms 0240: dt=1.280000, rms=0.677 (2.909%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34442.898 ms 0241: dt=0.448000, rms=0.672 (0.701%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34446.496 ms 0242: dt=0.448000, rms=0.668 (0.617%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36889.348 ms 0243: dt=1.792000, rms=0.654 (2.175%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36886.488 ms 0244: dt=1.792000, rms=0.645 (1.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37030.898 ms 0245: dt=1.792000, rms=0.640 (0.856%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36917.754 ms 0246: dt=1.792000, rms=0.636 (0.621%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36924.023 ms 0247: dt=1.792000, rms=0.633 (0.485%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36913.996 ms 0248: dt=1.792000, rms=0.630 (0.394%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41518.355 ms 0249: dt=5.120000, rms=0.624 (0.920%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37160.465 ms 0250: dt=1.792000, rms=0.623 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36905.492 ms 0251: dt=1.792000, rms=0.622 (0.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36980.094 ms 0252: dt=1.792000, rms=0.621 (0.187%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37004.883 ms 0253: dt=1.792000, rms=0.620 (0.164%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36987.340 ms 0254: dt=5.120000, rms=0.617 (0.426%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36914.449 ms 0255: dt=1.792000, rms=0.616 (0.119%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37748.664 ms 0256: dt=1.792000, rms=0.616 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36916.473 ms 0257: dt=5.000000, rms=0.614 (0.280%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37010.766 ms 0258: dt=1.280000, rms=0.613 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36952.035 ms 0259: dt=3.500000, rms=0.612 (0.163%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36963.395 ms 0260: dt=1.792000, rms=0.612 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37274.590 ms 0261: dt=5.120000, rms=0.611 (0.188%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34540.906 ms 0262: dt=0.458333, rms=0.611 (0.011%), neg=0, invalid=766 0263: dt=0.458333, rms=0.611 (0.023%), neg=0, invalid=766 0264: dt=0.458333, rms=0.611 (0.018%), neg=0, invalid=766 0265: dt=0.458333, rms=0.610 (0.029%), neg=0, invalid=766 0266: dt=0.458333, rms=0.610 (0.038%), neg=0, invalid=766 0267: dt=0.458333, rms=0.610 (0.048%), neg=0, invalid=766 0268: dt=0.458333, rms=0.609 (0.059%), neg=0, invalid=766 0269: dt=0.458333, rms=0.609 (0.063%), neg=0, invalid=766 0270: dt=0.458333, rms=0.609 (0.070%), neg=0, invalid=766 0271: dt=0.458333, rms=0.608 (0.070%), neg=0, invalid=766 0272: dt=0.458333, rms=0.608 (0.070%), neg=0, invalid=766 0273: dt=0.458333, rms=0.607 (0.072%), neg=0, invalid=766 0274: dt=0.458333, rms=0.607 (0.070%), neg=0, invalid=766 0275: dt=0.458333, rms=0.607 (0.068%), neg=0, invalid=766 0276: dt=0.458333, rms=0.606 (0.061%), neg=0, invalid=766 0277: dt=0.458333, rms=0.606 (0.057%), neg=0, invalid=766 0278: dt=0.458333, rms=0.605 (0.054%), neg=0, invalid=766 0279: dt=0.458333, rms=0.605 (0.050%), neg=0, invalid=766 0280: dt=0.458333, rms=0.605 (0.043%), neg=0, invalid=766 0281: dt=0.458333, rms=0.605 (0.042%), neg=0, invalid=766 0282: dt=0.458333, rms=0.604 (0.038%), neg=0, invalid=766 0283: dt=0.458333, rms=0.604 (0.033%), neg=0, invalid=766 0284: dt=0.458333, rms=0.604 (0.032%), neg=0, invalid=766 0285: dt=0.458333, rms=0.604 (0.032%), neg=0, invalid=766 0286: dt=0.458333, rms=0.604 (0.033%), neg=0, invalid=766 0287: dt=0.458333, rms=0.603 (0.028%), neg=0, invalid=766 0288: dt=0.458333, rms=0.603 (0.032%), neg=0, invalid=766 0289: dt=0.458333, rms=0.603 (0.032%), neg=0, invalid=766 0290: dt=0.458333, rms=0.603 (0.035%), neg=0, invalid=766 0291: dt=0.458333, rms=0.603 (0.033%), neg=0, invalid=766 0292: dt=0.458333, rms=0.602 (0.033%), neg=0, invalid=766 0293: dt=0.458333, rms=0.602 (0.034%), neg=0, invalid=766 0294: dt=0.458333, rms=0.602 (0.035%), neg=0, invalid=766 0295: dt=0.458333, rms=0.602 (0.034%), neg=0, invalid=766 0296: dt=0.458333, rms=0.602 (0.033%), neg=0, invalid=766 0297: dt=0.458333, rms=0.601 (0.032%), neg=0, invalid=766 0298: dt=0.458333, rms=0.601 (0.031%), neg=0, invalid=766 0299: dt=0.458333, rms=0.601 (0.035%), neg=0, invalid=766 0300: dt=0.458333, rms=0.601 (0.034%), neg=0, invalid=766 0301: dt=0.458333, rms=0.601 (0.032%), neg=0, invalid=766 0302: dt=0.458333, rms=0.601 (0.031%), neg=0, invalid=766 0303: dt=0.458333, rms=0.600 (0.031%), neg=0, invalid=766 0304: dt=0.458333, rms=0.600 (0.030%), neg=0, invalid=766 0305: dt=0.458333, rms=0.600 (0.030%), neg=0, invalid=766 0306: dt=0.458333, rms=0.600 (0.032%), neg=0, invalid=766 0307: dt=0.458333, rms=0.600 (0.028%), neg=0, invalid=766 0308: dt=0.458333, rms=0.599 (0.026%), neg=0, invalid=766 0309: dt=0.458333, rms=0.599 (0.029%), neg=0, invalid=766 0310: dt=0.458333, rms=0.599 (0.027%), neg=0, invalid=766 0311: dt=0.458333, rms=0.599 (0.025%), neg=0, invalid=766 0312: dt=0.458333, rms=0.599 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36912.062 ms 0313: dt=7.168000, rms=0.599 (0.018%), neg=0, invalid=766 0314: dt=1.792000, rms=0.599 (0.009%), neg=0, invalid=766 0315: dt=1.792000, rms=0.599 (0.002%), neg=0, invalid=766 0316: dt=1.792000, rms=0.599 (0.021%), neg=0, invalid=766 0317: dt=1.792000, rms=0.598 (0.011%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36817.332 ms 0318: dt=1.792000, rms=0.598 (0.155%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39244.219 ms 0319: dt=4.563380, rms=0.597 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34425.770 ms 0320: dt=0.000000, rms=0.597 (-0.009%), neg=0, invalid=766 0321: dt=0.100000, rms=0.597 (-0.001%), 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=0.581, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34688.414 ms 0322: dt=0.175373, rms=0.573 (1.500%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34351.020 ms 0323: dt=0.149332, rms=0.567 (0.920%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36807.242 ms 0324: dt=0.320000, rms=0.559 (1.532%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34317.992 ms 0325: dt=0.112000, rms=0.557 (0.311%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34411.199 ms 0326: dt=0.112000, rms=0.555 (0.271%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34411.996 ms 0327: dt=0.112000, rms=0.554 (0.242%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36914.266 ms 0328: dt=0.384000, rms=0.550 (0.737%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36819.957 ms 0329: dt=0.384000, rms=0.547 (0.497%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31941.281 ms 0330: dt=0.028000, rms=0.547 (0.029%), neg=0, invalid=766 0331: dt=0.028000, rms=0.547 (0.027%), neg=0, invalid=766 0332: dt=0.028000, rms=0.547 (0.052%), neg=0, invalid=766 0333: dt=0.028000, rms=0.546 (0.072%), neg=0, invalid=766 0334: dt=0.028000, rms=0.546 (0.089%), neg=0, invalid=766 0335: dt=0.028000, rms=0.545 (0.103%), neg=0, invalid=766 0336: dt=0.028000, rms=0.545 (0.115%), neg=0, invalid=766 0337: dt=0.028000, rms=0.544 (0.122%), neg=0, invalid=766 0338: dt=0.028000, rms=0.543 (0.128%), neg=0, invalid=766 0339: dt=0.028000, rms=0.543 (0.135%), neg=0, invalid=766 0340: dt=0.028000, rms=0.542 (0.134%), neg=0, invalid=766 0341: dt=0.028000, rms=0.541 (0.134%), neg=0, invalid=766 0342: dt=0.028000, rms=0.540 (0.131%), neg=0, invalid=766 0343: dt=0.028000, rms=0.540 (0.127%), neg=0, invalid=766 0344: dt=0.028000, rms=0.539 (0.122%), neg=0, invalid=766 0345: dt=0.028000, rms=0.538 (0.118%), neg=0, invalid=766 0346: dt=0.028000, rms=0.538 (0.112%), neg=0, invalid=766 0347: dt=0.028000, rms=0.537 (0.106%), neg=0, invalid=766 0348: dt=0.028000, rms=0.537 (0.099%), neg=0, invalid=766 0349: dt=0.028000, rms=0.536 (0.093%), neg=0, invalid=766 0350: dt=0.028000, rms=0.536 (0.085%), neg=0, invalid=766 0351: dt=0.028000, rms=0.535 (0.078%), neg=0, invalid=766 0352: dt=0.028000, rms=0.535 (0.071%), neg=0, invalid=766 0353: dt=0.028000, rms=0.535 (0.067%), neg=0, invalid=766 0354: dt=0.028000, rms=0.534 (0.062%), neg=0, invalid=766 0355: dt=0.028000, rms=0.534 (0.057%), neg=0, invalid=766 0356: dt=0.028000, rms=0.534 (0.049%), neg=0, invalid=766 0357: dt=0.028000, rms=0.533 (0.046%), neg=0, invalid=766 0358: dt=0.028000, rms=0.533 (0.042%), neg=0, invalid=766 0359: dt=0.028000, rms=0.533 (0.039%), neg=0, invalid=766 0360: dt=0.028000, rms=0.533 (0.036%), neg=0, invalid=766 0361: dt=0.028000, rms=0.533 (0.033%), neg=0, invalid=766 0362: dt=0.028000, rms=0.533 (0.030%), neg=0, invalid=766 0363: dt=0.028000, rms=0.532 (0.026%), neg=0, invalid=766 0364: dt=0.028000, rms=0.532 (0.026%), neg=0, invalid=766 0365: dt=0.028000, rms=0.532 (0.022%), neg=0, invalid=766 0366: dt=0.028000, rms=0.532 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36896.672 ms 0367: dt=0.448000, rms=0.532 (0.014%), neg=0, invalid=766 0368: dt=0.448000, rms=0.532 (0.015%), neg=0, invalid=766 0369: dt=0.448000, rms=0.532 (0.025%), neg=0, invalid=766 0370: dt=0.224000, rms=0.532 (0.008%), neg=0, invalid=766 0371: dt=0.224000, rms=0.532 (0.009%), neg=0, invalid=766 0372: dt=0.224000, rms=0.532 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34369.203 ms 0373: dt=0.112000, rms=0.532 (0.004%), neg=0, invalid=766 0374: dt=0.112000, rms=0.532 (0.004%), neg=0, invalid=766 0375: dt=0.112000, rms=0.532 (0.007%), neg=0, invalid=766 0376: dt=0.112000, rms=0.532 (0.002%), neg=0, invalid=766 0377: dt=0.112000, rms=0.531 (0.008%), neg=0, invalid=766 0378: dt=0.112000, rms=0.531 (0.011%), neg=0, invalid=766 0379: dt=0.112000, rms=0.531 (0.013%), neg=0, invalid=766 0380: dt=0.112000, rms=0.531 (0.016%), neg=0, invalid=766 0381: dt=0.112000, rms=0.531 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34392.105 ms 0382: dt=0.112000, rms=0.530 (0.247%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36844.992 ms 0383: dt=0.448000, rms=0.526 (0.689%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31990.072 ms 0384: dt=0.000000, rms=0.526 (0.000%), neg=0, invalid=766 0385: dt=0.050000, rms=0.526 (-0.004%), 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=0.523, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41669.637 ms iter 0, gcam->neg = 33 after 42 iterations, nbhd size=2, neg = 0 0386: dt=44.800000, rms=0.496 (5.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41659.164 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0387: dt=44.800000, rms=0.489 (1.483%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44109.812 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0388: dt=10.181818, rms=0.486 (0.479%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41639.000 ms 0389: dt=11.200000, rms=0.484 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41624.086 ms 0390: dt=11.200000, rms=0.484 (0.169%), neg=0, invalid=766 0391: dt=11.200000, rms=0.482 (0.253%), neg=0, invalid=766 0392: dt=11.200000, rms=0.481 (0.343%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 69 iterations, nbhd size=3, neg = 0 0393: dt=11.200000, rms=0.479 (0.378%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24450.898 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (15.282%) 0394: dt=11.200000, rms=0.477 (0.427%), neg=0, invalid=766 0395: dt=11.200000, rms=0.476 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24257.727 ms iter 1, dt=0.008000: new neg 0, old_neg 1, delta 1, rms=0.003 (6.716%) 0396: dt=11.200000, rms=0.475 (0.164%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24275.295 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (8.849%) 0397: dt=11.200000, rms=0.475 (0.075%), neg=0, invalid=766 0398: dt=11.200000, rms=0.474 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0399: dt=11.200000, rms=0.474 (0.149%), neg=0, invalid=766 0400: dt=11.200000, rms=0.473 (0.168%), neg=0, invalid=766 0401: dt=11.200000, rms=0.472 (0.230%), neg=0, invalid=766 0402: dt=11.200000, rms=0.471 (0.247%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0403: dt=11.200000, rms=0.470 (0.225%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0404: dt=11.200000, rms=0.469 (0.222%), neg=0, invalid=766 0405: dt=11.200000, rms=0.468 (0.232%), neg=0, invalid=766 0406: dt=11.200000, rms=0.466 (0.229%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0407: dt=11.200000, rms=0.465 (0.209%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0408: dt=11.200000, rms=0.465 (0.183%), neg=0, invalid=766 0409: dt=11.200000, rms=0.464 (0.189%), neg=0, invalid=766 0410: dt=11.200000, rms=0.463 (0.168%), neg=0, invalid=766 0411: dt=11.200000, rms=0.462 (0.125%), neg=0, invalid=766 0412: dt=11.200000, rms=0.462 (0.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41636.676 ms 0413: dt=11.200000, rms=0.462 (0.033%), neg=0, invalid=766 0414: dt=11.200000, rms=0.462 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41623.449 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24266.832 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.003 (10.944%) 0415: dt=44.800000, rms=0.460 (0.420%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44086.602 ms 0416: dt=8.406780, rms=0.459 (0.196%), neg=0, invalid=766 0417: dt=8.406780, rms=0.459 (0.037%), neg=0, invalid=766 0418: dt=8.406780, rms=0.458 (0.050%), neg=0, invalid=766 0419: dt=8.406780, rms=0.458 (0.123%), neg=0, invalid=766 0420: dt=8.406780, rms=0.458 (0.083%), neg=0, invalid=766 0421: dt=8.406780, rms=0.457 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41786.465 ms 0422: dt=6.400000, rms=0.457 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44117.273 ms 0423: dt=0.252000, rms=0.470 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44083.938 ms 0424: dt=0.252000, rms=0.470 (0.001%), neg=0, invalid=766 0425: dt=0.252000, rms=0.470 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44065.945 ms 0426: dt=1.008000, rms=0.470 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44059.539 ms 0427: dt=0.720000, rms=0.470 (0.005%), neg=0, invalid=766 0428: dt=0.720000, rms=0.470 (0.002%), neg=0, invalid=766 0429: dt=0.720000, rms=0.470 (-0.013%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44073.309 ms iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0430: dt=1.380783, rms=0.490 (0.414%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44075.352 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0431: dt=0.384000, rms=0.490 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0432: dt=0.384000, rms=0.490 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44089.434 ms iter 0, gcam->neg = 20 after 25 iterations, nbhd size=4, neg = 0 0433: dt=0.910180, rms=0.489 (0.130%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44060.551 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0434: dt=0.448000, rms=0.489 (0.026%), neg=0, invalid=766 0435: dt=0.448000, rms=0.489 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0436: dt=0.448000, rms=0.489 (-0.036%), 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=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44160.832 ms iter 0, gcam->neg = 916 after 19 iterations, nbhd size=2, neg = 0 0437: dt=2.188172, rms=0.425 (9.246%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44041.551 ms 0438: dt=0.000438, rms=0.425 (-0.000%), neg=0, invalid=766 0439: dt=0.000438, rms=0.425 (0.001%), neg=0, invalid=766 0440: dt=0.000438, rms=0.425 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44021.738 ms 0441: dt=0.001750, rms=0.425 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41586.531 ms 0442: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0443: dt=0.050000, rms=0.425 (-0.113%), 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=0.404, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43987.043 ms iter 0, gcam->neg = 477 after 13 iterations, nbhd size=1, neg = 0 0444: dt=0.676471, rms=0.393 (2.836%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44006.695 ms 0445: dt=0.000438, rms=0.393 (-0.003%), neg=0, invalid=766 0446: dt=0.000438, rms=0.393 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0447: dt=0.000438, rms=0.393 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44054.480 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0448: dt=0.000438, rms=0.393 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44032.098 ms 0449: dt=0.001750, rms=0.393 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44023.406 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0450: dt=0.007000, rms=0.393 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44008.625 ms iter 0, gcam->neg = 10 after 15 iterations, nbhd size=2, neg = 0 0451: dt=0.112000, rms=0.392 (0.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44028.965 ms 0452: dt=0.000438, rms=0.392 (0.006%), neg=0, invalid=766 0453: dt=0.000438, rms=0.392 (0.000%), neg=0, invalid=766 0454: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0455: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0456: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0457: dt=0.000438, rms=0.392 (0.002%), neg=0, invalid=766 0458: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0459: dt=0.000438, rms=0.392 (0.002%), neg=0, invalid=766 0460: dt=0.000438, rms=0.392 (0.003%), neg=0, invalid=766 0461: dt=0.000438, rms=0.392 (0.003%), 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=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44281.633 ms iter 0, gcam->neg = 174 after 17 iterations, nbhd size=2, neg = 0 0462: dt=0.227872, rms=0.387 (0.976%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44028.918 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0463: dt=0.001750, rms=0.387 (-0.000%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0464: dt=0.001750, rms=0.387 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0465: dt=0.001750, rms=0.387 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0466: dt=0.001750, rms=0.387 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0467: dt=0.001750, rms=0.387 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=0.001750, rms=0.387 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0469: dt=0.001750, rms=0.387 (0.018%), neg=0, invalid=766 0470: dt=0.001750, rms=0.387 (0.020%), neg=0, invalid=766 0471: dt=0.001750, rms=0.387 (0.021%), neg=0, invalid=766 0472: dt=0.001750, rms=0.387 (0.024%), neg=0, invalid=766 0473: dt=0.001750, rms=0.387 (0.025%), neg=0, invalid=766 0474: dt=0.001750, rms=0.387 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0475: dt=0.001750, rms=0.387 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0476: dt=0.001750, rms=0.386 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0477: dt=0.001750, rms=0.386 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0478: dt=0.001750, rms=0.386 (0.029%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44018.426 ms iter 0, gcam->neg = 150 after 16 iterations, nbhd size=2, neg = 0 0479: dt=0.260700, rms=0.383 (0.863%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44033.672 ms 0480: dt=0.003000, rms=0.383 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0481: dt=0.003000, rms=0.383 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0482: dt=0.003000, rms=0.383 (0.010%), neg=0, invalid=766 0483: dt=0.003000, rms=0.383 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0484: dt=0.003000, rms=0.383 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0485: dt=0.003000, rms=0.383 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0486: dt=0.003000, rms=0.382 (0.023%), neg=0, invalid=766 0487: dt=0.003000, rms=0.382 (0.026%), neg=0, invalid=766 0488: dt=0.003000, rms=0.382 (0.028%), neg=0, invalid=766 0489: dt=0.003000, rms=0.382 (0.028%), neg=0, invalid=766 0490: dt=0.003000, rms=0.382 (0.031%), neg=0, invalid=766 0491: dt=0.003000, rms=0.382 (0.030%), neg=0, invalid=766 0492: dt=0.003000, rms=0.382 (0.033%), neg=0, invalid=766 0493: dt=0.003000, rms=0.382 (0.033%), neg=0, invalid=766 0494: dt=0.003000, rms=0.382 (0.034%), neg=0, invalid=766 0495: dt=0.003000, rms=0.381 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44021.012 ms iter 0, gcam->neg = 42 after 16 iterations, nbhd size=2, neg = 0 0496: dt=0.096000, rms=0.381 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44014.078 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=0.004000, rms=0.381 (0.006%), 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=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41013.977 ms iter 0, gcam->neg = 51 after 61 iterations, nbhd size=2, neg = 0 0498: dt=11.200000, rms=0.380 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40856.727 ms iter 0, gcam->neg = 85 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30790.324 ms iter 1, dt=0.000080: new neg 0, old_neg 5, delta 5, rms=0.001 (66.649%) 0499: dt=8.000000, rms=0.380 (0.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40857.547 ms iter 0, gcam->neg = 68 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30503.398 ms iter 1, dt=0.000100: new neg 1, old_neg 9, delta 8, rms=0.002 (78.285%) gcamFindOptimalTimeStep: Complete in 24211.430 ms iter 2, dt=0.000492: new neg 0, old_neg 1, delta 1, rms=0.001 (38.753%) 0500: dt=11.200000, rms=0.380 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 200 iterations, nbhd size=4, neg = 19 starting rms=0.009, neg=19, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29259.102 ms iter 1, dt=0.000039: new neg 0, old_neg 19, delta 19, rms=0.002 (80.064%) 0501: dt=11.200000, rms=0.380 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 51 after 200 iterations, nbhd size=2, neg = 18 starting rms=0.010, neg=18, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22958.732 ms iter 1, dt=0.000039: new neg 1, old_neg 18, delta 17, rms=0.002 (75.822%) gcamFindOptimalTimeStep: Complete in 24227.080 ms iter 2, dt=0.000147: new neg 0, old_neg 1, delta 1, rms=0.002 (33.379%) 0502: dt=11.200000, rms=0.380 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 200 iterations, nbhd size=1, neg = 29 starting rms=0.012, neg=29, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22972.959 ms iter 1, dt=0.000039: new neg 1, old_neg 29, delta 28, rms=0.002 (80.780%) gcamFindOptimalTimeStep: Complete in 24272.943 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (30.218%) 0503: dt=11.200000, rms=0.380 (-0.052%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40861.656 ms iter 0, gcam->neg = 96 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.009, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30516.779 ms iter 1, dt=0.000080: new neg 0, old_neg 11, delta 11, rms=0.001 (82.801%) 0504: dt=25.600000, rms=0.378 (0.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40858.113 ms iter 0, gcam->neg = 82 after 200 iterations, nbhd size=1, neg = 14 starting rms=0.009, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23468.578 ms iter 1, dt=0.000023: new neg 1, old_neg 14, delta 13, rms=0.003 (67.479%) gcamFindOptimalTimeStep: Complete in 23173.947 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.002 (22.324%) 0505: dt=38.400000, rms=0.378 (0.214%), neg=0, invalid=766 iter 0, gcam->neg = 184 after 200 iterations, nbhd size=4, neg = 27 starting rms=0.011, neg=27, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22977.266 ms iter 1, dt=0.000031: new neg 1, old_neg 27, delta 26, rms=0.003 (67.967%) gcamFindOptimalTimeStep: Complete in 24235.479 ms iter 2, dt=0.000573: new neg 1, old_neg 1, delta 0, rms=0.001 (70.941%) gcamFindOptimalTimeStep: Complete in 22973.242 ms iter 3, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.001 (3.522%) gcamFindOptimalTimeStep: Complete in 22977.578 ms iter 4, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.001 (0.897%) gcamFindOptimalTimeStep: Complete in 22975.324 ms iter 5, dt=0.000026: new neg 1, old_neg 1, delta 0, rms=0.001 (0.434%) gcamFindOptimalTimeStep: Complete in 22975.477 ms iter 6, dt=0.000001: new neg 1, old_neg 1, delta 0, rms=0.001 (0.007%) ---------- unfolding failed - restoring original position -------------------- 0506: dt=38.400000, rms=0.378 (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=0.378, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43270.941 ms iter 0, gcam->neg = 99 after 200 iterations, nbhd size=3, neg = 20 starting rms=0.009, neg=20, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30574.846 ms iter 1, dt=0.000082: new neg 0, old_neg 20, delta 20, rms=0.002 (81.920%) 0507: dt=2.300000, rms=0.377 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43239.719 ms iter 0, gcam->neg = 93 after 200 iterations, nbhd size=4, neg = 16 starting rms=0.009, neg=16, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22975.182 ms iter 1, dt=0.000031: new neg 1, old_neg 16, delta 15, rms=0.002 (77.085%) gcamFindOptimalTimeStep: Complete in 24240.918 ms iter 2, dt=0.000149: new neg 0, old_neg 1, delta 1, rms=0.001 (35.366%) 0508: dt=2.967033, rms=0.377 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43410.008 ms iter 0, gcam->neg = 49 after 200 iterations, nbhd size=2, neg = 16 starting rms=0.009, neg=16, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23177.867 ms iter 1, dt=0.000031: new neg 1, old_neg 16, delta 15, rms=0.002 (78.879%) gcamFindOptimalTimeStep: Complete in 24426.715 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (34.891%) 0509: dt=2.123457, rms=0.376 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=4, neg = 20 starting rms=0.010, neg=20, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22982.461 ms iter 1, dt=0.000125: new neg 0, old_neg 20, delta 20, rms=0.001 (86.023%) 0510: dt=2.123457, rms=0.376 (0.084%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 200 iterations, nbhd size=1, neg = 15 starting rms=0.009, neg=15, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22964.400 ms iter 1, dt=0.000023: new neg 3, old_neg 15, delta 12, rms=0.002 (73.631%) gcamFindOptimalTimeStep: Complete in 22963.717 ms iter 2, dt=0.000009: new neg 0, old_neg 3, delta 3, rms=0.002 (19.282%) 0511: dt=2.123457, rms=0.376 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 97 after 200 iterations, nbhd size=3, neg = 15 starting rms=0.009, neg=15, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23114.236 ms iter 1, dt=0.000031: new neg 1, old_neg 15, delta 14, rms=0.002 (76.214%) gcamFindOptimalTimeStep: Complete in 24466.715 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (33.252%) 0512: dt=2.123457, rms=0.375 (0.089%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=2, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23282.197 ms iter 1, dt=0.000023: new neg 0, old_neg 12, delta 12, rms=0.002 (78.154%) 0513: dt=2.123457, rms=0.375 (0.078%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43246.184 ms iter 0, gcam->neg = 59 after 200 iterations, nbhd size=4, neg = 17 starting rms=0.008, neg=17, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23269.658 ms iter 1, dt=0.000023: new neg 0, old_neg 17, delta 17, rms=0.001 (81.421%) 0514: dt=2.533333, rms=0.374 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43246.242 ms iter 0, gcam->neg = 40 after 200 iterations, nbhd size=2, neg = 7 starting rms=0.005, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22990.891 ms iter 1, dt=0.000125: new neg 0, old_neg 7, delta 7, rms=0.001 (79.015%) 0515: dt=1.932203, rms=0.374 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.005, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22962.389 ms iter 1, dt=0.000023: new neg 0, old_neg 7, delta 7, rms=0.001 (71.669%) 0516: dt=1.932203, rms=0.374 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=2, neg = 8 starting rms=0.006, neg=8, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23000.973 ms iter 1, dt=0.000023: new neg 1, old_neg 8, delta 7, rms=0.002 (71.978%) gcamFindOptimalTimeStep: Complete in 24229.154 ms iter 2, dt=0.000410: new neg 1, old_neg 1, delta 0, rms=0.001 (34.785%) gcamFindOptimalTimeStep: Complete in 24233.971 ms iter 3, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (6.807%) 0517: dt=1.932203, rms=0.373 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.006, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22974.637 ms iter 1, dt=0.000023: new neg 0, old_neg 11, delta 11, rms=0.001 (79.595%) 0518: dt=1.932203, rms=0.373 (0.086%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30530.059 ms iter 1, dt=0.000080: new neg 0, old_neg 6, delta 6, rms=0.001 (78.359%) 0519: dt=1.932203, rms=0.373 (0.080%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43464.020 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.002, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22965.076 ms iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.001 (67.313%) 0520: dt=0.112000, rms=0.374 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43245.410 ms iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22968.162 ms iter 1, dt=0.000023: new neg 0, old_neg 4, delta 4, rms=0.001 (71.974%) 0521: dt=0.263636, rms=0.374 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43306.371 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0522: dt=0.112000, rms=0.374 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23186.633 ms iter 1, dt=0.000023: new neg 1, old_neg 3, delta 2, rms=0.001 (65.878%) gcamFindOptimalTimeStep: Complete in 24429.600 ms iter 2, dt=0.000102: new neg 0, old_neg 1, delta 1, rms=0.001 (33.528%) 0523: dt=0.112000, rms=0.374 (-0.001%), 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 43246.801 ms iter 0, gcam->neg = 24 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22966.975 ms iter 1, dt=0.000023: new neg 1, old_neg 6, delta 5, rms=0.003 (45.649%) gcamFindOptimalTimeStep: Complete in 22970.189 ms iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.001 (68.645%) 0524: dt=0.448000, rms=0.374 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43261.121 ms iter 0, gcam->neg = 13 after 50 iterations, nbhd size=3, neg = 0 0525: dt=0.286765, rms=0.374 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.002, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23428.639 ms iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0526: dt=0.286765, rms=0.374 (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=0.372, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43193.906 ms iter 0, gcam->neg = 35 after 63 iterations, nbhd size=1, neg = 0 0527: dt=0.064000, rms=0.371 (0.243%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43402.555 ms iter 0, gcam->neg = 27 after 26 iterations, nbhd size=3, neg = 0 0528: dt=0.048000, rms=0.370 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 10 iterations, nbhd size=1, neg = 0 0529: dt=0.048000, rms=0.370 (0.128%), neg=0, invalid=766 iter 0, gcam->neg = 82 after 36 iterations, nbhd size=4, neg = 0 0530: dt=0.048000, rms=0.369 (0.222%), neg=0, invalid=766 iter 0, gcam->neg = 138 after 32 iterations, nbhd size=4, neg = 0 0531: dt=0.048000, rms=0.368 (0.263%), neg=0, invalid=766 iter 0, gcam->neg = 218 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23154.361 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0532: dt=0.048000, rms=0.368 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43513.996 ms 0533: dt=0.000438, rms=0.368 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43282.652 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0534: dt=0.003000, rms=0.368 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43236.562 ms 0535: dt=0.007000, rms=0.368 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43234.133 ms 0536: dt=0.000438, rms=0.368 (0.001%), 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 43223.352 ms iter 0, gcam->neg = 53 after 29 iterations, nbhd size=3, neg = 0 0537: dt=0.096000, rms=0.367 (0.290%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43244.863 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0538: dt=0.005000, rms=0.367 (0.012%), neg=0, invalid=766 0539: dt=0.005000, rms=0.367 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0540: dt=0.005000, rms=0.367 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0541: dt=0.005000, rms=0.366 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=2, neg = 0 0542: dt=0.005000, rms=0.366 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.007, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23162.072 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0543: dt=0.005000, rms=0.366 (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=0.366, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43207.883 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0544: dt=0.001250, rms=0.366 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43426.402 ms iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0545: dt=0.020000, rms=0.366 (0.074%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43227.887 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0546: dt=0.003000, rms=0.366 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0547: dt=0.003000, rms=0.366 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0548: dt=0.003000, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0549: dt=0.003000, rms=0.365 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0550: dt=0.003000, rms=0.365 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0551: dt=0.003000, rms=0.365 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0552: dt=0.003000, rms=0.365 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0553: dt=0.003000, rms=0.365 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0554: dt=0.003000, rms=0.365 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0555: dt=0.003000, rms=0.364 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0556: dt=0.003000, rms=0.364 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0557: dt=0.003000, rms=0.364 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0558: dt=0.003000, rms=0.364 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0559: dt=0.003000, rms=0.364 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0560: dt=0.003000, rms=0.363 (0.060%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.363, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43477.406 ms iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0561: dt=0.016000, rms=0.363 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43247.461 ms 0562: dt=0.001750, rms=0.363 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0563: dt=0.001750, rms=0.363 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0564: dt=0.001750, rms=0.363 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0565: dt=0.001750, rms=0.363 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0566: dt=0.001750, rms=0.363 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0567: dt=0.001750, rms=0.363 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0568: dt=0.001750, rms=0.363 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0569: dt=0.001750, rms=0.363 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0570: dt=0.001750, rms=0.363 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0571: dt=0.001750, rms=0.362 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0572: dt=0.001750, rms=0.362 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0573: dt=0.001750, rms=0.362 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 27 iterations, nbhd size=4, neg = 0 0574: dt=0.001750, rms=0.362 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0575: dt=0.001750, rms=0.362 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 10 iterations, nbhd size=1, neg = 0 0576: dt=0.001750, rms=0.362 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0577: dt=0.001750, rms=0.362 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 13 iterations, nbhd size=2, neg = 0 0578: dt=0.001750, rms=0.362 (0.039%), 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 43193.406 ms iter 0, gcam->neg = 13 after 15 iterations, nbhd size=2, neg = 0 0579: dt=0.019802, rms=0.361 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43261.234 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0580: dt=0.007000, rms=0.361 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 16 iterations, nbhd size=2, neg = 0 0581: dt=0.007000, rms=0.361 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0582: dt=0.007000, rms=0.361 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0583: dt=0.007000, rms=0.361 (0.059%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 7 iterations, nbhd size=1, neg = 0 0584: dt=0.007000, rms=0.360 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 30 iterations, nbhd size=3, neg = 0 0585: dt=0.007000, rms=0.360 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 16 iterations, nbhd size=2, neg = 0 0586: dt=0.007000, rms=0.360 (0.087%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 17 iterations, nbhd size=2, neg = 0 0587: dt=0.007000, rms=0.359 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 16 iterations, nbhd size=2, neg = 0 0588: dt=0.007000, rms=0.359 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 42 after 15 iterations, nbhd size=2, neg = 0 0589: dt=0.007000, rms=0.359 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 45 after 12 iterations, nbhd size=1, neg = 0 0590: dt=0.007000, rms=0.358 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 43 after 29 iterations, nbhd size=4, neg = 0 0591: dt=0.007000, rms=0.358 (0.070%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.358, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43225.465 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0592: dt=0.001750, rms=0.358 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43224.035 ms iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0593: dt=0.016000, rms=0.358 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43234.105 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0594: dt=0.001750, rms=0.358 (0.005%), neg=0, invalid=766 0595: dt=0.001750, rms=0.358 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0596: dt=0.001750, rms=0.358 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0597: dt=0.001750, rms=0.358 (0.013%), neg=0, invalid=766 0598: dt=0.001750, rms=0.358 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0599: dt=0.001750, rms=0.358 (0.020%), neg=0, invalid=766 0600: dt=0.001750, rms=0.358 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0601: dt=0.001750, rms=0.357 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0602: dt=0.001750, rms=0.357 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0603: dt=0.001750, rms=0.357 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0604: dt=0.001750, rms=0.357 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=2, neg = 0 0605: dt=0.001750, rms=0.357 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0606: dt=0.001750, rms=0.357 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0607: dt=0.001750, rms=0.357 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0608: dt=0.001750, rms=0.357 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0609: dt=0.001750, rms=0.357 (0.031%), 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 6 hours, 33 minutes and 50 seconds. #-------------------------------------- #@# CA Reg Inv Tue May 12 00:01:50 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 00:03:01 EDT 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/autofs/space/plato_002/users/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... 11143983 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 18 seconds. #-------------------------------------- #@# SkullLTA Tue May 12 00:04:19 EDT 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /autofs/space/plato_002/users/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 '/autofs/space/plato_002/users/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=17.0 skull bounding box = (49, 27, 19) --> (212, 211, 234) using (103, 88, 127) as brain centroid... mean wm in atlas = 126, using box (83,65,100) --> (123, 110,153) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10338.0, old_max_log_p =-10356.5 (thresh=-10346.1) 1.077 0.010 0.035 -18.223; -0.019 1.256 0.341 -46.795; -0.018 -0.241 0.879 43.000; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10334.6, old_max_log_p =-10338.0 (thresh=-10327.6) 1.077 0.010 0.035 -18.223; -0.017 1.277 0.224 -37.131; -0.020 -0.075 0.916 21.623; 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=-10326.3, old_max_log_p =-10334.6 (thresh=-10324.3) 1.050 -0.155 -0.026 7.557; 0.129 1.340 0.237 -64.289; 0.014 -0.079 0.932 12.067; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10323.6, old_max_log_p =-10326.3 (thresh=-10316.0) 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 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 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 004: -log(p) = 10323.4 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) 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: 006: -log(p) = 10323.4 tol 0.000010 Resulting transform: 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10323.6 (old=-10356.5) transform before final EM align: 1.052 -0.133 -0.007 2.994; 0.111 1.342 0.222 -59.591; -0.001 -0.054 0.934 12.154; 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 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05198 -0.13348 -0.00707 2.99386; 0.11096 1.34183 0.22167 -59.59058; -0.00111 -0.05413 0.93428 12.15370; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1145759.8 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) dfp_em_step_func: 008: -log(p) = 1145748.8 after pass:transform: ( 1.05, -0.13, -0.01, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.00, -0.05, 0.93, 12.15) dfp_em_step_func: 009: -log(p) = 1145747.9 after pass:transform: ( 1.06, -0.13, -0.00, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.01, -0.06, 0.93, 12.15) 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) = 1145745.4 after pass:transform: ( 1.06, -0.13, -0.00, 2.99) ( 0.11, 1.34, 0.22, -59.59) ( -0.01, -0.06, 0.93, 12.15) 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... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 1145745.4 tol 0.000000 final transform: 1.056 -0.130 -0.004 2.994; 0.110 1.342 0.221 -59.591; -0.008 -0.060 0.930 12.154; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 26 seconds. #-------------------------------------- #@# SubCort Seg Tue May 12 00:21:45 EDT 2015 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute-0-65 machine x86_64 user mlapoint 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 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 = 0.12744 (21) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (9907 voxels, overlap=0.289) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (9907 voxels, peak = 20), gca=20.2 gca peak = 0.14982 (20) mri peak = 0.12685 (22) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (8880 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (8880 voxels, peak = 18), gca=18.0 gca peak = 0.28003 (97) mri peak = 0.12997 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, overlap=0.719) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.12261 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (410 voxels, overlap=0.820) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (410 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.09091 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (986 voxels, overlap=0.240) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (986 voxels, peak = 71), gca=71.3 gca peak = 0.32745 (63) mri peak = 0.07676 (72) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (947 voxels, overlap=0.634) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (947 voxels, peak = 68), gca=67.7 gca peak = 0.08597 (105) mri peak = 0.09584 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, peak = 105), gca=105.0 gca peak = 0.09209 (106) mri peak = 0.08532 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (25445 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (25445 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.03871 (73) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (30832 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (30832 voxels, peak = 72), gca=72.4 gca peak = 0.08598 (64) mri peak = 0.03788 (75) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (34464 voxels, overlap=0.330) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (34464 voxels, peak = 77), gca=76.8 gca peak = 0.24164 (71) mri peak = 0.12527 (86) Right_Caudate (50): linear fit = 1.17 x + 0.0 (718 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.17 x + 0.0 (718 voxels, peak = 83), gca=83.4 gca peak = 0.18227 (75) mri peak = 0.13480 (83) Left_Caudate (11): linear fit = 1.08 x + 0.0 (638 voxels, overlap=0.516) Left_Caudate (11): linear fit = 1.08 x + 0.0 (638 voxels, peak = 81), gca=80.6 gca peak = 0.10629 (62) mri peak = 0.06011 (68) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (22772 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (22772 voxels, peak = 71), gca=71.3 gca peak = 0.11668 (59) mri peak = 0.05980 (68) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25748 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (25748 voxels, peak = 66), gca=66.4 gca peak = 0.17849 (88) mri peak = 0.14498 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5310 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5310 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.14210 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5270 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5270 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.10247 (77) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (281 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (281 voxels, peak = 74), gca=73.6 gca peak = 0.42394 (62) mri peak = 0.09695 (79) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (277 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (277 voxels, peak = 74), gca=74.4 gca peak = 0.10041 (96) mri peak = 0.06372 (99) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3330 voxels, overlap=0.861) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3330 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.07220 (96) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3412 voxels, overlap=0.654) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3412 voxels, peak = 95), gca=94.6 gca peak = 0.08514 (81) mri peak = 0.07251 (93) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2035 voxels, overlap=0.545) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2035 voxels, peak = 89), gca=89.1 gca peak = 0.09624 (82) mri peak = 0.08383 (90) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1503 voxels, overlap=0.585) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1503 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.08155 (93) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12416 voxels, overlap=0.733) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12416 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.11040 (103) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1017 voxels, overlap=0.184) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1017 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.09052 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1131 voxels, overlap=0.410) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1131 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.15452 (26) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (341 voxels, overlap=0.038) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (341 voxels, peak = 23), gca=23.4 gca peak = 0.26069 (23) mri peak = 0.11477 (23) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (529 voxels, overlap=0.696) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (529 voxels, peak = 22), gca=21.9 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 1.15 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.87 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16292 (21) mri peak = 0.12744 (21) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (9907 voxels, overlap=0.915) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (9907 voxels, peak = 21), gca=21.0 gca peak = 0.15073 (19) mri peak = 0.12685 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (8880 voxels, overlap=0.808) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (8880 voxels, peak = 19), gca=19.5 gca peak = 0.25294 (100) mri peak = 0.12997 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (376 voxels, peak = 102), gca=102.5 gca peak = 0.18507 (101) mri peak = 0.12261 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (410 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (410 voxels, peak = 101), gca=101.0 gca peak = 0.24928 (71) mri peak = 0.09091 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (986 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (986 voxels, peak = 71), gca=71.0 gca peak = 0.31225 (68) mri peak = 0.07676 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (947 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (947 voxels, peak = 68), gca=68.0 gca peak = 0.08621 (105) mri peak = 0.09584 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24720 voxels, peak = 105), gca=105.0 gca peak = 0.08536 (108) mri peak = 0.08532 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (25445 voxels, overlap=0.763) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (25445 voxels, peak = 108), gca=108.0 gca peak = 0.06954 (72) mri peak = 0.03871 (73) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (30832 voxels, overlap=0.877) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (30832 voxels, peak = 72), gca=72.0 gca peak = 0.07345 (76) mri peak = 0.03788 (75) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34464 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34464 voxels, peak = 76), gca=76.0 gca peak = 0.21504 (83) mri peak = 0.12527 (86) Right_Caudate (50): linear fit = 1.00 x + 0.0 (718 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (718 voxels, peak = 83), gca=83.0 gca peak = 0.16044 (80) mri peak = 0.13480 (83) Left_Caudate (11): linear fit = 1.00 x + 0.0 (638 voxels, overlap=0.866) Left_Caudate (11): linear fit = 1.00 x + 0.0 (638 voxels, peak = 80), gca=80.0 gca peak = 0.09118 (70) mri peak = 0.06011 (68) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22772 voxels, overlap=0.969) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22772 voxels, peak = 68), gca=68.2 gca peak = 0.11770 (67) mri peak = 0.05980 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25748 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25748 voxels, peak = 67), gca=67.0 gca peak = 0.16848 (92) mri peak = 0.14498 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5310 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5310 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.14210 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5270 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5270 voxels, peak = 91), gca=91.0 gca peak = 0.32099 (73) mri peak = 0.10247 (77) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (281 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (281 voxels, peak = 75), gca=74.8 gca peak = 0.34937 (75) mri peak = 0.09695 (79) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (277 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (277 voxels, peak = 77), gca=76.9 gca peak = 0.10167 (99) mri peak = 0.06372 (99) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, overlap=0.968) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, peak = 99), gca=99.0 gca peak = 0.09750 (94) mri peak = 0.07220 (96) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3412 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3412 voxels, peak = 94), gca=94.0 gca peak = 0.08039 (91) mri peak = 0.07251 (93) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2035 voxels, overlap=0.903) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2035 voxels, peak = 91), gca=91.0 gca peak = 0.09054 (83) mri peak = 0.08383 (90) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1503 voxels, overlap=0.888) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1503 voxels, peak = 83), gca=83.0 gca peak = 0.07244 (90) mri peak = 0.08155 (93) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12416 voxels, overlap=0.833) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12416 voxels, peak = 90), gca=90.0 gca peak = 0.12058 (104) mri peak = 0.11040 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1017 voxels, overlap=0.778) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1017 voxels, peak = 104), gca=104.0 gca peak = 0.15598 (99) mri peak = 0.09052 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1131 voxels, overlap=0.873) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1131 voxels, peak = 99), gca=99.0 gca peak = 0.21185 (31) mri peak = 0.15452 (26) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (341 voxels, overlap=0.380) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (341 voxels, peak = 23), gca=23.2 gca peak = 0.20373 (22) mri peak = 0.11477 (23) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (529 voxels, overlap=0.776) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (529 voxels, peak = 21), gca=21.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26811 (38) gca peak CSF = 0.18566 (33) gca peak Left_Accumbens_area = 0.57937 (75) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.25693 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (37) gca peak WM_hypointensities = 0.15176 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34486 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 Right_Pallidum too bright - rescaling by 1.008 (from 1.025) to 103.3 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 26382 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 362 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 80783 changed. image ll: -2.243, PF=1.000 pass 2: 11402 changed. image ll: -2.241, PF=1.000 pass 3: 3810 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 29 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/cc_up.lta R01L019_MD_12m will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/norm.mgz 7726 voxels in left wm, 18659 in right wm, xrange [126, 132] searching rotation angles z=[-9 5], y=[-5 9] searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 global minimum found at slice 130.0, rotations (1.85, -1.36) final transformation (x=130.0, yr=1.848, zr=-1.364): 0.999 0.024 0.032 -7.564; -0.024 1.000 -0.001 27.199; -0.032 0.000 0.999 33.245; 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 128 132 125 eigenvectors: 0.000 -0.002 1.000; -0.094 -0.996 -0.002; 0.996 -0.094 -0.000; writing aseg with callosum to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Tue May 12 00:41:56 EDT 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 12 00:41:56 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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... 1612 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 3 minutes and 41 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 108 gm peak at 76 (76), valley at 57 (57) csf peak at 21, setting threshold to 57 white matter peak found at 111 white matter peak found at 109 gm peak at 77 (77), valley at 44 (44) csf peak at 21, setting threshold to 58 #-------------------------------------------- #@# Mask BFS Tue May 12 00:45:39 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1647048 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue May 12 00:45:41 EDT 2015 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-65 machine x86_64 user mlapoint 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 135 values in range Counting number of voxels Found 135 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-65 machine x86_64 user mlapoint 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 2 values in range Counting number of voxels Found 2 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 2 deletes, 135 fills cp wm.mgz wm.seg.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 (104.0): 104.5 +- 5.7 [80.0 --> 125.0] GM (73.0) : 69.9 +- 11.8 [30.0 --> 96.0] setting bottom of white matter range to 81.7 setting top of gray matter range to 93.5 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... 5164 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4482 filled 2957 bright non-wm voxels segmented. 3418 diagonally connected voxels added... white matter segmentation took 1.9 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.47 minutes reading wm segmentation from wm.seg.mgz... 116 voxels added to wm to prevent paths from MTL structures to cortex 3099 additional wm voxels added 0 additional wm voxels added SEG EDIT: 88266 voxels turned on, 51981 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 13 found - 13 modified | TOTAL: 31 pass 2 (xy-): 0 found - 13 modified | TOTAL: 31 pass 1 (yz+): 12 found - 12 modified | TOTAL: 43 pass 2 (yz+): 0 found - 12 modified | TOTAL: 43 pass 1 (yz-): 15 found - 15 modified | TOTAL: 58 pass 2 (yz-): 0 found - 15 modified | TOTAL: 58 pass 1 (xz+): 20 found - 20 modified | TOTAL: 78 pass 2 (xz+): 0 found - 20 modified | TOTAL: 78 pass 1 (xz-): 23 found - 23 modified | TOTAL: 101 pass 2 (xz-): 0 found - 23 modified | TOTAL: 101 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 10 found - 10 modified | TOTAL: 22 pass 2 (+++): 0 found - 10 modified | TOTAL: 22 pass 1 (+++): 4 found - 4 modified | TOTAL: 26 pass 2 (+++): 0 found - 4 modified | TOTAL: 26 Iteration Number : 1 pass 1 (++): 58 found - 58 modified | TOTAL: 58 pass 2 (++): 0 found - 58 modified | TOTAL: 58 pass 1 (+-): 78 found - 78 modified | TOTAL: 136 pass 2 (+-): 0 found - 78 modified | TOTAL: 136 pass 1 (--): 78 found - 78 modified | TOTAL: 214 pass 2 (--): 1 found - 79 modified | TOTAL: 215 pass 3 (--): 0 found - 79 modified | TOTAL: 215 pass 1 (-+): 74 found - 74 modified | TOTAL: 289 pass 2 (-+): 0 found - 74 modified | TOTAL: 289 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 4 found - 4 modified | TOTAL: 11 pass 2 (xz+): 0 found - 4 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 4 found - 4 modified | TOTAL: 5 pass 2 (+-): 0 found - 4 modified | TOTAL: 5 pass 1 (--): 1 found - 1 modified | TOTAL: 6 pass 2 (--): 0 found - 1 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 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 = 438 (out of 532267: 0.082290) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 135 WM ON voxels kept 2 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue May 12 00:48:20 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.002 0.009 0.032 -8.177; -0.018 1.169 0.318 -42.058; -0.019 -0.261 0.950 29.781; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1144 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 118, 155), TAL = (2.0, 27.0, 10.0) talairach voxel to voxel transform 0.997 -0.014 -0.029 8.418; 0.009 0.796 -0.266 41.493; 0.023 0.218 0.979 -19.794; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 118, 155) --> (2.0, 27.0, 10.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 27.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 10.00) SRC: (109.95, 95.12, 160.15) search lh wm seed point around talairach space (-16.00, 27.00, 10.00), SRC: (145.85, 95.44, 160.97) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue May 12 00:49:12 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 2 found - 2 modified | TOTAL: 2 pass 2 (yz-): 0 found - 2 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 252340: 0.001585) 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 40: 348 vertices, 419 faces slice 50: 5821 vertices, 6092 faces slice 60: 14572 vertices, 14949 faces slice 70: 25713 vertices, 26063 faces slice 80: 36483 vertices, 36877 faces slice 90: 46541 vertices, 46922 faces slice 100: 57575 vertices, 57972 faces slice 110: 69154 vertices, 69565 faces slice 120: 79819 vertices, 80224 faces slice 130: 90013 vertices, 90389 faces slice 140: 99509 vertices, 99888 faces slice 150: 108427 vertices, 108782 faces slice 160: 115764 vertices, 116049 faces slice 170: 122492 vertices, 122780 faces slice 180: 128475 vertices, 128713 faces slice 190: 132840 vertices, 133019 faces slice 200: 135508 vertices, 135591 faces slice 210: 135714 vertices, 135758 faces slice 220: 135714 vertices, 135758 faces slice 230: 135714 vertices, 135758 faces slice 240: 135714 vertices, 135758 faces slice 250: 135714 vertices, 135758 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... 135714 voxel in cpt #1: X=-44 [v=135714,e=407274,f=271516] located at (-30.334742, -17.490053, 25.924223) For the whole surface: X=-44 [v=135714,e=407274,f=271516] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue May 12 00:49:21 EDT 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 00:49:25 EDT 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts avg radius = 47.8 mm, total surface area = 71923 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue May 12 00:50:09 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 0.99 +- 0.59 (0.00-->6.61) (max @ vno 103787 --> 103788) face area 0.03 +- 0.03 (-0.08-->0.60) scaling brain by 0.310... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.684, avgs=0 005/300: dt: 0.9000, rms radial error=176.424, avgs=0 010/300: dt: 0.9000, rms radial error=175.867, avgs=0 015/300: dt: 0.9000, rms radial error=175.133, avgs=0 020/300: dt: 0.9000, rms radial error=174.297, avgs=0 025/300: dt: 0.9000, rms radial error=173.401, avgs=0 030/300: dt: 0.9000, rms radial error=172.472, avgs=0 035/300: dt: 0.9000, rms radial error=171.532, avgs=0 040/300: dt: 0.9000, rms radial error=170.586, avgs=0 045/300: dt: 0.9000, rms radial error=169.646, avgs=0 050/300: dt: 0.9000, rms radial error=168.708, avgs=0 055/300: dt: 0.9000, rms radial error=167.772, avgs=0 060/300: dt: 0.9000, rms radial error=166.840, avgs=0 065/300: dt: 0.9000, rms radial error=165.911, avgs=0 070/300: dt: 0.9000, rms radial error=164.987, avgs=0 075/300: dt: 0.9000, rms radial error=164.067, avgs=0 080/300: dt: 0.9000, rms radial error=163.152, avgs=0 085/300: dt: 0.9000, rms radial error=162.242, avgs=0 090/300: dt: 0.9000, rms radial error=161.337, avgs=0 095/300: dt: 0.9000, rms radial error=160.437, avgs=0 100/300: dt: 0.9000, rms radial error=159.541, avgs=0 105/300: dt: 0.9000, rms radial error=158.651, avgs=0 110/300: dt: 0.9000, rms radial error=157.765, avgs=0 115/300: dt: 0.9000, rms radial error=156.883, avgs=0 120/300: dt: 0.9000, rms radial error=156.006, avgs=0 125/300: dt: 0.9000, rms radial error=155.134, avgs=0 130/300: dt: 0.9000, rms radial error=154.267, avgs=0 135/300: dt: 0.9000, rms radial error=153.405, avgs=0 140/300: dt: 0.9000, rms radial error=152.547, avgs=0 145/300: dt: 0.9000, rms radial error=151.693, avgs=0 150/300: dt: 0.9000, rms radial error=150.844, avgs=0 155/300: dt: 0.9000, rms radial error=150.000, avgs=0 160/300: dt: 0.9000, rms radial error=149.160, avgs=0 165/300: dt: 0.9000, rms radial error=148.324, avgs=0 170/300: dt: 0.9000, rms radial error=147.493, avgs=0 175/300: dt: 0.9000, rms radial error=146.666, avgs=0 180/300: dt: 0.9000, rms radial error=145.844, avgs=0 185/300: dt: 0.9000, rms radial error=145.026, avgs=0 190/300: dt: 0.9000, rms radial error=144.212, avgs=0 195/300: dt: 0.9000, rms radial error=143.403, avgs=0 200/300: dt: 0.9000, rms radial error=142.598, avgs=0 205/300: dt: 0.9000, rms radial error=141.798, avgs=0 210/300: dt: 0.9000, rms radial error=141.001, avgs=0 215/300: dt: 0.9000, rms radial error=140.209, avgs=0 220/300: dt: 0.9000, rms radial error=139.421, avgs=0 225/300: dt: 0.9000, rms radial error=138.638, avgs=0 230/300: dt: 0.9000, rms radial error=137.859, avgs=0 235/300: dt: 0.9000, rms radial error=137.084, avgs=0 240/300: dt: 0.9000, rms radial error=136.313, avgs=0 245/300: dt: 0.9000, rms radial error=135.546, avgs=0 250/300: dt: 0.9000, rms radial error=134.784, avgs=0 255/300: dt: 0.9000, rms radial error=134.026, avgs=0 260/300: dt: 0.9000, rms radial error=133.272, avgs=0 265/300: dt: 0.9000, rms radial error=132.522, avgs=0 270/300: dt: 0.9000, rms radial error=131.776, avgs=0 275/300: dt: 0.9000, rms radial error=131.034, avgs=0 280/300: dt: 0.9000, rms radial error=130.297, avgs=0 285/300: dt: 0.9000, rms radial error=129.563, avgs=0 290/300: dt: 0.9000, rms radial error=128.834, avgs=0 295/300: dt: 0.9000, rms radial error=128.108, avgs=0 300/300: dt: 0.9000, rms radial error=127.387, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15897.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2690.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 3 (K=160.0), pass 1, starting sse = 294.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00874 epoch 4 (K=640.0), pass 1, starting sse = 18.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/17 = 0.01130 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue May 12 00:55:49 EDT 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 R01L019_MD_12m 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=-44 (nv=135714, nf=271516, ne=407274, g=23) 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 8 iterations marking ambiguous vertices... 3740 ambiguous faces found in tessellation segmenting defects... 33 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 16 32 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4162 (-4.7081) -vertex loglikelihood: -6.2407 (-3.1203) -normal dot loglikelihood: -3.6226 (-3.6226) -quad curv loglikelihood: -6.4379 (-3.2189) Total Loglikelihood : -25.7174 CORRECTING DEFECT 0 (vertices=36, convex hull=62) After retessellation of defect 0, euler #=-30 (133489,399693,266174) : difference with theory (-29) = 1 CORRECTING DEFECT 1 (vertices=36, convex hull=73) After retessellation of defect 1, euler #=-29 (133510,399784,266245) : difference with theory (-28) = 1 CORRECTING DEFECT 2 (vertices=18, convex hull=55) After retessellation of defect 2, euler #=-28 (133519,399833,266286) : difference with theory (-27) = 1 CORRECTING DEFECT 3 (vertices=105, convex hull=110) After retessellation of defect 3, euler #=-27 (133558,400004,266419) : difference with theory (-26) = 1 CORRECTING DEFECT 4 (vertices=42, convex hull=76) After retessellation of defect 4, euler #=-26 (133571,400075,266478) : difference with theory (-25) = 1 CORRECTING DEFECT 5 (vertices=7, convex hull=24) After retessellation of defect 5, euler #=-25 (133573,400087,266489) : difference with theory (-24) = 1 CORRECTING DEFECT 6 (vertices=23, convex hull=66) After retessellation of defect 6, euler #=-24 (133587,400157,266546) : difference with theory (-23) = 1 CORRECTING DEFECT 7 (vertices=31, convex hull=66) After retessellation of defect 7, euler #=-23 (133605,400236,266608) : difference with theory (-22) = 1 CORRECTING DEFECT 8 (vertices=47, convex hull=34) After retessellation of defect 8, euler #=-22 (133608,400253,266623) : difference with theory (-21) = 1 CORRECTING DEFECT 9 (vertices=57, convex hull=24) After retessellation of defect 9, euler #=-21 (133613,400280,266646) : difference with theory (-20) = 1 CORRECTING DEFECT 10 (vertices=33, convex hull=67) After retessellation of defect 10, euler #=-20 (133635,400373,266718) : difference with theory (-19) = 1 CORRECTING DEFECT 11 (vertices=34, convex hull=76) After retessellation of defect 11, euler #=-19 (133650,400451,266782) : difference with theory (-18) = 1 CORRECTING DEFECT 12 (vertices=28, convex hull=66) After retessellation of defect 12, euler #=-18 (133661,400508,266829) : difference with theory (-17) = 1 CORRECTING DEFECT 13 (vertices=9, convex hull=12) After retessellation of defect 13, euler #=-17 (133662,400514,266835) : difference with theory (-16) = 1 CORRECTING DEFECT 14 (vertices=20, convex hull=42) After retessellation of defect 14, euler #=-16 (133673,400562,266873) : difference with theory (-15) = 1 CORRECTING DEFECT 15 (vertices=13, convex hull=13) After retessellation of defect 15, euler #=-15 (133674,400567,266878) : difference with theory (-14) = 1 CORRECTING DEFECT 16 (vertices=688, convex hull=199) After retessellation of defect 16, euler #=-13 (133692,400717,267012) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=31, convex hull=27) After retessellation of defect 17, euler #=-12 (133694,400732,267026) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=25) After retessellation of defect 18, euler #=-11 (133695,400743,267037) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=51, convex hull=48) After retessellation of defect 19, euler #=-10 (133704,400784,267070) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=27, convex hull=32) After retessellation of defect 20, euler #=-9 (133709,400811,267093) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=26, convex hull=50) After retessellation of defect 21, euler #=-8 (133728,400887,267151) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=290, convex hull=40) After retessellation of defect 22, euler #=-7 (133737,400930,267186) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=196, convex hull=157) After retessellation of defect 23, euler #=-6 (133780,401133,267347) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=26, convex hull=58) After retessellation of defect 24, euler #=-5 (133789,401179,267385) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=88, convex hull=52) After retessellation of defect 25, euler #=-4 (133798,401225,267423) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=40, convex hull=33) After retessellation of defect 26, euler #=-3 (133806,401261,267452) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=9, convex hull=25) After retessellation of defect 27, euler #=-2 (133808,401276,267466) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=33, convex hull=30) After retessellation of defect 28, euler #=-1 (133810,401290,267479) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=79, convex hull=119) After retessellation of defect 29, euler #=0 (133832,401421,267589) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=67, convex hull=78) After retessellation of defect 30, euler #=1 (133866,401555,267690) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=46, convex hull=87) After retessellation of defect 31, euler #=2 (133894,401676,267784) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->6.67) (max @ vno 113651 --> 117657) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->6.67) (max @ vno 113651 --> 117657) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 139 mutations (36.8%), 239 crossovers (63.2%), 223 vertices were eliminated building final representation... 1820 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133894, nf=267784, ne=401676, g=0) writing corrected surface to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.7 minutes 0 defective edges removing intersecting faces 000: 277 intersecting 001: 15 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133894 - 401676 + 267784 = 2 --> 0 holes F =2V-4: 267784 = 267788-4 (0) 2E=3F: 803352 = 803352 (0) total defect index = 0 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 42 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue May 12 01:22:34 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 9996 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.orig... computing class statistics... border white: 262981 voxels (1.57%) border gray 285696 voxels (1.70%) WM (93.0): 94.5 +- 7.5 [70.0 --> 110.0] GM (83.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70) setting MAX_BORDER_WHITE to 109.5 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.2 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->2.90) (max @ vno 121082 --> 124513) face area 0.28 +- 0.12 (0.00-->2.23) mean absolute distance = 0.90 +- 1.11 4174 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=72 using class modes intead of means.... mean inside = 93.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=81.3, 379 (379) missing vertices, mean dist 0.3 [0.9 (%33.6)->0.9 (%66.4))] %31 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.10-->3.37) (max @ vno 97410 --> 98296) face area 0.28 +- 0.13 (0.00-->2.79) mean absolute distance = 0.46 +- 0.85 4373 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4845145.5, rms=9.84 001: dt: 0.5000, sse=5432619.5, rms=7.00 002: dt: 0.5000, sse=5730619.5, rms=5.23 003: dt: 0.5000, sse=6054396.0, rms=4.17 004: dt: 0.5000, sse=6255888.0, rms=3.54 005: dt: 0.5000, sse=6413032.0, rms=3.20 006: dt: 0.5000, sse=6511488.0, rms=3.01 007: dt: 0.5000, sse=6553705.5, rms=2.91 008: dt: 0.5000, sse=6578400.0, rms=2.86 rms = 2.83, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6594910.0, rms=2.83 010: dt: 0.2500, sse=4031906.0, rms=1.93 011: dt: 0.2500, sse=3747577.0, rms=1.74 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3628693.5, rms=1.71 rms = 1.67, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3569254.8, rms=1.67 positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=83.6, 260 (165) missing vertices, mean dist -0.3 [0.6 (%63.2)->0.3 (%36.8))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.08-->3.72) (max @ vno 53490 --> 54553) face area 0.35 +- 0.16 (0.00-->3.89) mean absolute distance = 0.36 +- 0.52 3784 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4042043.5, rms=4.01 014: dt: 0.5000, sse=4436008.5, rms=2.64 015: dt: 0.5000, sse=5012486.0, rms=2.42 016: dt: 0.5000, sse=5263274.0, rms=2.30 rms = 2.51, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4318093.5, rms=1.75 018: dt: 0.2500, sse=3993895.2, rms=1.50 019: dt: 0.2500, sse=3874838.0, rms=1.44 rms = 1.43, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3831545.8, rms=1.43 rms = 1.41, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3790165.8, rms=1.41 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.3, 225 (147) missing vertices, mean dist -0.2 [0.4 (%68.7)->0.2 (%31.3))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->3.98) (max @ vno 53490 --> 54553) face area 0.34 +- 0.16 (0.00-->3.83) mean absolute distance = 0.28 +- 0.40 2960 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4074828.0, rms=3.71 022: dt: 0.5000, sse=4357992.0, rms=2.14 rms = 2.19, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4139387.5, rms=1.69 024: dt: 0.2500, sse=4066110.2, rms=1.39 025: dt: 0.2500, sse=4019673.5, rms=1.31 rms = 1.31, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3991923.5, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3958327.5, rms=1.29 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.5, 197 (120) missing vertices, mean dist -0.1 [0.3 (%59.6)->0.2 (%40.4))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3998528.8, rms=1.97 028: dt: 0.5000, sse=4997731.0, rms=1.57 rms = 1.94, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4573031.0, rms=1.16 030: dt: 0.2500, sse=4371698.0, rms=1.07 rms = 1.03, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4431528.5, rms=1.03 rms = 1.03, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4425107.0, rms=1.03 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 10 non-cortical segments detected only using segment with 1831 vertices erasing segment 1 (vno[0] = 54481) erasing segment 2 (vno[0] = 79976) erasing segment 3 (vno[0] = 96302) erasing segment 4 (vno[0] = 98092) erasing segment 5 (vno[0] = 100679) erasing segment 6 (vno[0] = 101439) erasing segment 7 (vno[0] = 105512) erasing segment 8 (vno[0] = 107120) erasing segment 9 (vno[0] = 107168) writing cortex label to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.cortex.label writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->3.93) (max @ vno 53490 --> 54553) face area 0.34 +- 0.16 (0.00-->3.86) refinement took 5.6 minutes #-------------------------------------------- #@# Smooth2 lh Tue May 12 01:28:07 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 01:28:12 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.1 mm, total surface area = 81489 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 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 277 vertices thresholded to be in k1 ~ [-0.26 0.40], k2 ~ [-0.12 0.08] total integrated curvature = 0.458*4pi (5.758) --> 1 handles ICI = 1.6, FI = 11.9, variation=195.151 160 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 152 vertices thresholded to be in [-0.16 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.025 done. #-------------------------------------------- #@# Sphere lh Tue May 12 01:30:19 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.08 hours scaling brain by 0.291... pass 1: epoch 1 of 3 starting distance error %18.90 pass 1: epoch 2 of 3 starting distance error %18.83 unfolding complete - removing small folds... starting distance error %18.74 removing remaining folds... final distance error %18.76 #-------------------------------------------- #@# Surf Reg lh Tue May 12 02:35:19 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.599 curvature mean = 0.026, std = 0.934 curvature mean = 0.023, std = 0.869 curvature mean = 0.013, std = 0.960 curvature mean = 0.010, std = 0.944 curvature mean = 0.012, std = 0.974 curvature mean = 0.004, std = 0.975 curvature mean = 0.011, std = 0.976 curvature mean = 0.001, std = 0.989 curvature mean = -0.028, std = 0.274 curvature mean = 0.003, std = 0.068 curvature mean = 0.067, std = 0.367 curvature mean = 0.003, std = 0.080 curvature mean = 0.029, std = 0.571 curvature mean = 0.003, std = 0.086 curvature mean = 0.016, std = 0.715 curvature mean = 0.003, std = 0.089 curvature mean = 0.005, std = 0.821 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue May 12 03:10:43 EDT 2015 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 Tue May 12 03:10:46 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue May 12 03:10:48 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 1388 labels changed using aseg relabeling using gibbs priors... 000: 2824 changed, 133894 examined... 001: 652 changed, 12080 examined... 002: 143 changed, 3644 examined... 003: 40 changed, 825 examined... 004: 18 changed, 237 examined... 005: 6 changed, 121 examined... 006: 1 changed, 31 examined... 007: 3 changed, 10 examined... 008: 1 changed, 15 examined... 009: 2 changed, 11 examined... 010: 1 changed, 8 examined... 011: 1 changed, 7 examined... 012: 0 changed, 7 examined... 243 labels changed using aseg 000: 130 total segments, 85 labels (244 vertices) changed 001: 45 total segments, 5 labels (16 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 53 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1677 vertices marked for relabeling... 1677 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 49 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue May 12 03:11:37 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 9996 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.orig... computing class statistics... border white: 262981 voxels (1.57%) border gray 285696 voxels (1.70%) WM (93.0): 94.5 +- 7.5 [70.0 --> 110.0] GM (83.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.1 (was 70) setting MAX_BORDER_WHITE to 109.5 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.2 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=72 using class modes intead of means.... mean inside = 93.3, mean outside = 77.0 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->2.90) (max @ vno 121082 --> 124513) face area 0.28 +- 0.12 (0.00-->2.23) mean absolute distance = 0.90 +- 1.13 4120 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 648 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown mean border=81.3, 379 (379) missing vertices, mean dist 0.3 [1.0 (%33.6)->0.9 (%66.4))] %31 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.10-->3.37) (max @ vno 97410 --> 98296) face area 0.28 +- 0.13 (0.00-->2.79) mean absolute distance = 0.46 +- 0.85 4407 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4859936.5, rms=9.83 001: dt: 0.5000, sse=5451039.5, rms=6.99 002: dt: 0.5000, sse=5748572.5, rms=5.22 003: dt: 0.5000, sse=6075803.0, rms=4.16 004: dt: 0.5000, sse=6277558.0, rms=3.53 005: dt: 0.5000, sse=6435689.0, rms=3.19 006: dt: 0.5000, sse=6535020.0, rms=3.00 007: dt: 0.5000, sse=6576792.5, rms=2.91 008: dt: 0.5000, sse=6604066.0, rms=2.85 rms = 2.82, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6618736.0, rms=2.82 010: dt: 0.2500, sse=4049015.2, rms=1.93 011: dt: 0.2500, sse=3765610.5, rms=1.74 rms = 1.70, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3644700.5, rms=1.70 rms = 1.67, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3584462.5, rms=1.67 positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 360 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=83.6, 258 (165) missing vertices, mean dist -0.3 [0.6 (%63.2)->0.3 (%36.8))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.08-->3.72) (max @ vno 53490 --> 54553) face area 0.35 +- 0.16 (0.00-->3.89) mean absolute distance = 0.36 +- 0.52 3830 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4060342.0, rms=4.02 014: dt: 0.5000, sse=4458365.5, rms=2.64 015: dt: 0.5000, sse=5038018.0, rms=2.42 016: dt: 0.5000, sse=5287978.5, rms=2.30 rms = 2.51, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4336875.5, rms=1.75 018: dt: 0.2500, sse=4011120.8, rms=1.50 019: dt: 0.2500, sse=3891028.8, rms=1.44 rms = 1.43, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3848779.0, rms=1.43 rms = 1.41, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3806753.5, rms=1.41 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 421 points - only 0.00% unknown deleting segment 2 with 102 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown mean border=86.2, 224 (147) missing vertices, mean dist -0.2 [0.4 (%68.6)->0.2 (%31.4))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->3.98) (max @ vno 53490 --> 54553) face area 0.34 +- 0.16 (0.00-->3.83) mean absolute distance = 0.28 +- 0.40 3002 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4093398.0, rms=3.71 022: dt: 0.5000, sse=4377467.0, rms=2.14 rms = 2.18, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4158499.8, rms=1.69 024: dt: 0.2500, sse=4086241.0, rms=1.39 025: dt: 0.2500, sse=4039793.5, rms=1.31 rms = 1.31, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4012674.2, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3979550.5, rms=1.29 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 435 points - only 0.00% unknown deleting segment 3 with 156 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown mean border=87.5, 196 (120) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4020627.5, rms=1.96 028: dt: 0.5000, sse=5023091.5, rms=1.56 rms = 1.93, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4597359.0, rms=1.16 030: dt: 0.2500, sse=4393497.0, rms=1.07 rms = 1.03, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4454773.0, rms=1.03 rms = 1.03, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4447849.5, rms=1.03 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... mean border=60.1, 273 (273) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.2 (%100.0))] %43 local maxima, %43 large gradients and % 9 min vals, 486 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=22011472.0, rms=27.59 001: dt: 0.5000, sse=17366466.0, rms=24.08 002: dt: 0.5000, sse=13774751.0, rms=21.00 003: dt: 0.5000, sse=11340465.0, rms=18.41 004: dt: 0.5000, sse=9914483.0, rms=16.19 005: dt: 0.5000, sse=8859206.0, rms=14.26 006: dt: 0.5000, sse=8097751.0, rms=12.58 007: dt: 0.5000, sse=7479409.5, rms=11.03 008: dt: 0.5000, sse=7061900.0, rms=9.60 009: dt: 0.5000, sse=6782740.5, rms=8.28 010: dt: 0.5000, sse=6623856.5, rms=7.14 011: dt: 0.5000, sse=6545511.5, rms=6.22 012: dt: 0.5000, sse=6579427.0, rms=5.54 013: dt: 0.5000, sse=6620810.5, rms=5.07 014: dt: 0.5000, sse=6686744.5, rms=4.78 015: dt: 0.5000, sse=6717976.5, rms=4.56 016: dt: 0.5000, sse=6762796.5, rms=4.42 017: dt: 0.5000, sse=6766869.5, rms=4.30 018: dt: 0.5000, sse=6795926.0, rms=4.23 019: dt: 0.5000, sse=6765537.5, rms=4.15 rms = 4.12, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6782162.5, rms=4.12 021: dt: 0.2500, sse=4283247.5, rms=3.03 022: dt: 0.2500, sse=3977378.0, rms=2.71 023: dt: 0.2500, sse=3820434.5, rms=2.64 rms = 2.61, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3787839.2, rms=2.61 025: dt: 0.1250, sse=3630936.2, rms=2.49 rms = 2.47, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3601407.2, rms=2.47 positioning took 2.7 minutes mean border=56.2, 341 (9) missing vertices, mean dist 0.2 [0.2 (%35.1)->0.5 (%64.9))] %62 local maxima, %28 large gradients and % 6 min vals, 197 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4663748.5, rms=6.22 027: dt: 0.5000, sse=4708155.0, rms=4.36 028: dt: 0.5000, sse=5844671.5, rms=4.26 rms = 4.32, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4744687.0, rms=3.29 030: dt: 0.2500, sse=4360854.5, rms=2.86 031: dt: 0.2500, sse=4277735.5, rms=2.71 032: dt: 0.2500, sse=4233991.5, rms=2.64 rms = 2.60, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4223362.0, rms=2.60 034: dt: 0.1250, sse=4086527.0, rms=2.46 rms = 2.44, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4067930.5, rms=2.44 positioning took 1.0 minutes mean border=53.9, 453 (2) missing vertices, mean dist 0.1 [0.2 (%35.3)->0.3 (%64.7))] %72 local maxima, %18 large gradients and % 5 min vals, 217 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4297591.0, rms=3.74 rms = 3.94, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4121809.8, rms=2.97 037: dt: 0.2500, sse=4102689.5, rms=2.53 038: dt: 0.2500, sse=4207435.5, rms=2.40 rms = 2.36, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4215316.5, rms=2.36 040: dt: 0.1250, sse=4115369.5, rms=2.25 rms = 2.23, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4107284.0, rms=2.23 positioning took 0.7 minutes mean border=52.8, 805 (2) missing vertices, mean dist 0.1 [0.2 (%42.9)->0.3 (%57.1))] %76 local maxima, %14 large gradients and % 5 min vals, 216 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4151751.5, rms=2.61 rms = 3.33, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=4075342.8, rms=2.26 043: dt: 0.2500, sse=4161245.8, rms=2.17 rms = 2.12, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4196364.5, rms=2.12 045: dt: 0.1250, sse=4149742.8, rms=2.05 rms = 2.03, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=4146707.2, rms=2.03 positioning took 0.6 minutes writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.area.pial vertex spacing 1.01 +- 0.41 (0.08-->6.66) (max @ vno 100059 --> 100049) face area 0.41 +- 0.29 (0.00-->6.35) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133894 vertices processed 25000 of 133894 vertices processed 50000 of 133894 vertices processed 75000 of 133894 vertices processed 100000 of 133894 vertices processed 125000 of 133894 vertices processed 0 of 133894 vertices processed 25000 of 133894 vertices processed 50000 of 133894 vertices processed 75000 of 133894 vertices processed 100000 of 133894 vertices processed 125000 of 133894 vertices processed thickness calculation complete, 682:1228 truncations. 65851 vertices at 0 distance 86297 vertices at 1 distance 64740 vertices at 2 distance 25445 vertices at 3 distance 8506 vertices at 4 distance 2894 vertices at 5 distance 1197 vertices at 6 distance 497 vertices at 7 distance 287 vertices at 8 distance 163 vertices at 9 distance 97 vertices at 10 distance 77 vertices at 11 distance 45 vertices at 12 distance 27 vertices at 13 distance 28 vertices at 14 distance 21 vertices at 15 distance 19 vertices at 16 distance 16 vertices at 17 distance 8 vertices at 18 distance 13 vertices at 19 distance 16 vertices at 20 distance writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.thickness positioning took 11.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue May 12 03:22:46 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 03:22:46 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1397 1004 2245 2.268 0.559 0.120 0.031 11 1.8 bankssts 1047 720 2030 2.876 0.829 0.139 0.039 17 1.7 caudalanteriorcingulate 2886 1929 5176 2.393 0.603 0.126 0.046 32 5.2 caudalmiddlefrontal 2237 1370 2708 1.730 0.489 0.152 0.065 37 5.5 cuneus 500 363 1557 2.815 0.946 0.160 0.072 8 1.3 entorhinal 3980 2681 7960 2.572 0.860 0.159 0.068 74 11.2 fusiform 7376 4924 13147 2.365 0.604 0.144 0.054 114 15.7 inferiorparietal 4673 3175 10442 2.716 0.795 0.165 0.072 102 14.8 inferiortemporal 2116 1388 3189 2.137 0.749 0.143 0.058 36 4.8 isthmuscingulate 6768 4289 10308 2.041 0.659 0.149 0.055 115 15.4 lateraloccipital 3822 2576 6770 2.306 0.709 0.158 0.071 65 11.2 lateralorbitofrontal 4300 2769 5230 1.732 0.511 0.155 0.059 69 10.8 lingual 2934 1950 5142 2.288 0.821 0.149 0.067 81 7.5 medialorbitofrontal 4346 2935 9989 2.749 0.686 0.152 0.064 84 11.8 middletemporal 990 698 2286 2.599 0.879 0.130 0.048 12 2.0 parahippocampal 2121 1271 3044 2.205 0.578 0.124 0.045 24 4.3 paracentral 2699 1763 4972 2.432 0.579 0.130 0.046 36 4.9 parsopercularis 860 584 1789 2.452 0.612 0.195 0.087 22 3.0 parsorbitalis 1910 1298 3317 2.237 0.599 0.149 0.050 27 3.9 parstriangularis 1810 1245 1548 1.329 0.311 0.133 0.041 20 3.1 pericalcarine 6664 4264 8905 1.851 0.595 0.128 0.043 78 12.2 postcentral 1735 1207 3275 2.462 0.729 0.171 0.083 39 6.3 posteriorcingulate 7801 4877 12594 2.413 0.616 0.131 0.074 131 26.8 precentral 6264 4192 9391 2.076 0.587 0.148 0.069 103 14.5 precuneus 1497 982 3315 2.808 0.971 0.154 0.069 32 4.5 rostralanteriorcingulate 7621 5330 13987 2.168 0.664 0.165 0.077 154 21.8 rostralmiddlefrontal 9563 6589 19861 2.573 0.672 0.155 0.083 222 36.1 superiorfrontal 8885 5860 14247 2.145 0.567 0.138 0.049 122 16.5 superiorparietal 6101 4102 11523 2.451 0.718 0.122 0.040 65 9.6 superiortemporal 5841 4006 10903 2.463 0.593 0.162 0.074 115 15.2 supramarginal 261 185 722 2.678 0.695 0.204 0.100 7 0.9 frontalpole 565 418 2694 3.619 0.766 0.183 0.075 12 1.8 temporalpole 882 448 1157 2.409 0.423 0.129 0.092 16 2.7 transversetemporal 3535 2389 6715 2.811 1.003 0.117 0.055 53 8.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue May 12 03:23:01 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 16 labels changed using aseg relabeling using gibbs priors... 000: 9052 changed, 133894 examined... 001: 2115 changed, 34550 examined... 002: 637 changed, 10689 examined... 003: 282 changed, 3594 examined... 004: 126 changed, 1585 examined... 005: 68 changed, 717 examined... 006: 36 changed, 397 examined... 007: 23 changed, 224 examined... 008: 10 changed, 124 examined... 009: 5 changed, 68 examined... 010: 2 changed, 25 examined... 011: 0 changed, 13 examined... 6 labels changed using aseg 000: 253 total segments, 172 labels (1746 vertices) changed 001: 86 total segments, 5 labels (56 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 176 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1052 vertices marked for relabeling... 1052 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 56 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue May 12 03:23:56 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1113 767 1920 2.084 0.666 0.182 0.072 25 3.3 G_and_S_frontomargin 1595 1046 3204 2.314 0.881 0.152 0.056 23 3.8 G_and_S_occipital_inf 1653 907 2431 2.269 0.524 0.129 0.059 31 4.1 G_and_S_paracentral 1649 1068 2875 2.374 0.672 0.145 0.052 23 3.4 G_and_S_subcentral 549 377 1342 2.508 0.613 0.222 0.107 25 2.5 G_and_S_transv_frontopol 2543 1739 4967 2.558 0.771 0.148 0.066 47 7.1 G_and_S_cingul-Ant 1648 1166 2935 2.385 0.631 0.142 0.055 22 3.0 G_and_S_cingul-Mid-Ant 1236 883 2390 2.513 0.644 0.136 0.050 14 2.8 G_and_S_cingul-Mid-Post 660 452 1505 2.539 0.618 0.190 0.095 18 2.4 G_cingul-Post-dorsal 483 306 717 2.027 0.953 0.143 0.078 8 1.4 G_cingul-Post-ventral 1893 1159 2441 1.754 0.556 0.159 0.061 33 5.1 G_cuneus 1573 997 3133 2.567 0.538 0.141 0.055 25 3.5 G_front_inf-Opercular 225 150 393 2.301 0.527 0.184 0.075 5 0.6 G_front_inf-Orbital 1106 746 2324 2.438 0.599 0.169 0.065 23 2.9 G_front_inf-Triangul 3710 2587 8441 2.474 0.662 0.179 0.095 92 13.0 G_front_middle 6190 4154 14419 2.741 0.667 0.168 0.100 188 29.7 G_front_sup 553 355 1274 3.403 0.694 0.136 0.073 8 1.5 G_Ins_lg_and_S_cent_ins 659 428 1815 3.519 0.851 0.155 0.110 30 3.6 G_insular_short 2238 1393 4512 2.504 0.608 0.154 0.066 56 5.6 G_occipital_middle 1984 1180 2846 2.068 0.528 0.141 0.050 29 4.1 G_occipital_sup 1415 905 3289 2.808 0.713 0.167 0.072 35 4.2 G_oc-temp_lat-fusifor 3033 1880 3965 1.747 0.544 0.155 0.058 51 7.5 G_oc-temp_med-Lingual 1125 779 3226 2.944 0.910 0.156 0.080 21 3.3 G_oc-temp_med-Parahip 2567 1736 5484 2.448 0.716 0.178 0.083 56 8.8 G_orbital 2596 1710 5594 2.562 0.546 0.157 0.057 48 6.3 G_pariet_inf-Angular 3259 2235 7149 2.669 0.528 0.180 0.087 76 9.4 G_pariet_inf-Supramar 3461 2311 6790 2.370 0.566 0.155 0.060 64 7.2 G_parietal_sup 2480 1527 3727 1.964 0.530 0.136 0.050 37 5.4 G_postcentral 2937 1700 5463 2.605 0.535 0.127 0.113 67 15.9 G_precentral 3142 2087 5685 2.250 0.512 0.167 0.070 64 8.9 G_precuneus 1075 718 2500 2.651 0.729 0.189 0.092 40 3.5 G_rectus 373 232 518 2.008 0.959 0.101 0.065 11 1.3 G_subcallosal 618 323 867 2.290 0.399 0.124 0.074 12 2.1 G_temp_sup-G_T_transv 2342 1503 5427 2.641 0.654 0.143 0.054 39 4.9 G_temp_sup-Lateral 795 543 1886 3.015 0.682 0.100 0.029 5 0.8 G_temp_sup-Plan_polar 880 634 1778 2.470 0.580 0.097 0.022 6 0.8 G_temp_sup-Plan_tempo 2947 1948 7256 2.774 0.806 0.172 0.075 73 9.7 G_temporal_inf 2592 1726 6902 2.963 0.575 0.173 0.081 67 8.6 G_temporal_middle 355 241 541 2.225 0.533 0.142 0.034 4 0.5 Lat_Fis-ant-Horizont 244 170 328 2.084 0.509 0.114 0.032 1 0.3 Lat_Fis-ant-Vertical 1270 846 1526 2.089 0.629 0.119 0.039 9 2.0 Lat_Fis-post 2331 1462 2890 1.769 0.525 0.160 0.058 38 5.9 Pole_occipital 1489 1076 5932 3.273 0.940 0.190 0.108 39 7.2 Pole_temporal 2796 1893 2689 1.628 0.550 0.144 0.077 46 6.3 S_calcarine 3355 2256 3558 1.710 0.571 0.126 0.044 34 7.0 S_central 1118 759 1652 2.234 0.773 0.120 0.037 10 1.6 S_cingul-Marginalis 551 366 836 2.351 0.734 0.103 0.030 3 0.8 S_circular_insula_ant 1527 1014 2299 2.566 0.882 0.095 0.024 8 1.6 S_circular_insula_inf 2001 1394 2927 2.310 0.676 0.103 0.034 12 2.9 S_circular_insula_sup 918 653 1579 2.914 0.895 0.155 0.053 13 2.0 S_collat_transv_ant 437 279 434 1.762 0.388 0.145 0.048 5 0.8 S_collat_transv_post 2672 1809 4104 2.098 0.573 0.128 0.037 27 4.3 S_front_inf 1181 816 1742 1.950 0.624 0.139 0.082 15 2.5 S_front_middle 2512 1710 3992 2.264 0.578 0.109 0.033 18 3.5 S_front_sup 183 128 216 1.740 0.391 0.150 0.040 2 0.4 S_interm_prim-Jensen 3234 2209 4343 2.035 0.448 0.127 0.044 34 5.9 S_intrapariet_and_P_trans 879 575 1071 1.854 0.482 0.134 0.045 10 1.6 S_oc_middle_and_Lunatus 1497 997 1961 2.036 0.452 0.128 0.039 15 2.3 S_oc_sup_and_transversal 462 325 560 1.780 0.594 0.107 0.026 4 0.5 S_occipital_ant 916 647 1362 2.284 0.577 0.136 0.040 8 1.5 S_oc-temp_lat 1586 1165 2061 1.914 0.514 0.126 0.035 14 2.3 S_oc-temp_med_and_Lingual 523 367 837 2.088 0.627 0.183 0.072 10 1.4 S_orbital_lateral 881 594 1089 1.925 0.693 0.123 0.036 15 1.2 S_orbital_med-olfact 1263 871 2196 2.294 0.719 0.168 0.084 24 4.2 S_orbital-H_Shaped 2103 1386 2314 1.683 0.484 0.118 0.043 20 3.1 S_parieto_occipital 1607 1025 2066 2.422 1.093 0.157 0.072 38 4.8 S_pericallosal 3224 2171 4091 1.893 0.546 0.130 0.047 41 5.6 S_postcentral 1429 965 2170 2.278 0.584 0.132 0.042 14 2.5 S_precentral-inf-part 1279 885 1894 2.371 0.657 0.122 0.035 9 1.9 S_precentral-sup-part 698 474 1055 2.162 0.713 0.147 0.055 12 1.6 S_suborbital 1311 885 1730 1.938 0.502 0.132 0.046 13 2.3 S_subparietal 1184 820 1808 2.403 0.666 0.136 0.052 16 2.9 S_temporal_inf 5628 3906 8389 2.254 0.594 0.122 0.040 57 9.1 S_temporal_sup 446 286 511 1.863 0.515 0.127 0.083 5 0.7 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Tue May 12 03:24:13 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 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 261368: 0.000765) 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 40: 345 vertices, 391 faces slice 50: 4714 vertices, 4908 faces slice 60: 12904 vertices, 13267 faces slice 70: 23231 vertices, 23599 faces slice 80: 34986 vertices, 35384 faces slice 90: 46023 vertices, 46389 faces slice 100: 57606 vertices, 57994 faces slice 110: 69215 vertices, 69662 faces slice 120: 80642 vertices, 81043 faces slice 130: 91498 vertices, 91915 faces slice 140: 102119 vertices, 102544 faces slice 150: 111516 vertices, 111852 faces slice 160: 119261 vertices, 119579 faces slice 170: 126586 vertices, 126881 faces slice 180: 132785 vertices, 133037 faces slice 190: 137769 vertices, 137995 faces slice 200: 140428 vertices, 140554 faces slice 210: 140744 vertices, 140810 faces slice 220: 140744 vertices, 140810 faces slice 230: 140744 vertices, 140810 faces slice 240: 140744 vertices, 140810 faces slice 250: 140744 vertices, 140810 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... 140744 voxel in cpt #1: X=-66 [v=140744,e=422430,f=281620] located at (26.911585, -15.753013, 27.358467) For the whole surface: X=-66 [v=140744,e=422430,f=281620] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue May 12 03:24:22 EDT 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 03:24:26 EDT 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts avg radius = 47.2 mm, total surface area = 74276 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.034 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue May 12 03:25:12 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 0.98 +- 0.58 (0.00-->6.46) (max @ vno 107730 --> 107731) face area 0.02 +- 0.03 (-0.15-->0.55) scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.824, avgs=0 005/300: dt: 0.9000, rms radial error=176.566, avgs=0 010/300: dt: 0.9000, rms radial error=176.011, avgs=0 015/300: dt: 0.9000, rms radial error=175.283, avgs=0 020/300: dt: 0.9000, rms radial error=174.453, avgs=0 025/300: dt: 0.9000, rms radial error=173.566, avgs=0 030/300: dt: 0.9000, rms radial error=172.647, avgs=0 035/300: dt: 0.9000, rms radial error=171.711, avgs=0 040/300: dt: 0.9000, rms radial error=170.767, avgs=0 045/300: dt: 0.9000, rms radial error=169.821, avgs=0 050/300: dt: 0.9000, rms radial error=168.877, avgs=0 055/300: dt: 0.9000, rms radial error=167.934, avgs=0 060/300: dt: 0.9000, rms radial error=166.996, avgs=0 065/300: dt: 0.9000, rms radial error=166.061, avgs=0 070/300: dt: 0.9000, rms radial error=165.131, avgs=0 075/300: dt: 0.9000, rms radial error=164.206, avgs=0 080/300: dt: 0.9000, rms radial error=163.286, avgs=0 085/300: dt: 0.9000, rms radial error=162.370, avgs=0 090/300: dt: 0.9000, rms radial error=161.459, avgs=0 095/300: dt: 0.9000, rms radial error=160.553, avgs=0 100/300: dt: 0.9000, rms radial error=159.652, avgs=0 105/300: dt: 0.9000, rms radial error=158.756, avgs=0 110/300: dt: 0.9000, rms radial error=157.866, avgs=0 115/300: dt: 0.9000, rms radial error=156.980, avgs=0 120/300: dt: 0.9000, rms radial error=156.099, avgs=0 125/300: dt: 0.9000, rms radial error=155.223, avgs=0 130/300: dt: 0.9000, rms radial error=154.351, avgs=0 135/300: dt: 0.9000, rms radial error=153.485, avgs=0 140/300: dt: 0.9000, rms radial error=152.622, avgs=0 145/300: dt: 0.9000, rms radial error=151.765, avgs=0 150/300: dt: 0.9000, rms radial error=150.911, avgs=0 155/300: dt: 0.9000, rms radial error=150.063, avgs=0 160/300: dt: 0.9000, rms radial error=149.219, avgs=0 165/300: dt: 0.9000, rms radial error=148.380, avgs=0 170/300: dt: 0.9000, rms radial error=147.545, avgs=0 175/300: dt: 0.9000, rms radial error=146.715, avgs=0 180/300: dt: 0.9000, rms radial error=145.890, avgs=0 185/300: dt: 0.9000, rms radial error=145.069, avgs=0 190/300: dt: 0.9000, rms radial error=144.254, avgs=0 195/300: dt: 0.9000, rms radial error=143.443, avgs=0 200/300: dt: 0.9000, rms radial error=142.636, avgs=0 205/300: dt: 0.9000, rms radial error=141.834, avgs=0 210/300: dt: 0.9000, rms radial error=141.036, avgs=0 215/300: dt: 0.9000, rms radial error=140.243, avgs=0 220/300: dt: 0.9000, rms radial error=139.454, avgs=0 225/300: dt: 0.9000, rms radial error=138.670, avgs=0 230/300: dt: 0.9000, rms radial error=137.890, avgs=0 235/300: dt: 0.9000, rms radial error=137.114, avgs=0 240/300: dt: 0.9000, rms radial error=136.343, avgs=0 245/300: dt: 0.9000, rms radial error=135.576, avgs=0 250/300: dt: 0.9000, rms radial error=134.813, avgs=0 255/300: dt: 0.9000, rms radial error=134.054, avgs=0 260/300: dt: 0.9000, rms radial error=133.300, avgs=0 265/300: dt: 0.9000, rms radial error=132.550, avgs=0 270/300: dt: 0.9000, rms radial error=131.803, avgs=0 275/300: dt: 0.9000, rms radial error=131.062, avgs=0 280/300: dt: 0.9000, rms radial error=130.324, avgs=0 285/300: dt: 0.9000, rms radial error=129.590, avgs=0 290/300: dt: 0.9000, rms radial error=128.860, avgs=0 295/300: dt: 0.9000, rms radial error=128.134, avgs=0 300/300: dt: 0.9000, rms radial error=127.413, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16554.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2806.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 304.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00870 epoch 4 (K=640.0), pass 1, starting sse = 20.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/16 = 0.00943 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue May 12 03:30:54 EDT 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 R01L019_MD_12m 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=-66 (nv=140744, nf=281620, ne=422430, g=34) 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... 4709 ambiguous faces found in tessellation segmenting defects... 36 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 14 -merging segment 20 into 14 -merging segment 22 into 14 33 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4535 (-4.7268) -vertex loglikelihood: -6.1853 (-3.0926) -normal dot loglikelihood: -3.6284 (-3.6284) -quad curv loglikelihood: -6.5144 (-3.2572) Total Loglikelihood : -25.7815 CORRECTING DEFECT 0 (vertices=52, convex hull=93) After retessellation of defect 0, euler #=-32 (137940,412763,274791) : difference with theory (-30) = 2 CORRECTING DEFECT 1 (vertices=28, convex hull=59) After retessellation of defect 1, euler #=-31 (137957,412834,274846) : difference with theory (-29) = 2 CORRECTING DEFECT 2 (vertices=17, convex hull=42) After retessellation of defect 2, euler #=-30 (137961,412863,274872) : difference with theory (-28) = 2 CORRECTING DEFECT 3 (vertices=37, convex hull=92) After retessellation of defect 3, euler #=-29 (137984,412971,274958) : difference with theory (-27) = 2 CORRECTING DEFECT 4 (vertices=81, convex hull=124) After retessellation of defect 4, euler #=-28 (138032,413168,275108) : difference with theory (-26) = 2 CORRECTING DEFECT 5 (vertices=18, convex hull=54) After retessellation of defect 5, euler #=-27 (138040,413215,275148) : difference with theory (-25) = 2 CORRECTING DEFECT 6 (vertices=153, convex hull=116) After retessellation of defect 6, euler #=-26 (138087,413407,275294) : difference with theory (-24) = 2 CORRECTING DEFECT 7 (vertices=33, convex hull=28) After retessellation of defect 7, euler #=-25 (138089,413427,275313) : difference with theory (-23) = 2 CORRECTING DEFECT 8 (vertices=44, convex hull=59) After retessellation of defect 8, euler #=-24 (138097,413475,275354) : difference with theory (-22) = 2 CORRECTING DEFECT 9 (vertices=20, convex hull=26) After retessellation of defect 9, euler #=-23 (138100,413489,275366) : difference with theory (-21) = 2 CORRECTING DEFECT 10 (vertices=7, convex hull=18) After retessellation of defect 10, euler #=-22 (138102,413498,275374) : difference with theory (-20) = 2 CORRECTING DEFECT 11 (vertices=32, convex hull=50) After retessellation of defect 11, euler #=-21 (138119,413569,275429) : difference with theory (-19) = 2 CORRECTING DEFECT 12 (vertices=47, convex hull=41) After retessellation of defect 12, euler #=-20 (138128,413612,275464) : difference with theory (-18) = 2 CORRECTING DEFECT 13 (vertices=18, convex hull=19) After retessellation of defect 13, euler #=-19 (138131,413626,275476) : difference with theory (-17) = 2 CORRECTING DEFECT 14 (vertices=1582, convex hull=664) After retessellation of defect 14, euler #=-16 (138640,415561,276905) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=52, convex hull=44) After retessellation of defect 15, euler #=-15 (138653,415616,276948) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=6, convex hull=28) After retessellation of defect 16, euler #=-14 (138654,415628,276960) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=60, convex hull=38) After retessellation of defect 17, euler #=-13 (138660,415657,276984) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=11, convex hull=16) After retessellation of defect 18, euler #=-12 (138664,415673,276997) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=49) After retessellation of defect 19, euler #=-11 (138676,415726,277039) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=192, convex hull=52) After retessellation of defect 20, euler #=-10 (138688,415791,277093) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=14, convex hull=22) After retessellation of defect 21, euler #=-9 (138691,415805,277105) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=11, convex hull=22) After retessellation of defect 22, euler #=-8 (138691,415811,277112) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=6, convex hull=16) After retessellation of defect 23, euler #=-7 (138693,415821,277121) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=19, convex hull=51) After retessellation of defect 24, euler #=-6 (138702,415868,277160) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=27, convex hull=63) After retessellation of defect 25, euler #=-5 (138719,415949,277225) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=57, convex hull=95) After retessellation of defect 26, euler #=-4 (138741,416058,277313) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=21, convex hull=41) After retessellation of defect 27, euler #=-3 (138752,416105,277350) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=45, convex hull=77) After retessellation of defect 28, euler #=-2 (138767,416183,277414) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=47) After retessellation of defect 29, euler #=-1 (138779,416235,277455) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=55, convex hull=106) After retessellation of defect 30, euler #=0 (138791,416321,277530) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=24, convex hull=52) After retessellation of defect 31, euler #=1 (138801,416376,277576) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=23, convex hull=51) After retessellation of defect 32, euler #=2 (138811,416427,277618) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.06-->6.18) (max @ vno 115959 --> 120280) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.06-->6.18) (max @ vno 115959 --> 120280) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 139 mutations (38.4%), 223 crossovers (61.6%), 74 vertices were eliminated building final representation... 1933 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138811, nf=277618, ne=416427, g=0) writing corrected surface to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.3 minutes 0 defective edges removing intersecting faces 000: 394 intersecting 001: 5 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 138811 - 416427 + 277618 = 2 --> 0 holes F =2V-4: 277618 = 277622-4 (0) 2E=3F: 832854 = 832854 (0) total defect index = 0 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 209 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue May 12 03:50:16 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 10683 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... computing class statistics... border white: 262981 voxels (1.57%) border gray 285696 voxels (1.70%) WM (93.0): 94.4 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.1 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.2 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.3 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.26) (max @ vno 43040 --> 138076) face area 0.28 +- 0.12 (0.00-->2.15) mean absolute distance = 0.87 +- 1.11 4347 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=74 using class modes intead of means.... mean inside = 93.3, mean outside = 77.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.1, 338 (338) missing vertices, mean dist 0.2 [0.9 (%38.0)->0.9 (%62.0))] %33 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.08-->4.29) (max @ vno 138545 --> 138520) face area 0.28 +- 0.13 (0.00-->4.12) mean absolute distance = 0.45 +- 0.85 4546 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4844246.5, rms=9.28 001: dt: 0.5000, sse=5591106.0, rms=6.46 002: dt: 0.5000, sse=5932855.5, rms=4.78 003: dt: 0.5000, sse=6249733.5, rms=3.88 004: dt: 0.5000, sse=6456786.0, rms=3.35 005: dt: 0.5000, sse=6622690.0, rms=3.06 006: dt: 0.5000, sse=6662867.0, rms=2.89 007: dt: 0.5000, sse=6684016.5, rms=2.81 008: dt: 0.5000, sse=6716399.0, rms=2.74 rms = 2.71, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6698627.5, rms=2.71 010: dt: 0.2500, sse=4236771.0, rms=1.91 011: dt: 0.2500, sse=3962046.8, rms=1.74 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3860511.0, rms=1.71 rms = 1.68, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3794813.2, rms=1.68 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.1, 341 (194) missing vertices, mean dist -0.3 [0.6 (%61.7)->0.3 (%38.3))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 +- 0.25 (0.08-->4.37) (max @ vno 138545 --> 138520) face area 0.35 +- 0.17 (0.00-->6.04) mean absolute distance = 0.37 +- 0.52 4064 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4199166.5, rms=3.63 014: dt: 0.5000, sse=4568537.0, rms=2.41 015: dt: 0.5000, sse=5116130.0, rms=2.20 016: dt: 0.5000, sse=5336901.0, rms=2.13 rms = 2.31, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4472338.5, rms=1.67 018: dt: 0.2500, sse=4178417.2, rms=1.48 rms = 1.45, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4068421.5, rms=1.45 rms = 1.42, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4016513.5, rms=1.42 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.7, 320 (162) missing vertices, mean dist -0.2 [0.4 (%69.0)->0.2 (%31.0))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 +- 0.25 (0.06-->4.31) (max @ vno 138545 --> 138520) face area 0.34 +- 0.16 (0.00-->6.22) mean absolute distance = 0.28 +- 0.39 3215 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4299428.0, rms=3.65 021: dt: 0.5000, sse=4503849.5, rms=2.09 022: dt: 0.5000, sse=5007813.5, rms=2.03 rms = 2.05, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4477551.0, rms=1.57 024: dt: 0.2500, sse=4269827.0, rms=1.33 rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4212344.5, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4171456.5, rms=1.29 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.9, 304 (139) missing vertices, mean dist -0.1 [0.3 (%60.4)->0.2 (%39.6))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4206984.5, rms=1.92 027: dt: 0.5000, sse=5111949.0, rms=1.47 rms = 1.79, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4714338.0, rms=1.14 029: dt: 0.2500, sse=4542198.0, rms=1.07 rms = 1.04, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4587725.0, rms=1.04 rms = 1.04, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4581440.0, rms=1.04 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 17 non-cortical segments detected only using segment with 1895 vertices erasing segment 1 (vno[0] = 57896) erasing segment 2 (vno[0] = 60137) erasing segment 3 (vno[0] = 68318) erasing segment 4 (vno[0] = 76517) erasing segment 5 (vno[0] = 88079) erasing segment 6 (vno[0] = 100001) erasing segment 7 (vno[0] = 100933) erasing segment 8 (vno[0] = 101731) erasing segment 9 (vno[0] = 102588) erasing segment 10 (vno[0] = 102621) erasing segment 11 (vno[0] = 103485) erasing segment 12 (vno[0] = 104412) erasing segment 13 (vno[0] = 106158) erasing segment 14 (vno[0] = 107099) erasing segment 15 (vno[0] = 107987) erasing segment 16 (vno[0] = 111750) writing cortex label to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.cortex.label writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.area vertex spacing 0.89 +- 0.25 (0.07-->4.38) (max @ vno 138545 --> 138520) face area 0.33 +- 0.16 (0.00-->6.04) refinement took 5.6 minutes #-------------------------------------------- #@# Smooth2 rh Tue May 12 03:55:52 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 03:55:57 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.5 mm, total surface area = 83240 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 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 347 vertices thresholded to be in k1 ~ [-0.23 0.32], k2 ~ [-0.10 0.08] total integrated curvature = 0.490*4pi (6.162) --> 1 handles ICI = 1.5, FI = 11.6, variation=191.035 159 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 = 0.001 147 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #-------------------------------------------- #@# Sphere rh Tue May 12 03:58:10 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1.01 hours scaling brain by 0.287... pass 1: epoch 1 of 3 starting distance error %19.68 pass 1: epoch 2 of 3 starting distance error %19.63 unfolding complete - removing small folds... starting distance error %19.57 removing remaining folds... final distance error %19.59 #-------------------------------------------- #@# Surf Reg rh Tue May 12 04:58:58 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.000, std = 0.595 curvature mean = 0.019, std = 0.940 curvature mean = 0.027, std = 0.864 curvature mean = 0.002, std = 0.961 curvature mean = 0.011, std = 0.944 curvature mean = -0.003, std = 0.971 curvature mean = 0.005, std = 0.975 curvature mean = -0.005, std = 0.972 curvature mean = 0.001, std = 0.989 curvature mean = -0.031, std = 0.290 curvature mean = 0.004, std = 0.071 curvature mean = 0.074, std = 0.349 curvature mean = 0.004, std = 0.085 curvature mean = 0.034, std = 0.543 curvature mean = 0.004, std = 0.091 curvature mean = 0.017, std = 0.688 curvature mean = 0.004, std = 0.093 curvature mean = 0.005, std = 0.798 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue May 12 05:37:03 EDT 2015 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 Tue May 12 05:37:05 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue May 12 05:37:07 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 1469 labels changed using aseg relabeling using gibbs priors... 000: 2974 changed, 138811 examined... 001: 731 changed, 12745 examined... 002: 157 changed, 3923 examined... 003: 51 changed, 960 examined... 004: 26 changed, 328 examined... 005: 16 changed, 163 examined... 006: 8 changed, 95 examined... 007: 2 changed, 39 examined... 008: 1 changed, 14 examined... 009: 0 changed, 7 examined... 200 labels changed using aseg 000: 117 total segments, 78 labels (459 vertices) changed 001: 42 total segments, 4 labels (5 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2229 vertices marked for relabeling... 2229 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue May 12 05:37:58 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... 10683 bright wm thresholded. 4368 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.orig... computing class statistics... border white: 262981 voxels (1.57%) border gray 285696 voxels (1.70%) WM (93.0): 94.4 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.1 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.2 (was 70) setting MAX_BORDER_WHITE to 108.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.3 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=74 using class modes intead of means.... mean inside = 93.3, mean outside = 77.6 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.26) (max @ vno 43040 --> 138076) face area 0.28 +- 0.12 (0.00-->2.15) mean absolute distance = 0.88 +- 1.12 4429 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 106 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 33 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 73 points - only 0.00% unknown mean border=83.1, 338 (338) missing vertices, mean dist 0.2 [0.9 (%38.0)->0.9 (%62.0))] %33 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 +- 0.26 (0.08-->4.29) (max @ vno 138545 --> 138520) face area 0.28 +- 0.13 (0.00-->4.12) mean absolute distance = 0.46 +- 0.85 4622 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4848463.0, rms=9.27 001: dt: 0.5000, sse=5595110.5, rms=6.45 002: dt: 0.5000, sse=5935836.0, rms=4.78 003: dt: 0.5000, sse=6252610.0, rms=3.88 004: dt: 0.5000, sse=6459282.0, rms=3.35 005: dt: 0.5000, sse=6625106.5, rms=3.06 006: dt: 0.5000, sse=6664733.0, rms=2.89 007: dt: 0.5000, sse=6687151.5, rms=2.80 008: dt: 0.5000, sse=6721836.5, rms=2.74 rms = 2.71, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6703203.0, rms=2.71 010: dt: 0.2500, sse=4238689.0, rms=1.90 011: dt: 0.2500, sse=3963911.8, rms=1.74 rms = 1.71, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3861129.5, rms=1.71 rms = 1.68, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3795622.2, rms=1.68 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 2 with 231 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 25 points - only 0.00% unknown mean border=85.1, 341 (194) missing vertices, mean dist -0.2 [0.6 (%61.6)->0.3 (%38.4))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 +- 0.25 (0.08-->4.37) (max @ vno 138545 --> 138520) face area 0.35 +- 0.16 (0.00-->6.04) mean absolute distance = 0.37 +- 0.52 4131 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4208859.0, rms=3.64 014: dt: 0.5000, sse=4584679.0, rms=2.42 015: dt: 0.5000, sse=5133239.5, rms=2.21 016: dt: 0.5000, sse=5354911.5, rms=2.13 rms = 2.32, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4486110.5, rms=1.68 018: dt: 0.2500, sse=4191620.5, rms=1.49 rms = 1.45, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4081650.5, rms=1.45 rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4029013.0, rms=1.43 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 278 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 50 points - only 0.00% unknown mean border=87.7, 320 (162) missing vertices, mean dist -0.2 [0.4 (%68.9)->0.2 (%31.1))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 +- 0.25 (0.06-->4.31) (max @ vno 138545 --> 138520) face area 0.34 +- 0.16 (0.00-->6.22) mean absolute distance = 0.28 +- 0.39 3260 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4313177.5, rms=3.65 021: dt: 0.5000, sse=4516418.5, rms=2.10 022: dt: 0.5000, sse=5023554.5, rms=2.03 rms = 2.05, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4491543.5, rms=1.58 024: dt: 0.2500, sse=4281419.0, rms=1.34 rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4223064.5, rms=1.31 rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4180477.0, rms=1.29 positioning took 0.7 minutes 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 237 points - only 0.00% unknown deleting segment 3 with 22 points - only 0.00% unknown deleting segment 4 with 112 points - only 0.00% unknown mean border=88.9, 304 (139) missing vertices, mean dist -0.1 [0.3 (%60.4)->0.2 (%39.6))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4216609.5, rms=1.93 027: dt: 0.5000, sse=5127371.0, rms=1.47 rms = 1.79, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4729070.0, rms=1.14 029: dt: 0.2500, sse=4557297.0, rms=1.07 rms = 1.04, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4600918.0, rms=1.04 rms = 1.04, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4593950.5, rms=1.04 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=62.4, 355 (355) missing vertices, mean dist 1.9 [0.8 (%0.0)->2.1 (%100.0))] %40 local maxima, %43 large gradients and %13 min vals, 553 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21647096.0, rms=26.74 001: dt: 0.5000, sse=17271450.0, rms=23.44 002: dt: 0.5000, sse=13863056.0, rms=20.54 003: dt: 0.5000, sse=11567405.0, rms=18.08 004: dt: 0.5000, sse=10138300.0, rms=15.95 005: dt: 0.5000, sse=9049755.0, rms=14.05 006: dt: 0.5000, sse=8261005.5, rms=12.39 007: dt: 0.5000, sse=7671150.5, rms=10.87 008: dt: 0.5000, sse=7215164.5, rms=9.46 009: dt: 0.5000, sse=6953597.0, rms=8.16 010: dt: 0.5000, sse=6781217.5, rms=7.03 011: dt: 0.5000, sse=6726040.5, rms=6.09 012: dt: 0.5000, sse=6702583.5, rms=5.38 013: dt: 0.5000, sse=6769473.0, rms=4.89 014: dt: 0.5000, sse=6838047.5, rms=4.59 015: dt: 0.5000, sse=6909605.5, rms=4.40 016: dt: 0.5000, sse=6900720.0, rms=4.27 017: dt: 0.5000, sse=6923087.0, rms=4.19 018: dt: 0.5000, sse=6924447.0, rms=4.13 rms = 4.09, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6924941.0, rms=4.09 020: dt: 0.2500, sse=4397675.0, rms=3.03 021: dt: 0.2500, sse=4067268.0, rms=2.72 022: dt: 0.2500, sse=3906996.5, rms=2.65 rms = 2.62, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3858045.0, rms=2.62 024: dt: 0.1250, sse=3687175.8, rms=2.49 rms = 2.48, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3660365.2, rms=2.48 positioning took 2.7 minutes mean border=58.9, 473 (24) missing vertices, mean dist 0.2 [0.2 (%36.9)->0.5 (%63.1))] %60 local maxima, %28 large gradients and % 8 min vals, 219 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4611951.0, rms=5.78 026: dt: 0.5000, sse=4777389.5, rms=4.29 027: dt: 0.5000, sse=5922517.5, rms=4.21 rms = 4.24, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4806806.0, rms=3.27 029: dt: 0.2500, sse=4424281.5, rms=2.85 030: dt: 0.2500, sse=4341994.0, rms=2.72 031: dt: 0.2500, sse=4312071.5, rms=2.66 rms = 2.62, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4310002.5, rms=2.62 033: dt: 0.1250, sse=4153991.5, rms=2.49 rms = 2.47, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4132930.8, rms=2.47 positioning took 1.0 minutes mean border=56.9, 630 (17) missing vertices, mean dist 0.1 [0.2 (%36.4)->0.3 (%63.6))] %71 local maxima, %17 large gradients and % 7 min vals, 197 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4346984.0, rms=3.64 rms = 3.89, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4173736.2, rms=2.92 036: dt: 0.2500, sse=4176477.8, rms=2.54 037: dt: 0.2500, sse=4275360.0, rms=2.42 rms = 2.38, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4302348.0, rms=2.38 039: dt: 0.1250, sse=4191139.8, rms=2.28 rms = 2.27, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4191181.8, rms=2.27 positioning took 0.7 minutes mean border=55.8, 1091 (14) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %75 local maxima, %13 large gradients and % 7 min vals, 178 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4230803.0, rms=2.59 rms = 3.26, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4143899.2, rms=2.28 042: dt: 0.2500, sse=4230660.0, rms=2.19 rms = 2.15, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4266453.0, rms=2.15 044: dt: 0.1250, sse=4204892.5, rms=2.08 rms = 2.07, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4194203.0, rms=2.07 positioning took 0.6 minutes writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.area.pial vertex spacing 0.99 +- 0.40 (0.02-->7.23) (max @ vno 105535 --> 105534) face area 0.40 +- 0.28 (0.00-->6.86) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138811 vertices processed 25000 of 138811 vertices processed 50000 of 138811 vertices processed 75000 of 138811 vertices processed 100000 of 138811 vertices processed 125000 of 138811 vertices processed 0 of 138811 vertices processed 25000 of 138811 vertices processed 50000 of 138811 vertices processed 75000 of 138811 vertices processed 100000 of 138811 vertices processed 125000 of 138811 vertices processed thickness calculation complete, 413:651 truncations. 70919 vertices at 0 distance 85968 vertices at 1 distance 67282 vertices at 2 distance 27022 vertices at 3 distance 9339 vertices at 4 distance 3151 vertices at 5 distance 1195 vertices at 6 distance 481 vertices at 7 distance 267 vertices at 8 distance 161 vertices at 9 distance 108 vertices at 10 distance 98 vertices at 11 distance 74 vertices at 12 distance 50 vertices at 13 distance 27 vertices at 14 distance 20 vertices at 15 distance 21 vertices at 16 distance 12 vertices at 17 distance 13 vertices at 18 distance 8 vertices at 19 distance 10 vertices at 20 distance writing curvature file /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.thickness positioning took 11.3 minutes #-------------------------------------------- #@# Surf Volume rh Tue May 12 05:49:16 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 Tue May 12 05:49:16 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1393 964 2163 2.253 0.447 0.111 0.029 12 1.7 bankssts 1459 995 2661 2.474 0.958 0.162 0.067 33 3.8 caudalanteriorcingulate 3071 2072 5452 2.292 0.585 0.143 0.055 41 6.4 caudalmiddlefrontal 2295 1407 2600 1.637 0.409 0.155 0.060 38 5.3 cuneus 470 312 1070 2.530 0.866 0.195 0.133 58 2.5 entorhinal 3901 2602 6697 2.410 0.708 0.156 0.071 65 12.0 fusiform 8005 5279 13515 2.331 0.621 0.152 0.056 138 18.8 inferiorparietal 4998 3299 10153 2.625 0.724 0.166 0.086 137 17.9 inferiortemporal 1606 1015 2493 2.109 0.773 0.164 0.169 116 7.3 isthmuscingulate 6069 3831 8863 2.081 0.613 0.156 0.062 98 15.7 lateraloccipital 3783 2488 6368 2.275 0.780 0.162 0.072 106 11.9 lateralorbitofrontal 4259 2766 5543 1.817 0.581 0.157 0.067 74 13.1 lingual 3385 2243 5818 2.173 0.803 0.141 0.068 75 8.4 medialorbitofrontal 5498 3769 12240 2.711 0.680 0.149 0.062 101 13.6 middletemporal 910 629 1854 2.462 0.870 0.121 0.057 13 2.0 parahippocampal 2566 1535 3513 2.171 0.525 0.126 0.048 31 4.9 paracentral 2273 1564 4556 2.505 0.581 0.148 0.048 35 4.3 parsopercularis 1060 704 2163 2.538 0.644 0.163 0.097 24 4.7 parsorbitalis 2015 1372 3650 2.228 0.629 0.148 0.059 31 5.1 parstriangularis 1843 1198 1607 1.374 0.329 0.149 0.091 28 4.3 pericalcarine 6611 4115 8487 1.884 0.599 0.124 0.041 79 11.4 postcentral 1852 1275 3326 2.278 0.780 0.171 0.122 142 5.8 posteriorcingulate 7749 4803 12099 2.353 0.591 0.129 0.058 102 20.1 precentral 6636 4352 9576 2.010 0.573 0.142 0.052 97 14.4 precuneus 1289 834 2539 2.638 0.839 0.160 0.071 28 3.7 rostralanteriorcingulate 7929 5390 13729 2.091 0.683 0.167 0.075 201 24.2 rostralmiddlefrontal 9312 6295 18418 2.453 0.687 0.154 0.096 234 29.0 superiorfrontal 9645 6247 15169 2.134 0.577 0.140 0.050 143 18.1 superiorparietal 6615 4347 11745 2.417 0.620 0.126 0.047 89 12.8 superiortemporal 6880 4521 11970 2.445 0.615 0.143 0.054 105 16.6 supramarginal 490 320 1238 2.632 0.710 0.204 0.102 16 2.1 frontalpole 658 457 1856 3.007 0.641 0.161 0.068 10 1.8 temporalpole 691 368 796 1.945 0.492 0.129 0.050 8 1.3 transversetemporal 3528 2336 6818 2.865 0.992 0.139 0.113 110 10.9 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue May 12 05:49:32 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 R01L019_MD_12m rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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... 3 labels changed using aseg relabeling using gibbs priors... 000: 9524 changed, 138811 examined... 001: 2360 changed, 36544 examined... 002: 713 changed, 11851 examined... 003: 283 changed, 4034 examined... 004: 162 changed, 1646 examined... 005: 94 changed, 894 examined... 006: 49 changed, 531 examined... 007: 27 changed, 276 examined... 008: 7 changed, 132 examined... 009: 3 changed, 47 examined... 010: 1 changed, 14 examined... 011: 0 changed, 7 examined... 1 labels changed using aseg 000: 266 total segments, 184 labels (2028 vertices) changed 001: 93 total segments, 11 labels (50 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 150 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1368 vertices marked for relabeling... 1368 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue May 12 05:50:30 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 1046 683 1797 2.149 0.752 0.166 0.076 23 3.1 G_and_S_frontomargin 1213 825 1838 2.090 0.502 0.148 0.045 16 2.3 G_and_S_occipital_inf 1320 733 1735 2.048 0.470 0.135 0.060 20 3.1 G_and_S_paracentral 1429 912 2484 2.418 0.517 0.145 0.053 22 2.9 G_and_S_subcentral 1136 774 2729 2.476 0.727 0.222 0.171 66 5.8 G_and_S_transv_frontopol 3043 2077 5448 2.281 0.731 0.147 0.069 62 7.1 G_and_S_cingul-Ant 1584 1080 2906 2.447 0.736 0.156 0.150 47 4.6 G_and_S_cingul-Mid-Ant 1592 1089 2858 2.378 0.624 0.139 0.054 21 3.5 G_and_S_cingul-Mid-Post 671 422 1651 2.854 0.502 0.202 0.123 27 3.2 G_cingul-Post-dorsal 288 187 495 2.235 0.708 0.229 0.587 56 3.5 G_cingul-Post-ventral 2107 1278 2521 1.707 0.450 0.159 0.061 39 5.2 G_cuneus 1581 1067 3718 2.718 0.577 0.164 0.062 34 3.7 G_front_inf-Opercular 391 250 935 2.825 0.486 0.195 0.124 13 2.4 G_front_inf-Orbital 966 649 2105 2.461 0.540 0.167 0.066 19 2.7 G_front_inf-Triangul 3415 2301 7421 2.442 0.607 0.175 0.086 92 11.5 G_front_middle 6179 3984 13735 2.640 0.658 0.165 0.087 140 22.7 G_front_sup 492 331 1230 3.602 0.846 0.205 0.283 48 2.7 G_Ins_lg_and_S_cent_ins 622 365 1798 3.587 0.821 0.147 0.064 10 1.7 G_insular_short 1684 1088 3925 2.828 0.546 0.176 0.073 39 5.2 G_occipital_middle 2173 1280 3258 2.123 0.485 0.145 0.058 39 5.3 G_occipital_sup 1490 938 3047 2.558 0.718 0.154 0.093 29 6.0 G_oc-temp_lat-fusifor 2933 1819 4140 1.912 0.636 0.168 0.079 62 10.5 G_oc-temp_med-Lingual 1411 864 2910 2.676 0.805 0.181 0.180 107 8.6 G_oc-temp_med-Parahip 2571 1658 5315 2.494 0.740 0.182 0.094 70 10.3 G_orbital 3431 2231 6638 2.484 0.584 0.172 0.071 79 10.2 G_pariet_inf-Angular 3644 2390 7485 2.653 0.609 0.152 0.056 60 8.2 G_pariet_inf-Supramar 2983 1932 5950 2.430 0.543 0.153 0.067 60 6.8 G_parietal_sup 2466 1386 3275 1.965 0.512 0.133 0.048 39 5.1 G_postcentral 3032 1579 5244 2.594 0.522 0.128 0.082 58 11.8 G_precentral 3205 2081 6185 2.316 0.556 0.162 0.066 68 8.2 G_precuneus 857 567 1815 2.384 0.603 0.165 0.075 22 3.0 G_rectus 561 329 859 2.526 0.903 0.124 0.090 15 1.4 G_subcallosal 537 274 676 2.031 0.485 0.131 0.048 7 1.0 G_temp_sup-G_T_transv 2288 1426 5140 2.725 0.568 0.144 0.069 51 6.7 G_temp_sup-Lateral 700 482 1469 2.781 0.588 0.112 0.030 4 0.9 G_temp_sup-Plan_polar 1063 667 1676 2.228 0.465 0.116 0.034 10 1.4 G_temp_sup-Plan_tempo 3074 1987 7161 2.728 0.763 0.177 0.096 104 12.4 G_temporal_inf 3402 2247 8791 2.937 0.615 0.162 0.075 76 10.1 G_temporal_middle 366 255 429 1.822 0.493 0.119 0.028 2 0.5 Lat_Fis-ant-Horizont 119 92 199 2.244 0.457 0.121 0.043 1 0.2 Lat_Fis-ant-Vertical 1656 1114 2063 2.119 0.632 0.120 0.062 23 5.3 Lat_Fis-post 3062 1869 3801 1.802 0.497 0.157 0.062 49 7.9 Pole_occipital 1703 1152 4421 2.766 0.701 0.157 0.088 32 6.9 Pole_temporal 2370 1590 2284 1.579 0.531 0.142 0.077 30 5.0 S_calcarine 3234 2257 3415 1.647 0.559 0.116 0.033 20 4.7 S_central 1354 947 1802 1.974 0.537 0.117 0.041 12 2.4 S_cingul-Marginalis 542 382 875 2.547 0.469 0.126 0.042 5 1.1 S_circular_insula_ant 1562 1097 2413 2.419 0.893 0.103 0.032 11 1.7 S_circular_insula_inf 1647 1164 2511 2.391 0.547 0.106 0.030 9 2.1 S_circular_insula_sup 607 421 979 2.655 0.962 0.168 0.051 14 1.3 S_collat_transv_ant 439 286 422 1.561 0.430 0.163 0.060 6 1.0 S_collat_transv_post 1987 1364 2743 1.945 0.499 0.143 0.046 25 3.9 S_front_inf 2436 1683 3938 1.913 0.724 0.161 0.072 58 7.0 S_front_middle 2651 1822 3981 2.191 0.607 0.124 0.046 56 4.9 S_front_sup 546 350 634 2.017 0.431 0.133 0.042 6 0.9 S_interm_prim-Jensen 3834 2582 4582 1.852 0.462 0.125 0.037 35 6.0 S_intrapariet_and_P_trans 540 352 805 2.384 0.578 0.152 0.063 7 1.2 S_oc_middle_and_Lunatus 1615 1084 2035 2.006 0.509 0.134 0.036 16 2.4 S_oc_sup_and_transversal 393 255 587 2.081 0.519 0.127 0.070 5 0.7 S_occipital_ant 779 548 1135 2.360 0.550 0.152 0.050 9 1.7 S_oc-temp_lat 1590 1186 2065 2.014 0.516 0.119 0.030 13 2.1 S_oc-temp_med_and_Lingual 420 278 642 2.100 0.613 0.151 0.055 7 0.9 S_orbital_lateral 1002 677 1113 1.771 0.879 0.120 0.040 10 1.6 S_orbital_med-olfact 1285 848 1969 2.129 0.677 0.155 0.066 50 3.8 S_orbital-H_Shaped 2223 1431 2270 1.658 0.528 0.117 0.033 19 2.8 S_parieto_occipital 2157 1385 2400 1.895 0.905 0.157 0.105 176 5.8 S_pericallosal 2731 1849 3507 2.021 0.538 0.126 0.039 27 4.4 S_postcentral 1340 938 1992 2.161 0.567 0.121 0.036 10 1.9 S_precentral-inf-part 1420 954 1978 2.187 0.490 0.126 0.038 12 2.4 S_precentral-sup-part 554 373 544 1.612 0.504 0.092 0.019 3 0.4 S_suborbital 1519 1029 1853 1.860 0.506 0.147 0.052 18 3.3 S_subparietal 1712 1208 2354 2.321 0.505 0.134 0.042 18 2.8 S_temporal_inf 6419 4412 9256 2.219 0.561 0.125 0.039 71 10.0 S_temporal_sup 350 235 387 1.733 0.450 0.105 0.030 2 0.4 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue May 12 05:50:47 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon R01L019_MD_12m SUBJECTS_DIR is /autofs/cluster/hab/FreeSurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 4 writing volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue May 12 06:05:04 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m 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 /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject R01L019_MD_12m $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 /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject R01L019_MD_12m sysname Linux hostname compute-0-65 machine x86_64 user mlapoint atlas_icv (eTIV) = 1619216 mm^3 (det: 1.203117 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 211051 rh white matter volume 217091 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 245712.427901, pTot = 463375.588979 c = 217663.161078 rh surface-based volumes (mm3): wTot = 247127.546581, pTot = 462307.316238 c = 215179.769657 Computing SupraTentVolCor SupraTentVolCor = 57587.000 SupraTentVol = 983269.905 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 22183 22183 4 5 Left-Inf-Lat-Vent 959 959 5 7 Left-Cerebellum-White-Matter 12689 12689 6 8 Left-Cerebellum-Cortex 46359 46359 7 10 Left-Thalamus-Proper 5420 5420 8 11 Left-Caudate 3162 3162 9 12 Left-Putamen 5263 5263 10 13 Left-Pallidum 1517 1517 11 14 3rd-Ventricle 2052 2052 12 15 4th-Ventricle 3195 3195 13 16 Brain-Stem 20634 20634 14 17 Left-Hippocampus 3506 3506 15 18 Left-Amygdala 1095 1095 16 24 CSF 1962 1962 17 26 Left-Accumbens-area 472 472 18 28 Left-VentralDC 3426 3426 19 30 Left-vessel 127 127 20 31 Left-choroid-plexus 2857 2857 23 43 Right-Lateral-Ventricle 19592 19592 24 44 Right-Inf-Lat-Vent 1168 1168 25 46 Right-Cerebellum-White-Matter 12888 12888 26 47 Right-Cerebellum-Cortex 49752 49752 27 49 Right-Thalamus-Proper 5548 5548 28 50 Right-Caudate 3205 3205 29 51 Right-Putamen 4584 4584 30 52 Right-Pallidum 1370 1370 31 53 Right-Hippocampus 3440 3440 32 54 Right-Amygdala 1057 1057 33 58 Right-Accumbens-area 502 502 34 60 Right-VentralDC 3255 3255 35 62 Right-vessel 121 121 36 63 Right-choroid-plexus 3279 3279 37 72 5th-Ventricle 36 36 38 77 WM-hypointensities 5932 5932 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 51 51 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 375 375 45 251 CC_Posterior 720 720 46 252 CC_Mid_Posterior 261 261 47 253 CC_Central 359 359 48 254 CC_Mid_Anterior 336 336 49 255 CC_Anterior 603 603 Reporting on 45 segmentations SubCortGrayVol = 163567 #----------------------------------------- #@# AParc-to-ASeg Tue May 12 06:13:48 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --volmask SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 426979 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --volmask --a2009s SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 426979 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue May 12 06:16:14 EDT 2015 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m mri_aparc2aseg --s R01L019_MD_12m --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer subject R01L019_MD_12m outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading lh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial Loading lh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading rh pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial Loading rh annotations from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/ribbon.mgz Loading filled from /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7907 vertices from left hemi Ripped 8067 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 830758 Used brute-force search on 25 voxels Fixing Parahip LH WM Found 4 clusters 0 k 6.000000 1 k 1457.000000 2 k 2.000000 3 k 4.000000 Fixing Parahip RH WM Found 2 clusters 0 k 1411.000000 1 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m 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 R01L019_MD_12m --surf-wm-vol --ctab /autofs/space/plato_002/users/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 R01L019_MD_12m --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-65 machine x86_64 user mlapoint atlas_icv (eTIV) = 1619216 mm^3 (det: 1.203117 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 211051 rh white matter volume 217091 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1650567 # brainmaskvolume 1650567.0 # nbrainsegvoxels 246938 # brainsegvolume 246938.0 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 2798 2798 2 3002 wm-lh-caudalanteriorcingulate 3180 3180 3 3003 wm-lh-caudalmiddlefrontal 5387 5387 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2144 2144 6 3006 wm-lh-entorhinal 771 771 7 3007 wm-lh-fusiform 5268 5268 8 3008 wm-lh-inferiorparietal 10360 10360 9 3009 wm-lh-inferiortemporal 5880 5880 10 3010 wm-lh-isthmuscingulate 4671 4671 11 3011 wm-lh-lateraloccipital 7450 7450 12 3012 wm-lh-lateralorbitofrontal 6493 6493 13 3013 wm-lh-lingual 4575 4575 14 3014 wm-lh-medialorbitofrontal 3904 3904 15 3015 wm-lh-middletemporal 4646 4646 16 3016 wm-lh-parahippocampal 1675 1675 17 3017 wm-lh-paracentral 3053 3053 18 3018 wm-lh-parsopercularis 3325 3325 19 3019 wm-lh-parsorbitalis 849 849 20 3020 wm-lh-parstriangularis 2803 2803 21 3021 wm-lh-pericalcarine 2982 2982 22 3022 wm-lh-postcentral 6632 6632 23 3023 wm-lh-posteriorcingulate 4088 4088 24 3024 wm-lh-precentral 13019 13019 25 3025 wm-lh-precuneus 9586 9586 26 3026 wm-lh-rostralanteriorcingulate 2647 2647 27 3027 wm-lh-rostralmiddlefrontal 11243 11243 28 3028 wm-lh-superiorfrontal 14846 14846 29 3029 wm-lh-superiorparietal 12833 12833 30 3030 wm-lh-superiortemporal 7898 7898 31 3031 wm-lh-supramarginal 9074 9074 32 3032 wm-lh-frontalpole 231 231 33 3033 wm-lh-temporalpole 615 615 34 3034 wm-lh-transversetemporal 1078 1078 35 3035 wm-lh-insula 9801 9801 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 2637 2637 120 4002 wm-rh-caudalanteriorcingulate 3102 3102 121 4003 wm-rh-caudalmiddlefrontal 5124 5124 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 2206 2206 124 4006 wm-rh-entorhinal 580 580 125 4007 wm-rh-fusiform 5174 5174 126 4008 wm-rh-inferiorparietal 11023 11023 127 4009 wm-rh-inferiortemporal 5793 5793 128 4010 wm-rh-isthmuscingulate 3140 3140 129 4011 wm-rh-lateraloccipital 7723 7723 130 4012 wm-rh-lateralorbitofrontal 5747 5747 131 4013 wm-rh-lingual 4825 4825 132 4014 wm-rh-medialorbitofrontal 3938 3938 133 4015 wm-rh-middletemporal 5673 5673 134 4016 wm-rh-parahippocampal 1601 1601 135 4017 wm-rh-paracentral 4212 4212 136 4018 wm-rh-parsopercularis 3180 3180 137 4019 wm-rh-parsorbitalis 1083 1083 138 4020 wm-rh-parstriangularis 2933 2933 139 4021 wm-rh-pericalcarine 2621 2621 140 4022 wm-rh-postcentral 7206 7206 141 4023 wm-rh-posteriorcingulate 4035 4035 142 4024 wm-rh-precentral 12931 12931 143 4025 wm-rh-precuneus 10315 10315 144 4026 wm-rh-rostralanteriorcingulate 2690 2690 145 4027 wm-rh-rostralmiddlefrontal 11068 11068 146 4028 wm-rh-superiorfrontal 14798 14798 147 4029 wm-rh-superiorparietal 12700 12700 148 4030 wm-rh-superiortemporal 7793 7793 149 4031 wm-rh-supramarginal 10166 10166 150 4032 wm-rh-frontalpole 420 420 151 4033 wm-rh-temporalpole 676 676 152 4034 wm-rh-transversetemporal 708 708 153 4035 wm-rh-insula 9620 9620 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 17219 17219 237 5002 Right-UnsegmentedWhiteMatter 19366 19366 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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label #-------------------------------------------- #@# BA Labels lh Tue May 12 06:33:14 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA1.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 345 Checking for and removing duplicates Writing label file ./lh.BA1.label 4474 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA2.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 535 Checking for and removing duplicates Writing label file ./lh.BA2.label 8444 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3a.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 199 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4276 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3b.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 385 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6368 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4a.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 563 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6347 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4p.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 416 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4486 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA6.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1202 Checking for and removing duplicates Writing label file ./lh.BA6.label 14791 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA44.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 475 Checking for and removing duplicates Writing label file ./lh.BA44.label 4656 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA45.label --trgsubject R01L019_MD_12m --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 854 Checking for and removing duplicates Writing label file ./lh.BA45.label 4276 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V1.label --trgsubject R01L019_MD_12m --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1135 Checking for and removing duplicates Writing label file ./lh.V1.label 5776 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V2.label --trgsubject R01L019_MD_12m --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 2774 Checking for and removing duplicates Writing label file ./lh.V2.label 10888 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.MT.label --trgsubject R01L019_MD_12m --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 340 Checking for and removing duplicates Writing label file ./lh.MT.label 2358 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s R01L019_MD_12m --hemi lh --ctab /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label cmdline mris_label2annot --s R01L019_MD_12m --hemi lh --ctab /autofs/space/plato_002/users/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 compute-0-65 machine x86_64 user mlapoint subject R01L019_MD_12m hemi lh SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer ColorTable /autofs/space/plato_002/users/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 93682 unhit vertices Writing annot to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab R01L019_MD_12m lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /autofs/space/plato_002/users/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 1141 644 1646 1.962 0.410 0.155 0.065 24 3.4 BA1 3999 2686 5809 2.000 0.585 0.131 0.053 58 7.3 BA2 1003 697 817 1.432 0.360 0.146 0.045 11 1.9 BA3a 2485 1621 3069 1.707 0.640 0.126 0.042 27 4.3 BA3b 1824 984 2844 2.509 0.499 0.126 0.055 33 4.2 BA4a 1538 971 2125 2.229 0.498 0.126 0.056 19 4.4 BA4p 9080 5949 17780 2.597 0.647 0.143 0.094 219 41.4 BA6 2440 1590 4727 2.521 0.538 0.143 0.053 33 5.1 BA44 3280 2239 5746 2.175 0.613 0.147 0.051 51 6.9 BA45 3311 2149 3431 1.509 0.465 0.136 0.046 43 6.4 V1 8353 5214 10364 1.823 0.542 0.159 0.073 143 22.5 V2 1758 1162 2814 2.075 0.671 0.131 0.044 22 3.3 MT #-------------------------------------------- #@# BA Labels rh Tue May 12 06:35:14 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA1.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 391 Checking for and removing duplicates Writing label file ./rh.BA1.label 4353 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA2.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 579 Checking for and removing duplicates Writing label file ./rh.BA2.label 7266 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3a.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 156 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4136 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3b.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 286 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4808 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4a.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 553 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6300 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4p.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 187 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4660 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA6.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1161 Checking for and removing duplicates Writing label file ./rh.BA6.label 13417 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA44.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 772 Checking for and removing duplicates Writing label file ./rh.BA44.label 7684 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA45.label --trgsubject R01L019_MD_12m --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 880 Checking for and removing duplicates Writing label file ./rh.BA45.label 6235 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V1.label --trgsubject R01L019_MD_12m --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 1294 Checking for and removing duplicates Writing label file ./rh.V1.label 6021 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V2.label --trgsubject R01L019_MD_12m --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 2675 Checking for and removing duplicates Writing label file ./rh.V2.label 10691 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.MT.label --trgsubject R01L019_MD_12m --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/hab/FreeSurfer/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = R01L019_MD_12m 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 /autofs/cluster/hab/FreeSurfer FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/hab/FreeSurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white Reading target registration /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 = 320 Checking for and removing duplicates Writing label file ./rh.MT.label 2252 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s R01L019_MD_12m --hemi rh --ctab /autofs/space/plato_002/users/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 /autofs/space/plato_002/users/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 /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label cmdline mris_label2annot --s R01L019_MD_12m --hemi rh --ctab /autofs/space/plato_002/users/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 compute-0-65 machine x86_64 user mlapoint subject R01L019_MD_12m hemi rh SUBJECTS_DIR /autofs/cluster/hab/FreeSurfer ColorTable /autofs/space/plato_002/users/freesurfer/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 99209 unhit vertices Writing annot to /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab R01L019_MD_12m rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /autofs/space/plato_002/users/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 1077 539 1436 2.161 0.413 0.146 0.059 19 2.9 BA1 3523 2317 5033 2.089 0.547 0.127 0.042 41 5.9 BA2 1023 711 831 1.422 0.337 0.138 0.043 10 1.8 BA3a 2157 1360 2223 1.473 0.413 0.115 0.037 23 3.5 BA3b 1624 920 2391 2.299 0.451 0.117 0.038 17 2.7 BA4a 1297 872 1902 2.230 0.491 0.124 0.045 12 2.6 BA4p 8009 4875 14516 2.515 0.617 0.142 0.081 145 28.6 BA6 3700 2558 6944 2.411 0.601 0.144 0.048 51 7.0 BA44 3891 2640 6942 2.267 0.675 0.158 0.065 70 10.8 BA45 3588 2272 3852 1.543 0.450 0.156 0.059 58 9.1 V1 7915 4945 9600 1.808 0.528 0.157 0.074 138 22.2 V2 1798 1210 3040 2.326 0.630 0.127 0.042 19 3.0 MT /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue May 12 06:37:16 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o R01L019_MD_12m label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject R01L019_MD_12m. processing subject lh.EC_average... reading output surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 R01L019_MD_12m lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/lh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 297 210 951 2.870 0.833 0.145 0.057 3 0.7 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue May 12 06:37:34 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o R01L019_MD_12m label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject R01L019_MD_12m. processing subject rh.EC_average... reading output surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 711 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 R01L019_MD_12m rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/mri/wm.mgz... reading input surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.white... reading input pial surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/surf/rh.pial... reading input white surface /autofs/cluster/hab/FreeSurfer/R01L019_MD_12m/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 217 147 676 2.789 0.783 0.142 0.064 3 0.6 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s R01L019_MD_12m finished without error at Tue May 12 06:37:51 EDT 2015 New invocation of recon-all Thu Dec 14 17:02:02 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4015012 4618208 145292 15879356 19906120 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-22:02:02-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:02:02-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:02:02-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:02-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:02:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 17:02:06 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.761 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 17:02:06 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.761 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 17:02:07 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.761/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 17:02:07 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 17:20:48 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 3919840 4559688 164040 16033048 19984780 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:48-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:49-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:20:50-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 17:20:50 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.3320 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 17:20:50 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.3320 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 17:20:50 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.3320/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 17:20:50 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 17:30:41 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4180284 4297568 155272 16034724 19732880 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:41-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:42-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-22:30:43-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 17:30:43 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.4412 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 17:30:43 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.4412 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 17:30:43 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4412/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 17:30:44 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:07:19 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4138812 4345596 148428 16028168 19781228 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:07:19-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:07:19-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:07:19-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:19-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:19-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:20-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:07:21-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 18:07:22 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.7457 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 18:07:22 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.7457 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 18:07:22 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7457/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:07:22 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:09:06 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage/ subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4140600 4342176 148432 16029800 19779404 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:09:06-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:07-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:09:08-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:09-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:09-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:09-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:09:09-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage/ Thu Dec 14 18:09:09 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage/ --out lh.thickness.fsaverage/.mgh ERROR: format for lh.thickness.fsaverage/.mgh not recognized Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:09:09 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:13:03 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage/ subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4186040 4137536 148432 16189000 19733988 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:03-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:04-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:05-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage/ Thu Dec 14 18:13:05 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage/ --out lh.thickness.fsaverage/.mgh ERROR: format for lh.thickness.fsaverage/.mgh not recognized Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:13:05 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:13:29 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4187492 4136072 148432 16189012 19732548 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:30-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:31-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:13:32-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 18:13:32 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9850 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 18:13:32 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.9850 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 18:13:32 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9850/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:13:32 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:15:52 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -s B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4187984 4135624 148432 16188968 19732088 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:52-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:53-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:15:54-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 18:15:54 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10226 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 18:15:54 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.10226 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 18:15:54 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10226/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:15:54 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Dec 14 18:16:45 EST 2017 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14 /autofs/space/plato_002/users/freesurfer/bin/recon-all -subjid B_02PSWW_2187-09-14 -qcache -measure thickness -target fsaverage subjid B_02PSWW_2187-09-14 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 95612 maxlocks unlimited maxsignal 95612 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 24512576 4188856 4134472 148436 16189248 19731212 Swap: 25645028 6800 25638228 ######################################## 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: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:45-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:46-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 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: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/12/14-23:16:47-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: fdu0 Machine: plato.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-693.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Dec 14 18:16:47 EST 2017 mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10499 /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 14 18:16:47 EST 2017 setenv SUBJECTS_DIR /autofs/space/rincewind_002/users/R01_Awareness_ana cd /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf /autofs/space/plato_002/users/freesurfer/bin/mris_preproc --s B_02PSWW_2187-09-14 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.10499 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 B_02PSWW_2187-09-14 Thu Dec 14 18:16:47 EST 2017 -------------- ----------------------- mri_surf2surf --srcsubject B_02PSWW_2187-09-14 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10499/B_02PSWW_2187-09-14.1.mgh --sval /autofs/space/rincewind_002/users/R01_Awareness_ana/B_02PSWW_2187-09-14/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped) Linux plato.nmr.mgh.harvard.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_02PSWW_2187-09-14 exited with ERRORS at Thu Dec 14 18:16:48 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting