Thu Apr 14 20:03:48 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 /usr/local/freesurfer/stable5_3_0/bin/recon-all -all -subjid nmr01002 -i /cluster/neuromind/dwakeman/tsc_pilot/raw//nmr01002/mri_0/003_MEMPRAGE_unwarped.mgz -FLAIRpial -FLAIR /cluster/neuromind/dwakeman/tsc_pilot/raw//nmr01002/mri_0/013_FLAIR_unwarped.mgz -openmp 8 subjid nmr01002 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 58720256 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 1300140 31577112 168 190644 60940 -/+ buffers/cache: 1048556 31828696 Swap: 67108860 86336 67022524 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:49-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:50-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:52-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:53-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:53-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:54-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:55-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:55-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 8 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:55-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:56-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:56-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:56-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:57-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:57-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:57-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:57-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:57-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:58-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:58-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:59-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:59-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:03:59-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:01-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:01-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:02-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:02-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:04-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:04-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-00:04:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: dwakeman Machine: compute-0-68 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/003_MEMPRAGE_unwarped.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/001.mgz mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/003_MEMPRAGE_unwarped.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/003_MEMPRAGE_unwarped.mgz... TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Thu Apr 14 20:04:20 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/013_FLAIR_unwarped.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/013_FLAIR_unwarped.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/raw/nmr01002/mri_0/013_FLAIR_unwarped.mgz... TR=5000.00, TE=387.00, TI=1800.00, flip angle=120.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz... #-------------------------------------------- #@# MotionCor Thu Apr 14 20:04:26 EDT 2016 Found 1 runs /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/001.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz --conform mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz... TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/talairach.xfm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Apr 14 20:04:43 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Apr 14 20:07:31 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6134, pval=0.2817 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable5_3_0/bin/extract_talairach_avi_QA.awk /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/talairach_avi.log TalAviQA: 0.97622 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Apr 14 20:07:31 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri /usr/local/freesurfer/stable5_3_0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Apr 14 20:07:31 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.6786 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6786/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6786/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 5.21541e-08) j_ras = (-2.98023e-08, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6786/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Apr 14 20:07:35 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.6786/nu0.mnc ./tmp.mri_nu_correct.mni.6786/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6786/0/ [dwakeman@compute-0-68:/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/] [2016-04-14 20:07:35] running: /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6786/0/ ./tmp.mri_nu_correct.mni.6786/nu0.mnc ./tmp.mri_nu_correct.mni.6786/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 45 CV of field change: 0.000960291 [dwakeman@compute-0-68:/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/] [2016-04-14 20:08:30] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6786/nu0.mnc ./tmp.mri_nu_correct.mni.6786/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Apr 14 20:08:33 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.6786/nu1.mnc ./tmp.mri_nu_correct.mni.6786/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6786/1/ [dwakeman@compute-0-68:/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/] [2016-04-14 20:08:33] running: /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6786/1/ ./tmp.mri_nu_correct.mni.6786/nu1.mnc ./tmp.mri_nu_correct.mni.6786/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 31 CV of field change: 0.000987454 [dwakeman@compute-0-68:/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/] [2016-04-14 20:09:11] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6786/nu1.mnc ./tmp.mri_nu_correct.mni.6786/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.6786/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6786/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.6786/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6786/ones.mgz sysname Linux hostname compute-0-68 machine x86_64 user dwakeman input ./tmp.mri_nu_correct.mni.6786/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6786/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.6786/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6786/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6786/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6786/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6786/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6786/input.mean.dat sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6786/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6786/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6786/ones.mgz --i ./tmp.mri_nu_correct.mni.6786/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6786/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6786/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6786/ones.mgz --i ./tmp.mri_nu_correct.mni.6786/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6786/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6786/output.mean.dat sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6786/ones.mgz Loading ./tmp.mri_nu_correct.mni.6786/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6786/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6786/nu2.mnc ./tmp.mri_nu_correct.mni.6786/nu2.mnc mul .93178291812129416328 Saving result to './tmp.mri_nu_correct.mni.6786/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6786/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.6786/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.6786/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 5.21541e-08) j_ras = (-2.98023e-08, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (21, 141) to ( 3, 110) Thu Apr 14 20:10:03 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Apr 14 20:10:05 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.040 -0.044 -0.128 -6.109; 0.083 0.965 0.257 -25.099; 0.105 -0.216 0.978 11.354; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 31 (31) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 69 (69), valley at 30 (30) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 16 seconds. #-------------------------------------------- #@# Skull Stripping Thu Apr 14 20:12:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (46, 21, 32) --> (212, 255, 233) using (101, 99, 133) as brain centroid... mean wm in atlas = 126, using box (81,70,108) --> (121, 127,157) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.387005 @ (0.000, 0.000, 0.000) max log p = -4.310159 @ (4.545, 13.636, -4.545) max log p = -4.224803 @ (-2.273, -2.273, 6.818) max log p = -4.215783 @ (-1.136, -1.136, 1.136) max log p = -4.205330 @ (0.568, -1.705, -1.705) max log p = -4.204324 @ (-1.989, 0.284, 0.852) Found translation: (-0.3, 8.8, 2.6): log p = -4.204 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 0.991 -0.148 -0.022 19.716; 0.131 1.125 0.168 -31.567; 0.000 -0.103 0.922 22.246; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.991 -0.148 -0.022 19.716; 0.131 1.125 0.168 -31.567; 0.000 -0.103 0.922 22.246; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.007 -0.162 0.038 13.131; 0.133 1.137 0.232 -43.499; -0.075 -0.170 0.925 38.257; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.007 -0.162 0.038 13.131; 0.133 1.137 0.232 -43.499; -0.075 -0.170 0.925 38.257; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.002 -0.164 0.053 11.500; 0.134 1.140 0.224 -42.213; -0.090 -0.157 0.924 38.455; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.002 -0.164 0.053 11.500; 0.133 1.138 0.224 -42.021; -0.090 -0.157 0.924 38.455; 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 1.00172 -0.16445 0.05305 11.50043; 0.13343 1.13847 0.22423 -42.02117; -0.08989 -0.15728 0.92432 38.45479; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.00172 -0.16445 0.05305 11.50043; 0.13343 1.13847 0.22423 -42.02117; -0.08989 -0.15728 0.92432 38.45479; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.002 -0.164 0.053 11.500; 0.133 1.138 0.224 -42.021; -0.090 -0.157 0.924 38.455; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.4) transform before final EM align: 1.002 -0.164 0.053 11.500; 0.133 1.138 0.224 -42.021; -0.090 -0.157 0.924 38.455; 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 1.00172 -0.16445 0.05305 11.50043; 0.13343 1.13847 0.22423 -42.02117; -0.08989 -0.15728 0.92432 38.45479; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.00172 -0.16445 0.05305 11.50043; 0.13343 1.13847 0.22423 -42.02117; -0.08989 -0.15728 0.92432 38.45479; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.002 -0.164 0.053 11.500; 0.133 1.138 0.224 -42.021; -0.090 -0.157 0.924 38.455; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 19 minutes and 37 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=102 z=108 r=97 first estimation of the main basin volume: 3899326 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=105, y=94, z=63, Imax=255 CSF=15, 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=22340696446 voxels, voxel volume =1.000 = 22340696446 mmm3 = 22340696.064 cm3 done. PostAnalyze...Basin Prior 43 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=125,y=106, z=102, r=10259 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45081 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1030005474 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1084962674 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = 1085519519 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 1080386640 OTHER CSF_MIN=2, CSF_intensity=21, CSF_MAX=48 , nb = 1069307508 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 10, 46, 66 after analyzing : 5, 34, 46, 42 RIGHT_CER before analyzing : 4, 5, 40, 77 after analyzing : 4, 28, 40, 40 LEFT_CER before analyzing : 4, 6, 43, 74 after analyzing : 4, 30, 43, 41 RIGHT_BRAIN before analyzing : 16, 27, 45, 66 after analyzing : 16, 39, 45, 45 LEFT_BRAIN before analyzing : 19, 31, 46, 67 after analyzing : 19, 41, 46, 47 OTHER before analyzing : 48, 70, 80, 92 after analyzing : 48, 76, 80, 80 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.012 curvature mean = 73.141, std = 8.567 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.69, sigma = 3.33 after rotation: sse = 1.69, sigma = 3.33 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.79, its var is 3.14 before Erosion-Dilatation 0.34% 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...46 iterations mri_strip_skull: done peeling brain Brain Size = 1957838 voxels, voxel volume = 1.000 mm3 = 1957838 mmm3 = 1957.838 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Apr 14 20:32:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=31.1 skull bounding box = (59, 39, 21) --> (194, 180, 195) using (104, 86, 108) as brain centroid... mean wm in atlas = 107, using box (87,69,87) --> (120, 103,129) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.079038 @ (-9.091, 9.091, 9.091) max log p = -3.947038 @ (13.636, 4.545, -4.545) max log p = -3.811541 @ (-2.273, -2.273, -2.273) max log p = -3.759173 @ (-1.136, 3.409, -1.136) max log p = -3.754446 @ (-0.568, 1.705, -0.568) max log p = -3.742680 @ (-0.852, -1.420, -0.852) Found translation: (-0.3, 15.1, -0.3): log p = -3.743 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7) 1.066 -0.136 -0.036 9.258; 0.140 1.029 0.276 -34.970; 0.000 -0.239 0.893 43.317; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6) 1.059 -0.148 0.084 -0.382; 0.139 1.052 0.157 -25.560; -0.121 -0.084 0.919 32.310; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.059 -0.148 0.084 -0.382; 0.139 1.052 0.157 -25.560; -0.121 -0.084 0.919 32.310; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.023 -0.134 0.054 6.018; 0.129 1.078 0.256 -37.600; -0.098 -0.191 0.902 46.099; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.023 -0.134 0.054 6.018; 0.129 1.078 0.256 -37.600; -0.098 -0.191 0.902 46.099; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.025 -0.115 0.051 4.591; 0.112 1.080 0.255 -36.074; -0.089 -0.192 0.903 45.477; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 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 1.02446 -0.10601 0.05298 3.47265; 0.10362 1.07925 0.25475 -34.41947; -0.08922 -0.19168 0.90201 45.54724; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.02446 -0.10601 0.05298 3.47265; 0.10362 1.07925 0.25475 -34.41947; -0.08922 -0.19168 0.90201 45.54724; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.2) transform before final EM align: 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 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 1.02446 -0.10601 0.05298 3.47265; 0.10362 1.07925 0.25475 -34.41947; -0.08922 -0.19168 0.90201 45.54724; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.02446 -0.10601 0.05298 3.47265; 0.10362 1.07925 0.25475 -34.41947; -0.08922 -0.19168 0.90201 45.54724; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.8 tol 0.000000 final transform: 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 18 minutes and 10 seconds. #-------------------------------------- #@# CA Normalize Thu Apr 14 20:50:39 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=31.1 skull bounding box = (59, 39, 21) --> (194, 180, 195) using (104, 86, 108) as brain centroid... mean wm in atlas = 107, using box (87,69,87) --> (120, 103,129) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 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 (121, 44, 20) --> (191, 150, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 180.0 0 of 201 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 47, 17) --> (127, 151, 196) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 180.0 0 of 429 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 127, 50) --> (180, 165, 107) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 180.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 127, 45) --> (132, 170, 106) Right_Cerebellum_White_Matter: limiting intensities to 102.0 --> 180.0 2 of 15 (13.3%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 116, 86) --> (145, 180, 118) Brain_Stem: limiting intensities to 121.0 --> 180.0 13 of 15 (86.7%) samples deleted using 669 total control points for intensity normalization... bias field = 1.047 +- 0.070 2 of 654 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (121, 44, 20) --> (191, 150, 197) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 168.0 0 of 193 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 47, 17) --> (127, 151, 196) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 168.0 0 of 405 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 127, 50) --> (180, 165, 107) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 168.0 0 of 58 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 127, 45) --> (132, 170, 106) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 168.0 0 of 44 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 116, 86) --> (145, 180, 118) Brain_Stem: limiting intensities to 90.0 --> 168.0 0 of 80 (0.0%) samples deleted using 780 total control points for intensity normalization... bias field = 0.985 +- 0.083 0 of 780 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (121, 44, 20) --> (191, 150, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 159.0 0 of 276 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 47, 17) --> (127, 151, 196) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 159.0 0 of 454 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 127, 50) --> (180, 165, 107) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 159.0 0 of 84 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 127, 45) --> (132, 170, 106) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 159.0 0 of 68 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 116, 86) --> (145, 180, 118) Brain_Stem: limiting intensities to 91.0 --> 159.0 58 of 176 (33.0%) samples deleted using 1058 total control points for intensity normalization... bias field = 1.004 +- 0.056 0 of 1000 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 45 seconds. #-------------------------------------- #@# CA Reg Thu Apr 14 20:52:25 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 8 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.06 (predicted orig area = 7.5) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.785, neg=0, invalid=96777 0001: dt=129.472000, rms=0.736 (6.260%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.711 (3.372%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.705 (0.856%), neg=0, invalid=96777 0004: dt=517.888000, rms=0.694 (1.582%), neg=0, invalid=96777 0005: dt=92.480000, rms=0.690 (0.490%), neg=0, invalid=96777 0006: dt=517.888000, rms=0.684 (0.994%), neg=0, invalid=96777 0007: dt=110.976000, rms=0.682 (0.279%), neg=0, invalid=96777 0008: dt=369.920000, rms=0.679 (0.362%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.678 (0.237%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.677 (0.109%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.676 (0.168%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.674 (0.212%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.673 (0.235%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.671 (0.253%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.669 (0.260%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.667 (0.268%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.666 (0.294%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.664 (0.277%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.662 (0.254%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.660 (0.247%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.659 (0.221%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.658 (0.202%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.656 (0.183%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.655 (0.196%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.654 (0.202%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.653 (0.174%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.652 (0.145%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.651 (0.100%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.650 (0.112%), neg=0, invalid=96777 0030: dt=73.984000, rms=0.649 (0.131%), neg=0, invalid=96777 0031: dt=73.984000, rms=0.649 (0.123%), neg=0, invalid=96777 0032: dt=73.984000, rms=0.648 (0.107%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.648 (0.008%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.648 (0.032%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.647 (0.032%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.647 (0.054%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.647 (0.048%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.646 (0.059%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.646 (0.092%), neg=0, invalid=96777 0040: dt=129.472000, rms=0.645 (0.086%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=96777 0041: dt=129.472000, rms=0.645 (0.087%), neg=0, invalid=96777 0042: dt=517.888000, rms=0.644 (0.163%), neg=0, invalid=96777 0043: dt=5.780000, rms=0.644 (0.002%), neg=0, invalid=96777 0044: dt=5.780000, rms=0.644 (0.001%), neg=0, invalid=96777 0045: dt=5.780000, rms=0.644 (0.001%), neg=0, invalid=96777 0046: dt=5.780000, rms=0.644 (0.002%), neg=0, invalid=96777 0047: dt=5.780000, rms=0.644 (0.002%), neg=0, invalid=96777 0048: dt=5.780000, rms=0.644 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0049: dt=145.152000, rms=0.640 (1.306%), neg=0, invalid=96777 0050: dt=124.416000, rms=0.632 (1.244%), neg=0, invalid=96777 0051: dt=31.104000, rms=0.629 (0.555%), neg=0, invalid=96777 0052: dt=145.152000, rms=0.624 (0.751%), neg=0, invalid=96777 0053: dt=62.208000, rms=0.622 (0.351%), neg=0, invalid=96777 0054: dt=82.944000, rms=0.619 (0.468%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.618 (0.162%), neg=0, invalid=96777 0056: dt=31.104000, rms=0.617 (0.153%), neg=0, invalid=96777 0057: dt=31.104000, rms=0.615 (0.261%), neg=0, invalid=96777 0058: dt=31.104000, rms=0.613 (0.328%), neg=0, invalid=96777 0059: dt=31.104000, rms=0.611 (0.363%), neg=0, invalid=96777 0060: dt=31.104000, rms=0.609 (0.396%), neg=0, invalid=96777 0061: dt=31.104000, rms=0.606 (0.413%), neg=0, invalid=96777 0062: dt=31.104000, rms=0.604 (0.410%), neg=0, invalid=96777 0063: dt=31.104000, rms=0.601 (0.387%), neg=0, invalid=96777 0064: dt=31.104000, rms=0.599 (0.355%), neg=0, invalid=96777 0065: dt=31.104000, rms=0.597 (0.348%), neg=0, invalid=96777 0066: dt=31.104000, rms=0.595 (0.308%), neg=0, invalid=96777 0067: dt=31.104000, rms=0.594 (0.267%), neg=0, invalid=96777 0068: dt=31.104000, rms=0.592 (0.285%), neg=0, invalid=96777 0069: dt=31.104000, rms=0.590 (0.267%), neg=0, invalid=96777 0070: dt=31.104000, rms=0.589 (0.210%), neg=0, invalid=96777 0071: dt=31.104000, rms=0.588 (0.166%), neg=0, invalid=96777 0072: dt=31.104000, rms=0.587 (0.178%), neg=0, invalid=96777 0073: dt=31.104000, rms=0.586 (0.172%), neg=0, invalid=96777 0074: dt=31.104000, rms=0.585 (0.181%), neg=0, invalid=96777 0075: dt=31.104000, rms=0.584 (0.158%), neg=0, invalid=96777 0076: dt=31.104000, rms=0.583 (0.136%), neg=0, invalid=96777 0077: dt=31.104000, rms=0.583 (0.134%), neg=0, invalid=96777 0078: dt=31.104000, rms=0.582 (0.147%), neg=0, invalid=96777 0079: dt=31.104000, rms=0.581 (0.135%), neg=0, invalid=96777 0080: dt=31.104000, rms=0.580 (0.101%), neg=0, invalid=96777 0081: dt=31.104000, rms=0.580 (0.082%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.580 (0.007%), neg=0, invalid=96777 0083: dt=36.288000, rms=0.580 (0.035%), neg=0, invalid=96777 0084: dt=36.288000, rms=0.580 (0.020%), neg=0, invalid=96777 0085: dt=36.288000, rms=0.580 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.580, neg=0, invalid=96777 0086: dt=36.288000, rms=0.579 (0.083%), neg=0, invalid=96777 0087: dt=62.208000, rms=0.579 (0.048%), neg=0, invalid=96777 0088: dt=62.208000, rms=0.578 (0.047%), neg=0, invalid=96777 0089: dt=62.208000, rms=0.578 (0.046%), neg=0, invalid=96777 0090: dt=62.208000, rms=0.578 (-0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0091: dt=1.600000, rms=0.603 (0.006%), neg=0, invalid=96777 0092: dt=0.500000, rms=0.603 (0.002%), neg=0, invalid=96777 0093: dt=0.500000, rms=0.603 (0.000%), neg=0, invalid=96777 0094: dt=0.500000, rms=0.603 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0095: dt=0.000000, rms=0.603 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.673, neg=0, invalid=96777 0096: dt=5.274510, rms=0.651 (3.249%), neg=0, invalid=96777 0097: dt=3.000000, rms=0.650 (0.172%), neg=0, invalid=96777 0098: dt=3.000000, rms=0.650 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=96777 0099: dt=0.000000, rms=0.650 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.712, neg=0, invalid=96777 0100: dt=1.085648, rms=0.708 (0.564%), neg=0, invalid=96777 0101: dt=2.040462, rms=0.702 (0.789%), neg=0, invalid=96777 0102: dt=0.448000, rms=0.702 (0.059%), neg=0, invalid=96777 0103: dt=0.448000, rms=0.701 (0.032%), neg=0, invalid=96777 0104: dt=0.448000, rms=0.701 (0.024%), neg=0, invalid=96777 0105: dt=0.448000, rms=0.701 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.701, neg=0, invalid=96777 0106: dt=1.308511, rms=0.700 (0.177%), neg=0, invalid=96777 0107: dt=0.000078, rms=0.700 (0.001%), neg=0, invalid=96777 0108: dt=0.000078, rms=0.700 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0109: dt=0.448000, rms=0.640 (2.412%), neg=0, invalid=96777 0110: dt=0.000000, rms=0.640 (0.004%), neg=0, invalid=96777 0111: dt=0.050000, rms=0.640 (-0.336%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0112: dt=0.000000, rms=0.640 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12457 (16) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (2420 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (2420 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.10611 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (2078 voxels, overlap=0.230) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (2078 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.11630 (110) Right_Pallidum (52): linear fit = 1.12 x + 0.0 (560 voxels, overlap=0.035) Right_Pallidum (52): linear fit = 1.12 x + 0.0 (560 voxels, peak = 112), gca=111.5 gca peak = 0.19192 (97) mri peak = 0.07916 (107) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (427 voxels, overlap=0.830) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (427 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.08242 (71) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (846 voxels, overlap=0.131) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (846 voxels, peak = 70), gca=70.2 gca peak = 0.29892 (64) mri peak = 0.07367 (72) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (815 voxels, overlap=0.990) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (815 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.09517 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (85309 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (85309 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.07838 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84267 voxels, overlap=0.824) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84267 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03894 (67) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (30776 voxels, overlap=0.995) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (30776 voxels, peak = 66), gca=66.5 gca peak = 0.13270 (63) mri peak = 0.04364 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (35348 voxels, overlap=0.993) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (35348 voxels, peak = 62), gca=62.1 gca peak = 0.15182 (70) mri peak = 0.08859 (70) Right_Caudate (50): linear fit = 1.02 x + 0.0 (238 voxels, overlap=0.951) Right_Caudate (50): linear fit = 1.02 x + 0.0 (238 voxels, peak = 72), gca=71.8 gca peak = 0.14251 (76) mri peak = 0.08449 (81) Left_Caudate (11): linear fit = 1.04 x + 0.0 (960 voxels, overlap=0.892) Left_Caudate (11): linear fit = 1.04 x + 0.0 (960 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.04377 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (19374 voxels, overlap=0.891) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (19374 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.03970 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (26394 voxels, overlap=0.859) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (26394 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.09215 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10106 voxels, overlap=0.770) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10106 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.09352 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9700 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9700 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.09191 (72) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (453 voxels, overlap=0.887) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (453 voxels, peak = 67), gca=67.3 gca peak = 0.39668 (62) mri peak = 0.08335 (70) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (431 voxels, overlap=0.092) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (431 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.05997 (100) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6197 voxels, overlap=0.514) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6197 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.05931 (101) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4854 voxels, overlap=0.590) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4854 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.05628 (91) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2726 voxels, overlap=0.929) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2726 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.05296 (91) Right_Putamen (51): linear fit = 1.11 x + 0.0 (2946 voxels, overlap=0.989) Right_Putamen (51): linear fit = 1.11 x + 0.0 (2946 voxels, peak = 93), gca=92.8 gca peak = 0.08983 (85) mri peak = 0.05267 (97) Brain_Stem (16): linear fit = 1.13 x + 0.0 (14711 voxels, overlap=0.743) Brain_Stem (16): linear fit = 1.13 x + 0.0 (14711 voxels, peak = 96), gca=96.5 gca peak = 0.11809 (92) mri peak = 0.08054 (107) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1288 voxels, overlap=0.192) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1288 voxels, peak = 104), gca=103.5 gca peak = 0.12914 (94) mri peak = 0.07910 (107) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1599 voxels, overlap=0.613) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1599 voxels, peak = 106), gca=105.8 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.13967 (19) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (367 voxels, overlap=0.152) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (367 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.61 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.075) to 103.9 (was 104.3) Right_Pallidum too bright - rescaling by 0.932 (from 1.115) to 103.9 (was 111.5) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0113: dt=129.472000, rms=0.647 (0.825%), neg=0, invalid=96777 0114: dt=129.472000, rms=0.645 (0.257%), neg=0, invalid=96777 0115: dt=129.472000, rms=0.643 (0.301%), neg=0, invalid=96777 0116: dt=92.480000, rms=0.643 (0.125%), neg=0, invalid=96777 0117: dt=369.920000, rms=0.640 (0.364%), neg=0, invalid=96777 0118: dt=55.488000, rms=0.639 (0.167%), neg=0, invalid=96777 0119: dt=517.888000, rms=0.638 (0.248%), neg=0, invalid=96777 0120: dt=110.976000, rms=0.636 (0.268%), neg=0, invalid=96777 0121: dt=73.984000, rms=0.636 (0.031%), neg=0, invalid=96777 0122: dt=73.984000, rms=0.635 (0.048%), neg=0, invalid=96777 0123: dt=73.984000, rms=0.635 (0.082%), neg=0, invalid=96777 0124: dt=73.984000, rms=0.634 (0.103%), neg=0, invalid=96777 0125: dt=73.984000, rms=0.633 (0.129%), neg=0, invalid=96777 0126: dt=73.984000, rms=0.633 (0.141%), neg=0, invalid=96777 0127: dt=73.984000, rms=0.632 (0.139%), neg=0, invalid=96777 0128: dt=73.984000, rms=0.631 (0.141%), neg=0, invalid=96777 0129: dt=73.984000, rms=0.630 (0.145%), neg=0, invalid=96777 0130: dt=73.984000, rms=0.629 (0.140%), neg=0, invalid=96777 0131: dt=73.984000, rms=0.628 (0.121%), neg=0, invalid=96777 0132: dt=73.984000, rms=0.628 (0.102%), neg=0, invalid=96777 0133: dt=73.984000, rms=0.627 (0.112%), neg=0, invalid=96777 0134: dt=73.984000, rms=0.626 (0.108%), neg=0, invalid=96777 0135: dt=73.984000, rms=0.626 (0.101%), neg=0, invalid=96777 0136: dt=73.984000, rms=0.625 (0.086%), neg=0, invalid=96777 0137: dt=73.984000, rms=0.625 (0.082%), neg=0, invalid=96777 0138: dt=73.984000, rms=0.624 (0.085%), neg=0, invalid=96777 0139: dt=73.984000, rms=0.623 (0.097%), neg=0, invalid=96777 0140: dt=73.984000, rms=0.623 (0.087%), neg=0, invalid=96777 0141: dt=73.984000, rms=0.622 (0.069%), neg=0, invalid=96777 0142: dt=73.984000, rms=0.622 (0.050%), neg=0, invalid=96777 0143: dt=73.984000, rms=0.622 (0.059%), neg=0, invalid=96777 0144: dt=73.984000, rms=0.621 (0.091%), neg=0, invalid=96777 0145: dt=73.984000, rms=0.621 (0.081%), neg=0, invalid=96777 0146: dt=73.984000, rms=0.620 (0.072%), neg=0, invalid=96777 0147: dt=73.984000, rms=0.620 (0.067%), neg=0, invalid=96777 0148: dt=73.984000, rms=0.620 (0.033%), neg=0, invalid=96777 0149: dt=73.984000, rms=0.619 (0.066%), neg=0, invalid=96777 0150: dt=73.984000, rms=0.619 (0.067%), neg=0, invalid=96777 0151: dt=73.984000, rms=0.618 (0.048%), neg=0, invalid=96777 0152: dt=73.984000, rms=0.618 (0.059%), neg=0, invalid=96777 0153: dt=73.984000, rms=0.618 (0.046%), neg=0, invalid=96777 0154: dt=73.984000, rms=0.618 (0.044%), neg=0, invalid=96777 0155: dt=73.984000, rms=0.617 (0.057%), neg=0, invalid=96777 0156: dt=73.984000, rms=0.617 (0.057%), neg=0, invalid=96777 0157: dt=73.984000, rms=0.616 (0.060%), neg=0, invalid=96777 0158: dt=73.984000, rms=0.616 (0.051%), neg=0, invalid=96777 0159: dt=73.984000, rms=0.616 (0.031%), neg=0, invalid=96777 0160: dt=73.984000, rms=0.616 (0.050%), neg=0, invalid=96777 0161: dt=73.984000, rms=0.615 (0.049%), neg=0, invalid=96777 0162: dt=73.984000, rms=0.615 (0.044%), neg=0, invalid=96777 0163: dt=73.984000, rms=0.615 (0.043%), neg=0, invalid=96777 0164: dt=73.984000, rms=0.615 (0.041%), neg=0, invalid=96777 0165: dt=73.984000, rms=0.614 (0.034%), neg=0, invalid=96777 0166: dt=73.984000, rms=0.614 (0.036%), neg=0, invalid=96777 0167: dt=73.984000, rms=0.614 (0.034%), neg=0, invalid=96777 0168: dt=73.984000, rms=0.614 (0.027%), neg=0, invalid=96777 0169: dt=73.984000, rms=0.614 (0.037%), neg=0, invalid=96777 0170: dt=73.984000, rms=0.613 (0.035%), neg=0, invalid=96777 0171: dt=73.984000, rms=0.613 (0.017%), neg=0, invalid=96777 0172: dt=73.984000, rms=0.613 (0.041%), neg=0, invalid=96777 0173: dt=73.984000, rms=0.613 (0.022%), neg=0, invalid=96777 0174: dt=73.984000, rms=0.613 (0.021%), neg=0, invalid=96777 0175: dt=73.984000, rms=0.613 (0.010%), neg=0, invalid=96777 0176: dt=73.984000, rms=0.613 (0.001%), neg=0, invalid=96777 0177: dt=73.984000, rms=0.613 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=96777 0178: dt=129.472000, rms=0.612 (0.091%), neg=0, invalid=96777 0179: dt=295.936000, rms=0.611 (0.153%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.611 (0.016%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.611 (0.009%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.611 (0.002%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.611 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.612, neg=0, invalid=96777 0184: dt=145.152000, rms=0.606 (1.031%), neg=0, invalid=96777 0185: dt=103.680000, rms=0.601 (0.729%), neg=0, invalid=96777 0186: dt=31.104000, rms=0.598 (0.541%), neg=0, invalid=96777 0187: dt=36.288000, rms=0.597 (0.197%), neg=0, invalid=96777 0188: dt=103.680000, rms=0.595 (0.380%), neg=0, invalid=96777 0189: dt=20.736000, rms=0.593 (0.317%), neg=0, invalid=96777 0190: dt=580.608000, rms=0.584 (1.443%), neg=0, invalid=96777 0191: dt=31.104000, rms=0.579 (0.939%), neg=0, invalid=96777 0192: dt=31.104000, rms=0.578 (0.157%), neg=0, invalid=96777 0193: dt=124.416000, rms=0.576 (0.260%), neg=0, invalid=96777 0194: dt=20.736000, rms=0.576 (0.118%), neg=0, invalid=96777 0195: dt=124.416000, rms=0.575 (0.144%), neg=0, invalid=96777 0196: dt=36.288000, rms=0.573 (0.222%), neg=0, invalid=96777 0197: dt=62.208000, rms=0.573 (0.073%), neg=0, invalid=96777 0198: dt=62.208000, rms=0.572 (0.155%), neg=0, invalid=96777 0199: dt=25.920000, rms=0.572 (0.052%), neg=0, invalid=96777 0200: dt=580.608000, rms=0.567 (0.811%), neg=0, invalid=96777 0201: dt=31.104000, rms=0.566 (0.238%), neg=0, invalid=96777 0202: dt=103.680000, rms=0.565 (0.163%), neg=0, invalid=96777 0203: dt=20.736000, rms=0.565 (0.042%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.565 (0.020%), neg=0, invalid=96777 0205: dt=20.736000, rms=0.564 (0.042%), neg=0, invalid=96777 0206: dt=20.736000, rms=0.564 (0.059%), neg=0, invalid=96777 0207: dt=20.736000, rms=0.563 (0.096%), neg=0, invalid=96777 0208: dt=20.736000, rms=0.563 (0.114%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.563 (0.019%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.563 (0.027%), neg=0, invalid=96777 0211: dt=20.736000, rms=0.562 (0.036%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.562 (0.056%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.562 (0.082%), neg=0, invalid=96777 0214: dt=20.736000, rms=0.561 (0.094%), neg=0, invalid=96777 0215: dt=20.736000, rms=0.560 (0.099%), neg=0, invalid=96777 0216: dt=20.736000, rms=0.560 (0.113%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.559 (0.115%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.558 (0.134%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.558 (0.130%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.557 (0.133%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.556 (0.149%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.555 (0.136%), neg=0, invalid=96777 0223: dt=20.736000, rms=0.555 (0.124%), neg=0, invalid=96777 0224: dt=20.736000, rms=0.554 (0.127%), neg=0, invalid=96777 0225: dt=20.736000, rms=0.553 (0.125%), neg=0, invalid=96777 0226: dt=20.736000, rms=0.553 (0.132%), neg=0, invalid=96777 0227: dt=20.736000, rms=0.552 (0.116%), neg=0, invalid=96777 0228: dt=20.736000, rms=0.551 (0.116%), neg=0, invalid=96777 0229: dt=20.736000, rms=0.551 (0.104%), neg=0, invalid=96777 0230: dt=20.736000, rms=0.550 (0.109%), neg=0, invalid=96777 0231: dt=20.736000, rms=0.550 (0.112%), neg=0, invalid=96777 0232: dt=20.736000, rms=0.549 (0.110%), neg=0, invalid=96777 0233: dt=20.736000, rms=0.548 (0.105%), neg=0, invalid=96777 0234: dt=20.736000, rms=0.548 (0.094%), neg=0, invalid=96777 0235: dt=20.736000, rms=0.547 (0.082%), neg=0, invalid=96777 0236: dt=20.736000, rms=0.547 (0.084%), neg=0, invalid=96777 0237: dt=20.736000, rms=0.546 (0.080%), neg=0, invalid=96777 0238: dt=20.736000, rms=0.546 (0.084%), neg=0, invalid=96777 0239: dt=20.736000, rms=0.546 (0.076%), neg=0, invalid=96777 0240: dt=20.736000, rms=0.545 (0.076%), neg=0, invalid=96777 0241: dt=20.736000, rms=0.545 (0.069%), neg=0, invalid=96777 0242: dt=20.736000, rms=0.544 (0.074%), neg=0, invalid=96777 0243: dt=20.736000, rms=0.544 (0.076%), neg=0, invalid=96777 0244: dt=20.736000, rms=0.544 (0.059%), neg=0, invalid=96777 0245: dt=20.736000, rms=0.543 (0.059%), neg=0, invalid=96777 0246: dt=20.736000, rms=0.543 (0.066%), neg=0, invalid=96777 0247: dt=20.736000, rms=0.543 (0.067%), neg=0, invalid=96777 0248: dt=20.736000, rms=0.542 (0.063%), neg=0, invalid=96777 0249: dt=20.736000, rms=0.542 (0.060%), neg=0, invalid=96777 0250: dt=20.736000, rms=0.542 (0.059%), neg=0, invalid=96777 0251: dt=20.736000, rms=0.541 (0.053%), neg=0, invalid=96777 0252: dt=20.736000, rms=0.541 (0.054%), neg=0, invalid=96777 0253: dt=20.736000, rms=0.541 (0.065%), neg=0, invalid=96777 0254: dt=20.736000, rms=0.540 (0.057%), neg=0, invalid=96777 0255: dt=20.736000, rms=0.540 (0.057%), neg=0, invalid=96777 0256: dt=20.736000, rms=0.540 (0.050%), neg=0, invalid=96777 0257: dt=20.736000, rms=0.540 (0.050%), neg=0, invalid=96777 0258: dt=20.736000, rms=0.539 (0.047%), neg=0, invalid=96777 0259: dt=20.736000, rms=0.539 (0.046%), neg=0, invalid=96777 0260: dt=20.736000, rms=0.539 (0.044%), neg=0, invalid=96777 0261: dt=20.736000, rms=0.539 (0.039%), neg=0, invalid=96777 0262: dt=20.736000, rms=0.538 (0.044%), neg=0, invalid=96777 0263: dt=20.736000, rms=0.538 (0.046%), neg=0, invalid=96777 0264: dt=20.736000, rms=0.538 (0.044%), neg=0, invalid=96777 0265: dt=20.736000, rms=0.538 (0.042%), neg=0, invalid=96777 0266: dt=20.736000, rms=0.537 (0.038%), neg=0, invalid=96777 0267: dt=20.736000, rms=0.537 (0.037%), neg=0, invalid=96777 0268: dt=20.736000, rms=0.537 (0.036%), neg=0, invalid=96777 0269: dt=20.736000, rms=0.537 (0.032%), neg=0, invalid=96777 0270: dt=20.736000, rms=0.537 (0.028%), neg=0, invalid=96777 0271: dt=20.736000, rms=0.537 (0.035%), neg=0, invalid=96777 0272: dt=20.736000, rms=0.536 (0.032%), neg=0, invalid=96777 0273: dt=20.736000, rms=0.536 (0.031%), neg=0, invalid=96777 0274: dt=20.736000, rms=0.536 (0.029%), neg=0, invalid=96777 0275: dt=20.736000, rms=0.536 (0.034%), neg=0, invalid=96777 0276: dt=20.736000, rms=0.536 (0.041%), neg=0, invalid=96777 0277: dt=20.736000, rms=0.535 (0.033%), neg=0, invalid=96777 0278: dt=20.736000, rms=0.535 (0.025%), neg=0, invalid=96777 0279: dt=20.736000, rms=0.535 (0.017%), neg=0, invalid=96777 0280: dt=62.208000, rms=0.535 (0.017%), neg=0, invalid=96777 0281: dt=62.208000, rms=0.535 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=96777 0282: dt=124.416000, rms=0.534 (0.269%), neg=0, invalid=96777 0283: dt=36.288000, rms=0.533 (0.060%), neg=0, invalid=96777 0284: dt=36.288000, rms=0.533 (0.040%), neg=0, invalid=96777 0285: dt=36.288000, rms=0.533 (0.026%), neg=0, invalid=96777 0286: dt=36.288000, rms=0.533 (0.056%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.532 (0.056%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.532 (0.072%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.532 (0.047%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.532 (0.055%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.531 (0.077%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.531 (0.056%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.531 (0.048%), neg=0, invalid=96777 0294: dt=18.144000, rms=0.530 (0.009%), neg=0, invalid=96777 0295: dt=18.144000, rms=0.530 (0.007%), neg=0, invalid=96777 0296: dt=124.416000, rms=0.530 (0.015%), neg=0, invalid=96777 0297: dt=82.944000, rms=0.530 (0.036%), neg=0, invalid=96777 0298: dt=6.480000, rms=0.530 (0.004%), neg=0, invalid=96777 0299: dt=0.405000, rms=0.530 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=96777 0300: dt=38.400000, rms=0.536 (0.558%), neg=0, invalid=96777 0301: dt=11.200000, rms=0.535 (0.257%), neg=0, invalid=96777 0302: dt=11.200000, rms=0.534 (0.191%), neg=0, invalid=96777 0303: dt=76.800000, rms=0.530 (0.700%), neg=0, invalid=96777 0304: dt=7.600000, rms=0.528 (0.362%), neg=0, invalid=96777 0305: dt=44.800000, rms=0.527 (0.300%), neg=0, invalid=96777 0306: dt=8.947867, rms=0.525 (0.328%), neg=0, invalid=96777 0307: dt=25.600000, rms=0.524 (0.200%), neg=0, invalid=96777 0308: dt=11.200000, rms=0.523 (0.181%), neg=0, invalid=96777 0309: dt=19.200000, rms=0.522 (0.136%), neg=0, invalid=96777 0310: dt=11.200000, rms=0.522 (0.142%), neg=0, invalid=96777 0311: dt=32.000000, rms=0.521 (0.134%), neg=0, invalid=96777 0312: dt=9.600000, rms=0.520 (0.169%), neg=0, invalid=96777 0313: dt=25.600000, rms=0.519 (0.124%), neg=0, invalid=96777 0314: dt=11.200000, rms=0.519 (0.147%), neg=0, invalid=96777 0315: dt=19.200000, rms=0.518 (0.104%), neg=0, invalid=96777 0316: dt=11.200000, rms=0.518 (0.102%), neg=0, invalid=96777 0317: dt=25.600000, rms=0.517 (0.099%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.516 (0.128%), neg=0, invalid=96777 0319: dt=11.200000, rms=0.516 (0.063%), neg=0, invalid=96777 0320: dt=44.800000, rms=0.515 (0.229%), neg=0, invalid=96777 0321: dt=11.200000, rms=0.515 (0.068%), neg=0, invalid=96777 0322: dt=11.200000, rms=0.514 (0.066%), neg=0, invalid=96777 0323: dt=44.800000, rms=0.514 (0.106%), neg=0, invalid=96777 0324: dt=9.600000, rms=0.513 (0.121%), neg=0, invalid=96777 0325: dt=25.600000, rms=0.513 (0.073%), neg=0, invalid=96777 0326: dt=9.600000, rms=0.512 (0.084%), neg=0, invalid=96777 0327: dt=19.200000, rms=0.512 (0.053%), neg=0, invalid=96777 0328: dt=11.200000, rms=0.512 (0.066%), neg=0, invalid=96777 0329: dt=25.600000, rms=0.511 (0.053%), neg=0, invalid=96777 0330: dt=11.200000, rms=0.511 (0.077%), neg=0, invalid=96777 0331: dt=11.200000, rms=0.511 (0.039%), neg=0, invalid=96777 0332: dt=11.200000, rms=0.511 (0.051%), neg=0, invalid=96777 0333: dt=11.200000, rms=0.510 (0.067%), neg=0, invalid=96777 0334: dt=11.200000, rms=0.510 (0.102%), neg=0, invalid=96777 0335: dt=11.200000, rms=0.509 (0.108%), neg=0, invalid=96777 0336: dt=11.200000, rms=0.508 (0.167%), neg=0, invalid=96777 0337: dt=11.200000, rms=0.507 (0.153%), neg=0, invalid=96777 0338: dt=11.200000, rms=0.507 (0.166%), neg=0, invalid=96777 0339: dt=11.200000, rms=0.506 (0.167%), neg=0, invalid=96777 0340: dt=11.200000, rms=0.505 (0.166%), neg=0, invalid=96777 0341: dt=11.200000, rms=0.504 (0.169%), neg=0, invalid=96777 0342: dt=11.200000, rms=0.503 (0.171%), neg=0, invalid=96777 0343: dt=11.200000, rms=0.503 (0.147%), neg=0, invalid=96777 0344: dt=11.200000, rms=0.502 (0.132%), neg=0, invalid=96777 0345: dt=11.200000, rms=0.501 (0.168%), neg=0, invalid=96777 0346: dt=11.200000, rms=0.500 (0.145%), neg=0, invalid=96777 0347: dt=11.200000, rms=0.500 (0.017%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.500 (0.020%), neg=0, invalid=96777 0349: dt=11.200000, rms=0.500 (0.038%), neg=0, invalid=96777 0350: dt=11.200000, rms=0.500 (0.035%), neg=0, invalid=96777 0351: dt=11.200000, rms=0.500 (0.029%), neg=0, invalid=96777 0352: dt=11.200000, rms=0.499 (0.032%), neg=0, invalid=96777 0353: dt=11.200000, rms=0.499 (0.044%), neg=0, invalid=96777 0354: dt=11.200000, rms=0.499 (0.013%), neg=0, invalid=96777 0355: dt=5.600000, rms=0.499 (0.023%), neg=0, invalid=96777 0356: dt=5.600000, rms=0.499 (0.007%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.499 (0.008%), neg=0, invalid=96777 0358: dt=11.200000, rms=0.499 (0.018%), neg=0, invalid=96777 0359: dt=11.200000, rms=0.499 (0.018%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.499 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=96777 0361: dt=32.000000, rms=0.498 (0.208%), neg=0, invalid=96777 0362: dt=9.600000, rms=0.497 (0.095%), neg=0, invalid=96777 0363: dt=25.600000, rms=0.497 (0.062%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.497 (0.054%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.497 (0.024%), neg=0, invalid=96777 0366: dt=11.200000, rms=0.497 (0.004%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.496 (0.021%), neg=0, invalid=96777 0368: dt=11.200000, rms=0.496 (0.025%), neg=0, invalid=96777 0369: dt=11.200000, rms=0.496 (0.023%), neg=0, invalid=96777 0370: dt=11.200000, rms=0.496 (0.025%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.496 (0.008%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.496 (0.011%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.496 (0.004%), neg=0, invalid=96777 0374: dt=19.200000, rms=0.496 (0.066%), neg=0, invalid=96777 0375: dt=8.000000, rms=0.496 (0.016%), neg=0, invalid=96777 0376: dt=8.000000, rms=0.495 (0.016%), neg=0, invalid=96777 0377: dt=8.000000, rms=0.495 (0.008%), neg=0, invalid=96777 0378: dt=8.000000, rms=0.495 (0.024%), neg=0, invalid=96777 0379: dt=8.000000, rms=0.495 (0.048%), neg=0, invalid=96777 0380: dt=8.000000, rms=0.495 (0.044%), neg=0, invalid=96777 0381: dt=8.000000, rms=0.495 (0.044%), neg=0, invalid=96777 0382: dt=8.000000, rms=0.494 (0.043%), neg=0, invalid=96777 0383: dt=8.000000, rms=0.494 (0.042%), neg=0, invalid=96777 0384: dt=8.000000, rms=0.494 (0.042%), neg=0, invalid=96777 0385: dt=8.000000, rms=0.494 (0.045%), neg=0, invalid=96777 0386: dt=8.000000, rms=0.494 (0.035%), neg=0, invalid=96777 0387: dt=8.000000, rms=0.493 (0.048%), neg=0, invalid=96777 0388: dt=8.000000, rms=0.493 (0.038%), neg=0, invalid=96777 0389: dt=8.000000, rms=0.493 (0.007%), neg=0, invalid=96777 0390: dt=8.000000, rms=0.493 (-0.003%), neg=0, invalid=96777 0391: dt=11.200000, rms=0.493 (0.003%), neg=0, invalid=96777 0392: dt=11.200000, rms=0.493 (0.008%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.493 (0.018%), neg=0, invalid=96777 0394: dt=2.800000, rms=0.493 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.512, neg=0, invalid=96777 0395: dt=0.000000, rms=0.512 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=96777 0396: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.551, neg=0, invalid=96777 0397: dt=1.228700, rms=0.549 (0.495%), neg=0, invalid=96777 0398: dt=0.256000, rms=0.549 (0.017%), neg=0, invalid=96777 0399: dt=0.256000, rms=0.549 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=96777 0400: dt=0.538462, rms=0.548 (0.079%), neg=0, invalid=96777 0401: dt=0.340909, rms=0.548 (0.013%), neg=0, invalid=96777 0402: dt=0.340909, rms=0.548 (-0.008%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.503, neg=0, invalid=96777 0403: dt=0.448000, rms=0.488 (2.899%), neg=0, invalid=96777 0404: dt=0.448000, rms=0.485 (0.514%), neg=0, invalid=96777 0405: dt=0.448000, rms=0.484 (0.336%), neg=0, invalid=96777 0406: dt=0.448000, rms=0.483 (0.229%), neg=0, invalid=96777 0407: dt=0.448000, rms=0.482 (0.150%), neg=0, invalid=96777 0408: dt=0.448000, rms=0.481 (0.128%), neg=0, invalid=96777 0409: dt=0.448000, rms=0.481 (0.092%), neg=0, invalid=96777 0410: dt=0.448000, rms=0.481 (0.077%), neg=0, invalid=96777 0411: dt=0.448000, rms=0.480 (0.061%), neg=0, invalid=96777 0412: dt=0.448000, rms=0.480 (0.056%), neg=0, invalid=96777 0413: dt=0.007000, rms=0.480 (-0.003%), neg=0, invalid=96777 0414: dt=0.007000, rms=0.480 (0.001%), neg=0, invalid=96777 0415: dt=0.007000, rms=0.480 (0.001%), neg=0, invalid=96777 0416: dt=0.007000, rms=0.480 (0.003%), neg=0, invalid=96777 0417: dt=0.007000, rms=0.480 (0.003%), neg=0, invalid=96777 0418: dt=0.007000, rms=0.480 (0.002%), neg=0, invalid=96777 0419: dt=0.007000, rms=0.480 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=96777 0420: dt=0.448000, rms=0.475 (0.978%), neg=0, invalid=96777 0421: dt=0.320000, rms=0.475 (0.036%), neg=0, invalid=96777 0422: dt=0.010000, rms=0.475 (-0.004%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 0423: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 0424: dt=295.936000, rms=0.473 (0.062%), neg=0, invalid=96777 0425: dt=55.488000, rms=0.473 (0.018%), neg=0, invalid=96777 0426: dt=55.488000, rms=0.473 (0.006%), neg=0, invalid=96777 0427: dt=55.488000, rms=0.473 (0.015%), neg=0, invalid=96777 0428: dt=55.488000, rms=0.473 (0.013%), neg=0, invalid=96777 0429: dt=55.488000, rms=0.473 (0.017%), neg=0, invalid=96777 0430: dt=55.488000, rms=0.472 (0.022%), neg=0, invalid=96777 0431: dt=55.488000, rms=0.472 (0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0432: dt=36.288000, rms=0.472 (0.093%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0433: dt=36.288000, rms=0.472 (0.057%), neg=0, invalid=96777 0434: dt=36.288000, rms=0.471 (0.047%), neg=0, invalid=96777 0435: dt=36.288000, rms=0.471 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=36.288000, rms=0.471 (0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 0437: dt=103.680000, rms=0.469 (0.505%), neg=0, invalid=96777 0438: dt=36.288000, rms=0.468 (0.157%), neg=0, invalid=96777 0439: dt=36.288000, rms=0.468 (0.064%), neg=0, invalid=96777 0440: dt=36.288000, rms=0.467 (0.070%), neg=0, invalid=96777 0441: dt=36.288000, rms=0.467 (0.107%), neg=0, invalid=96777 0442: dt=36.288000, rms=0.466 (0.124%), neg=0, invalid=96777 0443: dt=36.288000, rms=0.466 (0.133%), neg=0, invalid=96777 0444: dt=36.288000, rms=0.465 (0.107%), neg=0, invalid=96777 0445: dt=36.288000, rms=0.465 (0.097%), neg=0, invalid=96777 0446: dt=36.288000, rms=0.465 (0.031%), neg=0, invalid=96777 0447: dt=36.288000, rms=0.465 (0.015%), neg=0, invalid=96777 0448: dt=36.288000, rms=0.464 (0.030%), neg=0, invalid=96777 0449: dt=36.288000, rms=0.464 (0.015%), neg=0, invalid=96777 0450: dt=36.288000, rms=0.464 (0.043%), neg=0, invalid=96777 0451: dt=36.288000, rms=0.464 (0.034%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0452: dt=32.000000, rms=0.462 (0.410%), neg=0, invalid=96777 0453: dt=11.200000, rms=0.462 (0.164%), neg=0, invalid=96777 0454: dt=11.200000, rms=0.461 (0.147%), neg=0, invalid=96777 0455: dt=11.200000, rms=0.460 (0.182%), neg=0, invalid=96777 0456: dt=11.200000, rms=0.459 (0.183%), neg=0, invalid=96777 0457: dt=11.200000, rms=0.458 (0.200%), neg=0, invalid=96777 0458: dt=11.200000, rms=0.458 (0.148%), neg=0, invalid=96777 0459: dt=11.200000, rms=0.457 (0.127%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0460: dt=11.200000, rms=0.457 (0.147%), neg=0, invalid=96777 0461: dt=11.200000, rms=0.456 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0462: dt=11.200000, rms=0.455 (0.168%), neg=0, invalid=96777 0463: dt=11.200000, rms=0.454 (0.145%), neg=0, invalid=96777 0464: dt=11.200000, rms=0.453 (0.175%), neg=0, invalid=96777 0465: dt=11.200000, rms=0.453 (0.157%), neg=0, invalid=96777 0466: dt=11.200000, rms=0.452 (0.169%), neg=0, invalid=96777 0467: dt=11.200000, rms=0.451 (0.146%), neg=0, invalid=96777 0468: dt=11.200000, rms=0.451 (0.132%), neg=0, invalid=96777 0469: dt=11.200000, rms=0.450 (0.110%), neg=0, invalid=96777 0470: dt=11.200000, rms=0.450 (0.101%), neg=0, invalid=96777 0471: dt=25.600000, rms=0.450 (0.052%), neg=0, invalid=96777 0472: dt=25.600000, rms=0.450 (-0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=96777 0473: dt=38.400000, rms=0.447 (0.492%), neg=0, invalid=96777 0474: dt=8.000000, rms=0.446 (0.258%), neg=0, invalid=96777 0475: dt=32.000000, rms=0.445 (0.213%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0476: dt=32.000000, rms=0.445 (-0.387%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0477: dt=6.200000, rms=0.452 (0.345%), neg=0, invalid=96777 0478: dt=4.285714, rms=0.452 (0.121%), neg=0, invalid=96777 0479: dt=4.285714, rms=0.451 (0.090%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0480: dt=4.285714, rms=0.451 (0.073%), neg=0, invalid=96777 0481: dt=4.285714, rms=0.451 (-0.025%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=96777 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=1, neg = 0 0482: dt=8.761905, rms=0.449 (0.378%), neg=0, invalid=96777 0483: dt=5.052632, rms=0.448 (0.213%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0484: dt=5.052632, rms=0.448 (0.184%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 1 iterations, nbhd size=0, neg = 0 0485: dt=5.052632, rms=0.447 (0.242%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0486: dt=5.052632, rms=0.446 (0.180%), neg=0, invalid=96777 iter 0, gcam->neg = 25 after 4 iterations, nbhd size=0, neg = 0 0487: dt=5.052632, rms=0.445 (0.070%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 9 iterations, nbhd size=1, neg = 0 0488: dt=5.052632, rms=0.445 (0.143%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0489: dt=5.052632, rms=0.444 (0.217%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0490: dt=5.052632, rms=0.442 (0.315%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 8 iterations, nbhd size=1, neg = 0 0491: dt=5.052632, rms=0.441 (0.324%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 8 iterations, nbhd size=1, neg = 0 0492: dt=5.052632, rms=0.440 (0.293%), neg=0, invalid=96777 iter 0, gcam->neg = 26 after 10 iterations, nbhd size=1, neg = 0 0493: dt=5.052632, rms=0.439 (0.225%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 10 iterations, nbhd size=1, neg = 0 0494: dt=5.052632, rms=0.438 (0.178%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0495: dt=5.052632, rms=0.437 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0496: dt=5.052632, rms=0.437 (0.063%), neg=0, invalid=96777 0497: dt=4.032000, rms=0.437 (0.052%), neg=0, invalid=96777 0498: dt=4.032000, rms=0.437 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0499: dt=4.032000, rms=0.437 (-0.016%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 0500: dt=0.000000, rms=0.442 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 0501: dt=0.000000, rms=0.442 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=96777 iter 0, gcam->neg = 405 after 10 iterations, nbhd size=1, neg = 0 0502: dt=1.896854, rms=0.404 (6.660%), neg=0, invalid=96777 0503: dt=0.000438, rms=0.404 (0.007%), neg=0, invalid=96777 0504: dt=0.000438, rms=0.404 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0505: dt=0.001750, rms=0.404 (0.001%), neg=0, invalid=96777 0506: dt=0.001750, rms=0.404 (0.001%), neg=0, invalid=96777 0507: dt=0.001000, rms=0.404 (-0.001%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0508: dt=2.023000, rms=0.391 (-0.234%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0509: dt=18.496000, rms=0.391 (0.002%), neg=0, invalid=96777 0510: dt=2.023000, rms=0.391 (0.000%), neg=0, invalid=96777 0511: dt=2.023000, rms=0.391 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0512: dt=2.268000, rms=0.391 (0.001%), neg=0, invalid=96777 0513: dt=1.296000, rms=0.391 (0.000%), neg=0, invalid=96777 0514: dt=1.296000, rms=0.391 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0515: dt=25.920000, rms=0.391 (0.014%), neg=0, invalid=96777 0516: dt=36.288000, rms=0.391 (0.007%), neg=0, invalid=96777 0517: dt=36.288000, rms=0.391 (0.009%), neg=0, invalid=96777 0518: dt=36.288000, rms=0.391 (0.007%), neg=0, invalid=96777 0519: dt=36.288000, rms=0.391 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0520: dt=11.200000, rms=0.391 (0.085%), neg=0, invalid=96777 0521: dt=8.000000, rms=0.391 (0.017%), neg=0, invalid=96777 0522: dt=8.000000, rms=0.391 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0523: dt=8.000000, rms=0.391 (-0.039%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0524: dt=44.800000, rms=0.389 (0.430%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0525: dt=32.000000, rms=0.389 (0.203%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0526: dt=32.000000, rms=0.389 (-0.094%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0527: dt=1.008000, rms=0.391 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 40 after 16 iterations, nbhd size=1, neg = 0 0528: dt=8.075117, rms=0.390 (0.183%), neg=0, invalid=96777 0529: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0530: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0531: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0532: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0533: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0534: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0535: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0536: dt=0.011250, rms=0.390 (0.000%), neg=0, invalid=96777 0537: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0538: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0539: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0540: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0541: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0542: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0543: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0544: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0545: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0546: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0547: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0548: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0549: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0550: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0551: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0552: dt=0.011250, rms=0.390 (0.001%), neg=0, invalid=96777 0553: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0554: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0555: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0556: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0557: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0558: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 0559: dt=0.011250, rms=0.390 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 iter 0, gcam->neg = 43 after 33 iterations, nbhd size=3, neg = 0 0560: dt=16.128000, rms=0.388 (0.616%), neg=0, invalid=96777 0561: dt=0.015750, rms=0.388 (0.000%), neg=0, invalid=96777 0562: dt=0.015750, rms=0.388 (0.000%), neg=0, invalid=96777 0563: dt=0.015750, rms=0.388 (0.000%), neg=0, invalid=96777 0564: dt=0.015750, rms=0.388 (0.001%), neg=0, invalid=96777 0565: dt=0.015750, rms=0.388 (0.001%), neg=0, invalid=96777 0566: dt=0.015750, rms=0.388 (0.001%), neg=0, invalid=96777 0567: dt=0.015750, rms=0.388 (0.001%), neg=0, invalid=96777 0568: dt=0.015750, rms=0.388 (0.001%), neg=0, invalid=96777 0569: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0570: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0571: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0572: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0573: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0574: dt=0.015750, rms=0.388 (0.002%), neg=0, invalid=96777 0575: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0576: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0577: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0578: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0579: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0580: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0581: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0582: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0583: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0584: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0585: dt=0.015750, rms=0.388 (0.003%), neg=0, invalid=96777 0586: dt=0.015750, rms=0.387 (0.003%), neg=0, invalid=96777 0587: dt=0.015750, rms=0.387 (0.003%), neg=0, invalid=96777 0588: dt=0.015750, rms=0.387 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 45 after 39 iterations, nbhd size=4, neg = 0 0589: dt=16.128000, rms=0.387 (0.056%), neg=0, invalid=96777 0590: dt=0.011250, rms=0.387 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0591: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0592: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.384, neg=0, invalid=96777 iter 0, gcam->neg = 407 after 33 iterations, nbhd size=3, neg = 0 0593: dt=0.987013, rms=0.373 (2.884%), neg=0, invalid=96777 0594: dt=0.000020, rms=0.373 (0.001%), neg=0, invalid=96777 0595: dt=0.000020, rms=0.373 (0.000%), neg=0, invalid=96777 0596: dt=0.000020, rms=0.373 (0.000%), neg=0, invalid=96777 0597: dt=0.000020, rms=0.373 (0.000%), neg=0, invalid=96777 0598: dt=0.000020, rms=0.373 (0.000%), neg=0, invalid=96777 0599: dt=0.000078, rms=0.373 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=96777 0600: dt=0.000750, rms=0.373 (0.001%), neg=0, invalid=96777 0601: dt=0.000438, rms=0.373 (0.000%), neg=0, invalid=96777 0602: dt=0.000438, rms=0.373 (0.000%), neg=0, invalid=96777 0603: dt=0.000438, rms=0.373 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 42 minutes and 35 seconds. #-------------------------------------- #@# CA Reg Inv Thu Apr 14 22:35:00 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Apr 14 22:36:04 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10591669 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 10 seconds. #-------------------------------------- #@# SkullLTA Thu Apr 14 22:37:14 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (43, 21, 0) --> (213, 212, 223) using (100, 85, 112) as brain centroid... mean wm in atlas = 126, using box (79,61,84) --> (120, 108,139) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-578.5 (thresh=-577.9) 1.024 -0.106 0.053 3.473; 0.116 1.099 0.117 -24.009; -0.082 -0.072 0.982 23.463; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.024 -0.106 0.053 3.473; 0.104 1.080 0.244 -33.546; -0.096 -0.215 0.958 43.112; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.023 -0.136 0.015 10.798; 0.140 1.096 0.245 -39.763; -0.058 -0.211 0.905 43.435; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.023 -0.136 0.015 10.798; 0.139 1.082 0.211 -34.652; -0.054 -0.175 0.913 38.205; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.023 -0.136 0.015 10.798; 0.139 1.082 0.211 -34.652; -0.054 -0.175 0.913 38.205; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.023 -0.103 0.037 4.960; 0.105 1.087 0.226 -33.338; -0.073 -0.190 0.907 42.332; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.023 -0.103 0.037 4.960; 0.105 1.088 0.226 -33.519; -0.073 -0.190 0.907 42.332; 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 1.02335 -0.10317 0.03681 4.95957; 0.10498 1.08811 0.22578 -33.51855; -0.07252 -0.19028 0.90693 42.33232; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02335 -0.10317 0.03681 4.95957; 0.10498 1.08811 0.22578 -33.51855; -0.07252 -0.19028 0.90693 42.33232; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.023 -0.103 0.037 4.960; 0.105 1.088 0.226 -33.519; -0.073 -0.190 0.907 42.332; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-578.5) transform before final EM align: 1.023 -0.103 0.037 4.960; 0.105 1.088 0.226 -33.519; -0.073 -0.190 0.907 42.332; 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 1.02335 -0.10317 0.03681 4.95957; 0.10498 1.08811 0.22578 -33.51855; -0.07252 -0.19028 0.90693 42.33232; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02335 -0.10317 0.03681 4.95957; 0.10498 1.08811 0.22578 -33.51855; -0.07252 -0.19028 0.90693 42.33232; 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) = 4.3 tol 0.000000 final transform: 1.023 -0.103 0.037 4.960; 0.105 1.088 0.226 -33.519; -0.073 -0.190 0.907 42.332; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 19 minutes and 55 seconds. #-------------------------------------- #@# SubCort Seg Thu Apr 14 22:57:09 EDT 2016 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-68 machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/stable5_3_0/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 = 0.11777 (16) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (5268 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (5268 voxels, peak = 15), gca=15.3 gca peak = 0.14982 (20) mri peak = 0.10317 (17) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (3892 voxels, overlap=0.284) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (3892 voxels, peak = 13), gca=12.9 gca peak = 0.28003 (97) mri peak = 0.13371 (109) Right_Pallidum (52): linear fit = 1.12 x + 0.0 (360 voxels, overlap=0.032) Right_Pallidum (52): linear fit = 1.12 x + 0.0 (360 voxels, peak = 108), gca=108.2 gca peak = 0.18160 (96) mri peak = 0.10680 (110) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (302 voxels, overlap=0.236) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (302 voxels, peak = 106), gca=106.1 gca peak = 0.27536 (62) mri peak = 0.08371 (71) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (889 voxels, overlap=0.404) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (889 voxels, peak = 69), gca=68.5 gca peak = 0.32745 (63) mri peak = 0.08334 (69) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (842 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (842 voxels, peak = 68), gca=67.7 gca peak = 0.08597 (105) mri peak = 0.09669 (107) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54173 voxels, overlap=0.700) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (54173 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.08171 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52967 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52967 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.03886 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32829 voxels, overlap=0.982) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32829 voxels, peak = 65), gca=64.6 gca peak = 0.08598 (64) mri peak = 0.04664 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31344 voxels, overlap=0.933) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31344 voxels, peak = 63), gca=63.0 gca peak = 0.24164 (71) mri peak = 0.09189 (78) Right_Caudate (50): linear fit = 1.08 x + 0.0 (554 voxels, overlap=1.006) Right_Caudate (50): linear fit = 1.08 x + 0.0 (554 voxels, peak = 76), gca=76.3 gca peak = 0.18227 (75) mri peak = 0.10163 (83) Left_Caudate (11): linear fit = 1.03 x + 0.0 (738 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.03 x + 0.0 (738 voxels, peak = 78), gca=77.6 gca peak = 0.10629 (62) mri peak = 0.04803 (65) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (17382 voxels, overlap=0.790) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (17382 voxels, peak = 69), gca=68.5 gca peak = 0.11668 (59) mri peak = 0.04758 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20228 voxels, overlap=0.873) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20228 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.11085 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6831 voxels, overlap=0.815) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6831 voxels, peak = 91), gca=91.1 gca peak = 0.16819 (86) mri peak = 0.11011 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6461 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6461 voxels, peak = 89), gca=89.0 gca peak = 0.41688 (64) mri peak = 0.09562 (69) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (374 voxels, overlap=0.567) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (374 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.10119 (70) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (334 voxels, overlap=0.478) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (334 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.07830 (99) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4341 voxels, overlap=0.592) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4341 voxels, peak = 103), gca=103.2 gca peak = 0.13978 (88) mri peak = 0.06368 (99) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3955 voxels, overlap=0.521) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3955 voxels, peak = 98), gca=98.1 gca peak = 0.08514 (81) mri peak = 0.06139 (89) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2047 voxels, overlap=0.831) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2047 voxels, peak = 85), gca=85.5 gca peak = 0.09624 (82) mri peak = 0.05192 (87) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2135 voxels, overlap=0.815) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2135 voxels, peak = 87), gca=86.5 gca peak = 0.07543 (88) mri peak = 0.05619 (97) Brain_Stem (16): linear fit = 1.09 x + 0.0 (14638 voxels, overlap=0.659) Brain_Stem (16): linear fit = 1.09 x + 0.0 (14638 voxels, peak = 95), gca=95.5 gca peak = 0.12757 (95) mri peak = 0.08067 (107) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1133 voxels, overlap=0.281) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1133 voxels, peak = 107), gca=106.9 gca peak = 0.17004 (92) mri peak = 0.07946 (107) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1238 voxels, overlap=0.543) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1238 voxels, peak = 101), gca=100.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.13044 (17) Fourth_Ventricle (15): linear fit = 0.69 x + 0.0 (173 voxels, overlap=0.436) Fourth_Ventricle (15): linear fit = 0.69 x + 0.0 (173 voxels, peak = 16), gca=15.8 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 1.07 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.63 x + 0.0 Left_Pallidum too bright - rescaling by 0.979 (from 1.105) to 103.9 (was 106.1) Right_Pallidum too bright - rescaling by 0.960 (from 1.115) to 103.9 (was 108.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21849 (15) mri peak = 0.11777 (16) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (5268 voxels, overlap=0.967) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (5268 voxels, peak = 16), gca=15.5 gca peak = 0.22431 (13) mri peak = 0.10317 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3892 voxels, overlap=0.962) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3892 voxels, peak = 13), gca=13.5 gca peak = 0.20415 (105) mri peak = 0.13371 (109) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (360 voxels, overlap=0.931) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (360 voxels, peak = 109), gca=108.7 gca peak = 0.17046 (104) mri peak = 0.10680 (110) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (302 voxels, overlap=0.976) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (302 voxels, peak = 106), gca=105.6 gca peak = 0.23406 (68) mri peak = 0.08371 (71) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (889 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (889 voxels, peak = 68), gca=68.0 gca peak = 0.34123 (68) mri peak = 0.08334 (69) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (842 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (842 voxels, peak = 68), gca=68.0 gca peak = 0.08546 (107) mri peak = 0.09669 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54173 voxels, overlap=0.742) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54173 voxels, peak = 108), gca=107.5 gca peak = 0.08678 (107) mri peak = 0.08171 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52967 voxels, overlap=0.786) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52967 voxels, peak = 107), gca=107.0 gca peak = 0.07462 (65) mri peak = 0.03886 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (32829 voxels, overlap=0.936) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (32829 voxels, peak = 64), gca=64.0 gca peak = 0.08737 (63) mri peak = 0.04664 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31344 voxels, overlap=0.952) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (31344 voxels, peak = 65), gca=64.6 gca peak = 0.27738 (79) mri peak = 0.09189 (78) Right_Caudate (50): linear fit = 0.99 x + 0.0 (554 voxels, overlap=1.009) Right_Caudate (50): linear fit = 0.99 x + 0.0 (554 voxels, peak = 78), gca=77.8 gca peak = 0.17639 (77) mri peak = 0.10163 (83) Left_Caudate (11): linear fit = 1.00 x + 0.0 (738 voxels, overlap=1.003) Left_Caudate (11): linear fit = 1.00 x + 0.0 (738 voxels, peak = 77), gca=77.0 gca peak = 0.09417 (69) mri peak = 0.04803 (65) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (17382 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (17382 voxels, peak = 68), gca=68.0 gca peak = 0.12026 (64) mri peak = 0.04758 (65) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20228 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20228 voxels, peak = 66), gca=65.6 gca peak = 0.16847 (91) mri peak = 0.11085 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6831 voxels, overlap=0.957) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6831 voxels, peak = 91), gca=90.5 gca peak = 0.16223 (89) mri peak = 0.11011 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6461 voxels, overlap=0.967) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6461 voxels, peak = 89), gca=88.6 gca peak = 0.30598 (70) mri peak = 0.09562 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (374 voxels, overlap=1.023) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (374 voxels, peak = 70), gca=70.0 gca peak = 0.30975 (71) mri peak = 0.10119 (70) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (334 voxels, overlap=1.012) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (334 voxels, peak = 73), gca=73.5 gca peak = 0.10909 (103) mri peak = 0.07830 (99) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4341 voxels, overlap=0.920) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4341 voxels, peak = 103), gca=103.0 gca peak = 0.11982 (98) mri peak = 0.06368 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3955 voxels, overlap=0.984) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3955 voxels, peak = 98), gca=98.0 gca peak = 0.08917 (92) mri peak = 0.06139 (89) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2047 voxels, overlap=0.990) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2047 voxels, peak = 91), gca=90.6 gca peak = 0.10379 (80) mri peak = 0.05192 (87) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2135 voxels, overlap=0.996) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2135 voxels, peak = 81), gca=81.2 gca peak = 0.06975 (93) mri peak = 0.05619 (97) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14638 voxels, overlap=0.850) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14638 voxels, peak = 93), gca=93.5 gca peak = 0.10323 (102) mri peak = 0.08067 (107) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1133 voxels, overlap=0.815) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1133 voxels, peak = 102), gca=102.0 gca peak = 0.16939 (101) mri peak = 0.07946 (107) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1238 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1238 voxels, peak = 102), gca=101.5 gca peak = 0.25894 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26696 (16) mri peak = 0.13044 (17) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (173 voxels, overlap=0.948) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (173 voxels, peak = 16), gca=15.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak Third_Ventricle = 0.25894 (24) gca peak CSF = 0.24713 (29) gca peak Left_Accumbens_area = 0.44003 (72) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.28428 (35) gca peak Right_Accumbens_area = 0.43827 (77) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (28) gca peak WM_hypointensities = 0.17534 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 Left_Pallidum too bright - rescaling by 0.986 (from 1.015) to 104.0 (was 105.6) Right_Pallidum too bright - rescaling by 0.957 (from 1.035) to 104.0 (was 108.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 23079 gm and wm labels changed (%19 to gray, %81 to white out of all changed labels) 408 hippocampal voxels changed. 8 amygdala voxels changed. pass 1: 89147 changed. image ll: -2.230, PF=1.000 pass 2: 13519 changed. image ll: -2.228, PF=1.000 pass 3: 4443 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 17 minutes and 33 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/cc_up.lta nmr01002 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/norm.mgz 97556 voxels in left wm, 75550 in right wm, xrange [116, 132] searching rotation angles z=[-0 14], y=[-5 9] 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 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.6 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.1 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.6 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.1 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.6 searching scale 1 Z rot 12.9 searching scale 1 Z rot 13.1 searching scale 1 Z rot 13.4 global minimum found at slice 122.9, rotations (2.35, 6.62) final transformation (x=122.9, yr=2.347, zr=6.618): 0.993 -0.115 0.041 12.484; 0.115 0.993 0.005 25.000; -0.041 -0.000 0.999 39.111; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 156 117 eigenvectors: 0.001 0.003 1.000; -0.131 -0.991 0.003; 0.991 -0.131 -0.001; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.7 minutes #-------------------------------------- #@# Merge ASeg Thu Apr 14 23:16:27 EDT 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Apr 14 23:16:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2917 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 37 seconds. #-------------------------------------------- #@# Mask BFS Thu Apr 14 23:20:06 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1879483 voxels in mask (pct= 11.20) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Apr 14 23:20:09 EDT 2016 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.7 +- 6.5 [80.0 --> 125.0] GM (73.0) : 71.8 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.4 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5521 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6051 filled 337 bright non-wm voxels segmented. 3333 diagonally connected voxels added... white matter segmentation took 1.8 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 0.62 minutes reading wm segmentation from wm.seg.mgz... 219 voxels added to wm to prevent paths from MTL structures to cortex 2739 additional wm voxels added 0 additional wm voxels added SEG EDIT: 76008 voxels turned on, 58347 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+): 25 found - 25 modified | TOTAL: 25 pass 2 (xy+): 0 found - 25 modified | TOTAL: 25 pass 1 (xy-): 32 found - 32 modified | TOTAL: 57 pass 2 (xy-): 0 found - 32 modified | TOTAL: 57 pass 1 (yz+): 31 found - 31 modified | TOTAL: 88 pass 2 (yz+): 0 found - 31 modified | TOTAL: 88 pass 1 (yz-): 15 found - 15 modified | TOTAL: 103 pass 2 (yz-): 0 found - 15 modified | TOTAL: 103 pass 1 (xz+): 22 found - 22 modified | TOTAL: 125 pass 2 (xz+): 0 found - 22 modified | TOTAL: 125 pass 1 (xz-): 18 found - 18 modified | TOTAL: 143 pass 2 (xz-): 0 found - 18 modified | TOTAL: 143 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 16 found - 16 modified | TOTAL: 29 pass 2 (+++): 0 found - 16 modified | TOTAL: 29 pass 1 (+++): 12 found - 12 modified | TOTAL: 41 pass 2 (+++): 0 found - 12 modified | TOTAL: 41 pass 1 (+++): 15 found - 15 modified | TOTAL: 56 pass 2 (+++): 0 found - 15 modified | TOTAL: 56 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 84 found - 84 modified | TOTAL: 208 pass 2 (+-): 0 found - 84 modified | TOTAL: 208 pass 1 (--): 90 found - 90 modified | TOTAL: 298 pass 2 (--): 0 found - 90 modified | TOTAL: 298 pass 1 (-+): 104 found - 104 modified | TOTAL: 402 pass 2 (-+): 0 found - 104 modified | TOTAL: 402 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 619 (out of 716492: 0.086393) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Apr 14 23:22:39 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3639 (min = 350, max = 1400), aspect = 1.41 (min = 0.10, max = 0.75) need search nearby using seed (127, 121, 155), TAL = (1.0, 27.0, 7.0) talairach voxel to voxel transform 0.961 0.080 -0.079 3.033; -0.109 0.873 -0.240 41.374; 0.072 0.194 1.050 -41.403; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 121, 155) --> (1.0, 27.0, 7.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (1.00, 27.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 7.00) SRC: (105.25, 97.89, 152.56) search lh wm seed point around talairach space (-17.00, 27.00, 7.00), SRC: (139.85, 93.96, 155.14) 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 Apr 14 23:23:28 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 19 (out of 347268: 0.005471) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 2944 vertices, 3132 faces slice 40: 10921 vertices, 11278 faces slice 50: 22273 vertices, 22668 faces slice 60: 34740 vertices, 35181 faces slice 70: 47149 vertices, 47532 faces slice 80: 59678 vertices, 60114 faces slice 90: 72395 vertices, 72851 faces slice 100: 85976 vertices, 86438 faces slice 110: 98341 vertices, 98802 faces slice 120: 111100 vertices, 111556 faces slice 130: 123616 vertices, 124049 faces slice 140: 134919 vertices, 135312 faces slice 150: 144969 vertices, 145304 faces slice 160: 153120 vertices, 153436 faces slice 170: 160115 vertices, 160371 faces slice 180: 166375 vertices, 166591 faces slice 190: 171266 vertices, 171444 faces slice 200: 172828 vertices, 172866 faces slice 210: 172828 vertices, 172866 faces slice 220: 172828 vertices, 172866 faces slice 230: 172828 vertices, 172866 faces slice 240: 172828 vertices, 172866 faces slice 250: 172828 vertices, 172866 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... 172828 voxel in cpt #1: X=-38 [v=172828,e=518598,f=345732] located at (-23.818184, -26.572702, 31.230940) For the whole surface: X=-38 [v=172828,e=518598,f=345732] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Apr 14 23:23:37 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 14 23:23:43 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts avg radius = 51.0 mm, total surface area = 90513 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Apr 14 23:24:37 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.54 (0.00-->6.55) (max @ vno 129289 --> 130308) face area 0.02 +- 0.03 (-0.09-->0.52) scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.808, avgs=0 005/300: dt: 0.9000, rms radial error=176.547, avgs=0 010/300: dt: 0.9000, rms radial error=175.989, avgs=0 015/300: dt: 0.9000, rms radial error=175.257, avgs=0 020/300: dt: 0.9000, rms radial error=174.425, avgs=0 025/300: dt: 0.9000, rms radial error=173.535, avgs=0 030/300: dt: 0.9000, rms radial error=172.613, avgs=0 035/300: dt: 0.9000, rms radial error=171.674, avgs=0 040/300: dt: 0.9000, rms radial error=170.728, avgs=0 045/300: dt: 0.9000, rms radial error=169.779, avgs=0 050/300: dt: 0.9000, rms radial error=168.830, avgs=0 055/300: dt: 0.9000, rms radial error=167.885, avgs=0 060/300: dt: 0.9000, rms radial error=166.943, avgs=0 065/300: dt: 0.9000, rms radial error=166.005, avgs=0 070/300: dt: 0.9000, rms radial error=165.073, avgs=0 075/300: dt: 0.9000, rms radial error=164.145, avgs=0 080/300: dt: 0.9000, rms radial error=163.222, avgs=0 085/300: dt: 0.9000, rms radial error=162.304, avgs=0 090/300: dt: 0.9000, rms radial error=161.392, avgs=0 095/300: dt: 0.9000, rms radial error=160.484, avgs=0 100/300: dt: 0.9000, rms radial error=159.581, avgs=0 105/300: dt: 0.9000, rms radial error=158.683, avgs=0 110/300: dt: 0.9000, rms radial error=157.790, avgs=0 115/300: dt: 0.9000, rms radial error=156.902, avgs=0 120/300: dt: 0.9000, rms radial error=156.019, avgs=0 125/300: dt: 0.9000, rms radial error=155.140, avgs=0 130/300: dt: 0.9000, rms radial error=154.267, avgs=0 135/300: dt: 0.9000, rms radial error=153.398, avgs=0 140/300: dt: 0.9000, rms radial error=152.534, avgs=0 145/300: dt: 0.9000, rms radial error=151.675, avgs=0 150/300: dt: 0.9000, rms radial error=150.820, avgs=0 155/300: dt: 0.9000, rms radial error=149.971, avgs=0 160/300: dt: 0.9000, rms radial error=149.125, avgs=0 165/300: dt: 0.9000, rms radial error=148.285, avgs=0 170/300: dt: 0.9000, rms radial error=147.449, avgs=0 175/300: dt: 0.9000, rms radial error=146.618, avgs=0 180/300: dt: 0.9000, rms radial error=145.791, avgs=0 185/300: dt: 0.9000, rms radial error=144.969, avgs=0 190/300: dt: 0.9000, rms radial error=144.152, avgs=0 195/300: dt: 0.9000, rms radial error=143.339, avgs=0 200/300: dt: 0.9000, rms radial error=142.530, avgs=0 205/300: dt: 0.9000, rms radial error=141.726, avgs=0 210/300: dt: 0.9000, rms radial error=140.927, avgs=0 215/300: dt: 0.9000, rms radial error=140.132, avgs=0 220/300: dt: 0.9000, rms radial error=139.341, avgs=0 225/300: dt: 0.9000, rms radial error=138.555, avgs=0 230/300: dt: 0.9000, rms radial error=137.773, avgs=0 235/300: dt: 0.9000, rms radial error=136.996, avgs=0 240/300: dt: 0.9000, rms radial error=136.223, avgs=0 245/300: dt: 0.9000, rms radial error=135.454, avgs=0 250/300: dt: 0.9000, rms radial error=134.690, avgs=0 255/300: dt: 0.9000, rms radial error=133.930, avgs=0 260/300: dt: 0.9000, rms radial error=133.174, avgs=0 265/300: dt: 0.9000, rms radial error=132.422, avgs=0 270/300: dt: 0.9000, rms radial error=131.675, avgs=0 275/300: dt: 0.9000, rms radial error=130.932, avgs=0 280/300: dt: 0.9000, rms radial error=130.193, avgs=0 285/300: dt: 0.9000, rms radial error=129.458, avgs=0 290/300: dt: 0.9000, rms radial error=128.727, avgs=0 295/300: dt: 0.9000, rms radial error=128.001, avgs=0 300/300: dt: 0.9000, rms radial error=127.278, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20908.40 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 = 3769.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 431.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00517 epoch 4 (K=640.0), pass 1, starting sse = 25.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/17 = 0.01369 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Apr 14 23:31:45 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=172828, nf=345732, ne=518598, g=20) 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... 3174 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3257 (-4.6629) -vertex loglikelihood: -6.1497 (-3.0749) -normal dot loglikelihood: -3.6182 (-3.6182) -quad curv loglikelihood: -6.3064 (-3.1532) Total Loglikelihood : -25.4000 CORRECTING DEFECT 0 (vertices=18, convex hull=22) After retessellation of defect 0, euler #=-22 (170915,512130,341193) : difference with theory (-23) = -1 CORRECTING DEFECT 1 (vertices=27, convex hull=75) After retessellation of defect 1, euler #=-21 (170927,512198,341250) : difference with theory (-22) = -1 CORRECTING DEFECT 2 (vertices=69, convex hull=64) After retessellation of defect 2, euler #=-20 (170936,512254,341298) : difference with theory (-21) = -1 CORRECTING DEFECT 3 (vertices=26, convex hull=32) After retessellation of defect 3, euler #=-19 (170940,512276,341317) : difference with theory (-20) = -1 CORRECTING DEFECT 4 (vertices=22, convex hull=61) After retessellation of defect 4, euler #=-18 (170952,512336,341366) : difference with theory (-19) = -1 CORRECTING DEFECT 5 (vertices=80, convex hull=86) After retessellation of defect 5, euler #=-17 (170964,512403,341422) : difference with theory (-18) = -1 CORRECTING DEFECT 6 (vertices=26, convex hull=69) After retessellation of defect 6, euler #=-16 (170979,512475,341480) : difference with theory (-17) = -1 CORRECTING DEFECT 7 (vertices=819, convex hull=349) After retessellation of defect 7, euler #=-16 (171193,513301,342092) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=25, convex hull=31) After retessellation of defect 8, euler #=-15 (171197,513322,342110) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=34) After retessellation of defect 9, euler #=-14 (171202,513350,342134) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=50, convex hull=26) After retessellation of defect 10, euler #=-13 (171207,513374,342154) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-12 (171214,513405,342179) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=363, convex hull=95) After retessellation of defect 12, euler #=-11 (171237,513513,342265) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=10, convex hull=23) After retessellation of defect 13, euler #=-10 (171239,513523,342274) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=9, convex hull=25) After retessellation of defect 14, euler #=-9 (171242,513540,342289) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=79, convex hull=67) After retessellation of defect 15, euler #=-8 (171258,513622,342356) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=32) After retessellation of defect 16, euler #=-7 (171264,513648,342377) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=19) After retessellation of defect 17, euler #=-6 (171265,513657,342386) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=51) After retessellation of defect 18, euler #=-5 (171280,513717,342432) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=76) After retessellation of defect 19, euler #=-4 (171303,513814,342507) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=42, convex hull=50) After retessellation of defect 20, euler #=-3 (171318,513876,342555) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=69) After retessellation of defect 21, euler #=-2 (171329,513934,342603) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=41, convex hull=76) After retessellation of defect 22, euler #=-1 (171350,514030,342679) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=16, convex hull=27) After retessellation of defect 23, euler #=0 (171354,514050,342696) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=8, convex hull=18) After retessellation of defect 24, euler #=1 (171355,514057,342703) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=15, convex hull=15) After retessellation of defect 25, euler #=2 (171356,514062,342708) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (33.6%), 160 crossovers (66.4%), 94 vertices were eliminated building final representation... 1472 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=171356, nf=342708, ne=514062, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.8 minutes 0 defective edges removing intersecting faces 000: 141 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 171356 - 514062 + 342708 = 2 --> 0 holes F =2V-4: 342708 = 342712-4 (0) 2E=3F: 1028124 = 1028124 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Apr 14 23:49:42 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs nmr01002 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4843 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=81.7, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.9)->0.8 (%65.1))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.57 4093 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6547922.5, rms=10.18 001: dt: 0.5000, sse=7446320.0, rms=7.191 (0.000%) 002: dt: 0.5000, sse=7917418.5, rms=5.426 (0.000%) 003: dt: 0.5000, sse=8368811.0, rms=4.396 (0.000%) 004: dt: 0.5000, sse=8621337.0, rms=3.764 (0.000%) 005: dt: 0.5000, sse=8797901.0, rms=3.473 (0.000%) 006: dt: 0.5000, sse=8843084.0, rms=3.279 (0.000%) 007: dt: 0.5000, sse=8900322.0, rms=3.227 (0.000%) 008: dt: 0.5000, sse=8859434.0, rms=3.143 (0.000%) rms = 3.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6121292.0, rms=2.322 (0.000%) 010: dt: 0.2500, sse=5105471.5, rms=1.911 (0.000%) 011: dt: 0.2500, sse=4845299.0, rms=1.818 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4744487.5, rms=1.783 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4664090.5, rms=1.741 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.9, 92 (24) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.28) mean absolute distance = 0.26 +- 0.38 4748 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5489666.0, rms=4.84 014: dt: 0.5000, sse=5829010.0, rms=3.047 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6452591.0, rms=3.019 (0.000%) 016: dt: 0.2500, sse=5449506.0, rms=1.840 (0.000%) 017: dt: 0.2500, sse=5277622.5, rms=1.594 (0.000%) 018: dt: 0.2500, sse=5121994.0, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5088431.0, rms=1.481 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5008896.5, rms=1.448 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.5, 88 (6) missing vertices, mean dist -0.1 [0.3 (%75.1)->0.2 (%24.9))] %90 local maxima, % 5 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 (0.07-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.16 (0.00-->2.57) mean absolute distance = 0.20 +- 0.31 4616 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5289109.0, rms=3.43 021: dt: 0.5000, sse=5532589.0, rms=2.553 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5188599.5, rms=1.785 (0.000%) 023: dt: 0.2500, sse=5095104.5, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5080774.5, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5048881.0, rms=1.295 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.3, 87 (6) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %92 local maxima, % 3 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5065500.0, rms=1.63 rms = 1.76, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5111591.0, rms=1.206 (0.000%) 027: dt: 0.2500, sse=5293448.5, rms=0.997 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5290424.5, rms=0.993 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 18 non-cortical segments detected only using segment with 2146 vertices erasing segment 1 (vno[0] = 84151) erasing segment 2 (vno[0] = 95362) erasing segment 3 (vno[0] = 101746) erasing segment 4 (vno[0] = 105209) erasing segment 5 (vno[0] = 110214) erasing segment 6 (vno[0] = 118503) erasing segment 7 (vno[0] = 123094) erasing segment 8 (vno[0] = 123467) erasing segment 9 (vno[0] = 124283) erasing segment 10 (vno[0] = 124325) erasing segment 11 (vno[0] = 124399) erasing segment 12 (vno[0] = 125521) erasing segment 13 (vno[0] = 126884) erasing segment 14 (vno[0] = 127923) erasing segment 15 (vno[0] = 129137) erasing segment 16 (vno[0] = 171209) erasing segment 17 (vno[0] = 171261) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area vertex spacing 0.88 +- 0.25 (0.02-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.55) refinement took 6.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu Apr 14 23:56:23 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 14 23:56:28 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.2 mm, total surface area = 102629 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.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=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 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 229 vertices thresholded to be in k1 ~ [-0.33 0.44], k2 ~ [-0.09 0.08] total integrated curvature = 0.473*4pi (5.946) --> 1 handles ICI = 1.7, FI = 11.7, variation=196.595 163 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 159 vertices thresholded to be in [-0.13 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Thu Apr 14 23:59:08 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm nmr01002 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 [ nmr01002/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 [ 270 ] Gb_filter = 0 WARN: S lookup min: -0.446790 WARN: S explicit min: 0.000000 vertex = 560 #-------------------------------------------- #@# Sphere lh Thu Apr 14 23:59:15 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.262... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.73 pass 1: epoch 2 of 3 starting distance error %19.60 unfolding complete - removing small folds... starting distance error %19.51 removing remaining folds... final distance error %19.53 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.06 hours #-------------------------------------------- #@# Surf Reg lh Fri Apr 15 01:03:00 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.584 curvature mean = 0.019, std = 0.938 curvature mean = 0.025, std = 0.832 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 0.00) sse = 336897.8, tmin=2.9510 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 314532.9, tmin=4.4333 d=8.00 min @ (0.00, -2.00, 0.00) sse = 308756.3, tmin=5.9296 d=2.00 min @ (0.00, 0.50, 0.00) sse = 308642.5, tmin=8.9358 d=1.00 min @ (0.00, -0.25, -0.25) sse = 308511.6, tmin=10.4306 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 308488.6, tmin=11.9426 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 11.94 min curvature mean = -0.019, std = 0.931 curvature mean = 0.011, std = 0.923 curvature mean = -0.026, std = 0.935 curvature mean = 0.005, std = 0.963 curvature mean = -0.032, std = 0.930 curvature mean = 0.001, std = 0.982 2 Reading smoothwm curvature mean = -0.023, std = 0.291 curvature mean = 0.001, std = 0.066 curvature mean = 0.064, std = 0.313 curvature mean = 0.002, std = 0.077 curvature mean = 0.030, std = 0.508 curvature mean = 0.002, std = 0.082 curvature mean = 0.016, std = 0.657 curvature mean = 0.002, std = 0.085 curvature mean = 0.005, std = 0.772 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Apr 15 01:45:25 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Apr 15 01:45:28 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Apr 15 01:45:32 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 1413 labels changed using aseg relabeling using gibbs priors... 000: 3753 changed, 171356 examined... 001: 889 changed, 15700 examined... 002: 240 changed, 4861 examined... 003: 90 changed, 1375 examined... 004: 33 changed, 499 examined... 005: 13 changed, 188 examined... 006: 8 changed, 77 examined... 007: 2 changed, 42 examined... 008: 0 changed, 17 examined... 267 labels changed using aseg 000: 126 total segments, 71 labels (312 vertices) changed 001: 56 total segments, 2 labels (2 vertices) changed 002: 54 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 70 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2099 vertices marked for relabeling... 2099 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 7 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Apr 15 01:46:39 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs nmr01002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4872 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 390 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 24 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 77 points - only 0.00% unknown mean border=81.7, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.9)->0.8 (%65.1))] %75 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.57 4095 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6558650.5, rms=10.17 001: dt: 0.5000, sse=7461575.0, rms=7.184 (0.000%) 002: dt: 0.5000, sse=7937947.5, rms=5.422 (0.000%) 003: dt: 0.5000, sse=8386512.0, rms=4.392 (0.000%) 004: dt: 0.5000, sse=8645279.0, rms=3.761 (0.000%) 005: dt: 0.5000, sse=8819796.0, rms=3.472 (0.000%) 006: dt: 0.5000, sse=8868165.0, rms=3.278 (0.000%) 007: dt: 0.5000, sse=8922629.0, rms=3.225 (0.000%) 008: dt: 0.5000, sse=8885561.0, rms=3.142 (0.000%) rms = 3.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6136683.0, rms=2.321 (0.000%) 010: dt: 0.2500, sse=5116696.5, rms=1.910 (0.000%) 011: dt: 0.2500, sse=4856406.0, rms=1.817 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4754709.5, rms=1.782 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4674394.5, rms=1.740 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 4 with 301 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown deleting segment 9 with 30 points - only 20.00% unknown deleting segment 10 with 19 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 92 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown mean border=84.9, 105 (30) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.28) mean absolute distance = 0.26 +- 0.38 4755 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5503923.5, rms=4.84 014: dt: 0.5000, sse=5841640.0, rms=3.044 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6470345.0, rms=3.017 (0.000%) 016: dt: 0.2500, sse=5463847.0, rms=1.839 (0.000%) 017: dt: 0.2500, sse=5292212.0, rms=1.593 (0.000%) 018: dt: 0.2500, sse=5135784.5, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5102400.0, rms=1.481 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5022256.5, rms=1.448 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 2 with 326 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 30 points - only 20.00% unknown deleting segment 8 with 32 points - only 0.00% unknown deleting segment 9 with 29 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 87 points - only 0.00% unknown mean border=87.5, 128 (20) missing vertices, mean dist -0.1 [0.3 (%75.1)->0.2 (%24.9))] %91 local maxima, % 5 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 +- 0.24 (0.07-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.57) mean absolute distance = 0.20 +- 0.31 4623 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5304547.0, rms=3.42 021: dt: 0.5000, sse=5546052.5, rms=2.552 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5202303.5, rms=1.785 (0.000%) 023: dt: 0.2500, sse=5110339.5, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5094723.5, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5062705.0, rms=1.295 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 332 points - only 0.00% unknown deleting segment 2 with 43 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 30 points - only 20.00% unknown deleting segment 6 with 30 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown deleting segment 8 with 92 points - only 0.00% unknown mean border=88.3, 123 (16) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))] %93 local maxima, % 3 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=5079317.0, rms=1.63 rms = 1.76, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5126277.5, rms=1.206 (0.000%) 027: dt: 0.2500, sse=5308623.0, rms=0.997 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5305788.5, rms=0.993 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.5, 176 (176) missing vertices, mean dist 1.6 [0.2 (%0.0)->2.6 (%100.0))] %17 local maxima, %43 large gradients and %37 min vals, 2145 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=28900546.0, rms=27.87 001: dt: 0.5000, sse=22001930.0, rms=23.793 (0.000%) 002: dt: 0.5000, sse=16941796.0, rms=20.336 (0.000%) 003: dt: 0.5000, sse=13329012.0, rms=17.474 (0.000%) 004: dt: 0.5000, sse=10894143.0, rms=15.121 (0.000%) 005: dt: 0.5000, sse=9323342.0, rms=13.211 (0.000%) 006: dt: 0.5000, sse=8390207.0, rms=11.660 (0.000%) 007: dt: 0.5000, sse=7872577.0, rms=10.305 (0.000%) 008: dt: 0.5000, sse=7561293.5, rms=9.091 (0.000%) 009: dt: 0.5000, sse=7345375.0, rms=7.962 (0.000%) 010: dt: 0.5000, sse=7262029.5, rms=6.950 (0.000%) 011: dt: 0.5000, sse=7251921.0, rms=6.069 (0.000%) 012: dt: 0.5000, sse=7407465.5, rms=5.388 (0.000%) 013: dt: 0.5000, sse=7505711.5, rms=4.872 (0.000%) 014: dt: 0.5000, sse=7663648.0, rms=4.498 (0.000%) 015: dt: 0.5000, sse=7685889.0, rms=4.233 (0.000%) 016: dt: 0.5000, sse=7789745.5, rms=4.045 (0.000%) 017: dt: 0.5000, sse=7779108.0, rms=3.915 (0.000%) 018: dt: 0.5000, sse=7850615.0, rms=3.805 (0.000%) 019: dt: 0.5000, sse=7793289.5, rms=3.725 (0.000%) 020: dt: 0.5000, sse=7866527.5, rms=3.647 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=7811858.5, rms=3.610 (0.000%) 022: dt: 0.2500, sse=5386800.5, rms=2.900 (0.000%) 023: dt: 0.2500, sse=5150997.0, rms=2.704 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5033083.5, rms=2.672 (0.000%) 025: dt: 0.1250, sse=4789146.5, rms=2.554 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4753057.5, rms=2.535 (0.000%) positioning took 3.4 minutes mean border=58.4, 1548 (20) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.6 (%52.5))] %35 local maxima, %31 large gradients and %29 min vals, 956 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=5431901.5, rms=4.42 027: dt: 0.5000, sse=5754976.5, rms=3.604 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5346831.5, rms=3.055 (0.000%) 029: dt: 0.2500, sse=5444522.0, rms=2.803 (0.000%) 030: dt: 0.2500, sse=5373422.5, rms=2.683 (0.000%) 031: dt: 0.2500, sse=5426433.5, rms=2.630 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5410621.0, rms=2.590 (0.000%) 033: dt: 0.1250, sse=5227589.0, rms=2.463 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5219373.0, rms=2.436 (0.000%) positioning took 1.1 minutes mean border=56.9, 1924 (10) missing vertices, mean dist 0.1 [0.2 (%39.3)->0.4 (%60.7))] %50 local maxima, %17 large gradients and %29 min vals, 1010 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=5392991.0, rms=3.26 rms = 3.40, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5198340.5, rms=2.823 (0.000%) 036: dt: 0.2500, sse=5239759.0, rms=2.573 (0.000%) 037: dt: 0.2500, sse=5447061.0, rms=2.505 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5521635.5, rms=2.492 (0.000%) 039: dt: 0.1250, sse=5354938.0, rms=2.386 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5375163.5, rms=2.366 (0.000%) positioning took 0.9 minutes mean border=56.2, 3760 (4) missing vertices, mean dist 0.0 [0.2 (%45.0)->0.3 (%55.0))] %52 local maxima, %14 large gradients and %28 min vals, 841 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5410502.5, rms=2.58 rms = 3.02, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5304744.5, rms=2.423 (0.000%) 042: dt: 0.2500, sse=5522243.5, rms=2.371 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=5601827.5, rms=2.365 (0.000%) 044: dt: 0.1250, sse=5496024.0, rms=2.283 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=5519702.5, rms=2.267 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.05-->6.31) (max @ vno 117187 --> 117166) face area 0.38 +- 0.29 (0.00-->7.02) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1358:1800 truncations. 35553 vertices at 0 distance 111789 vertices at 1 distance 107609 vertices at 2 distance 48592 vertices at 3 distance 17069 vertices at 4 distance 5533 vertices at 5 distance 1854 vertices at 6 distance 620 vertices at 7 distance 250 vertices at 8 distance 134 vertices at 9 distance 90 vertices at 10 distance 62 vertices at 11 distance 38 vertices at 12 distance 39 vertices at 13 distance 37 vertices at 14 distance 20 vertices at 15 distance 20 vertices at 16 distance 13 vertices at 17 distance 13 vertices at 18 distance 14 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness positioning took 13.9 minutes #-------------------------------------------- #@# Surf Volume lh Fri Apr 15 02:00:30 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Fri Apr 15 02:00:30 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts pctsurfcon --s nmr01002 --lh-only Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts/pctsurfcon.log Fri Apr 15 02:00:30 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.wm.mgh --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 93026 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.wm.mgh Dim: 171356 1 1 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.gm.mgh --projfrac 0.3 --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 110983 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.gm.mgh Dim: 171356 1 1 mri_concat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.wm.mgh /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.16285/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh --annot nmr01002 lh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh --annot nmr01002 lh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh Vertex Area is 0.653288 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1628 1095.248 2 1002 caudalanteriorcingulate 1267 852.491 3 1003 caudalmiddlefrontal 4661 2993.004 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2569 1638.091 6 1006 entorhinal 781 512.957 7 1007 fusiform 6473 4301.817 8 1008 inferiorparietal 9158 6029.126 9 1009 inferiortemporal 6799 4474.829 10 1010 isthmuscingulate 2042 1346.021 11 1011 lateraloccipital 9091 5807.110 12 1012 lateralorbitofrontal 4808 3182.915 13 1013 lingual 5918 3943.176 14 1014 medialorbitofrontal 3625 2353.873 15 1015 middletemporal 5984 3925.383 16 1016 parahippocampal 1419 911.175 17 1017 paracentral 1895 1179.488 18 1018 parsopercularis 2609 1719.767 19 1019 parsorbitalis 1193 787.067 20 1020 parstriangularis 2503 1647.294 21 1021 pericalcarine 2469 1585.254 22 1022 postcentral 7777 4899.180 23 1023 posteriorcingulate 1736 1193.859 24 1024 precentral 8885 5548.221 25 1025 precuneus 7980 5278.827 26 1026 rostralanteriorcingulate 1512 1014.819 27 1027 rostralmiddlefrontal 11811 7743.463 28 1028 superiorfrontal 13663 9135.432 29 1029 superiorparietal 10030 6451.680 30 1030 superiortemporal 7358 4778.141 31 1031 supramarginal 8212 5455.665 32 1032 frontalpole 432 267.123 33 1033 temporalpole 882 618.226 34 1034 transversetemporal 1079 657.037 35 1035 insula 3896 2502.375 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Apr 15 02:00:43 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1628 1095 3052 2.784 0.606 0.111 0.025 13 1.7 bankssts 1267 852 2556 2.705 0.664 0.159 0.041 25 2.0 caudalanteriorcingulate 4661 2993 8713 2.624 0.506 0.127 0.041 53 7.5 caudalmiddlefrontal 2569 1638 3351 1.921 0.479 0.165 0.060 45 6.5 cuneus 781 513 2225 3.302 0.710 0.140 0.050 9 1.7 entorhinal 6473 4302 12958 2.702 0.594 0.145 0.067 152 15.0 fusiform 9158 6029 16627 2.487 0.498 0.135 0.043 137 15.9 inferiorparietal 6799 4475 14105 2.730 0.737 0.132 0.050 125 13.6 inferiortemporal 2042 1346 3376 2.504 0.751 0.170 0.203 267 5.3 isthmuscingulate 9091 5807 14639 2.330 0.736 0.154 0.071 232 25.6 lateraloccipital 4808 3183 8495 2.473 0.625 0.157 0.083 223 16.5 lateralorbitofrontal 5918 3943 8255 1.991 0.613 0.164 0.063 106 15.7 lingual 3625 2354 5809 2.320 0.734 0.151 0.100 178 15.0 medialorbitofrontal 5984 3925 15427 3.182 0.787 0.147 0.058 114 14.5 middletemporal 1419 911 2517 2.404 0.665 0.111 0.034 14 2.0 parahippocampal 1895 1179 2952 2.385 0.513 0.121 0.055 27 5.0 paracentral 2609 1720 4965 2.579 0.481 0.130 0.038 32 3.9 parsopercularis 1193 787 2495 2.553 0.490 0.162 0.062 27 2.9 parsorbitalis 2503 1647 4790 2.496 0.487 0.134 0.040 35 3.9 parstriangularis 2469 1585 2544 1.709 0.435 0.149 0.085 46 7.9 pericalcarine 7777 4899 11754 2.158 0.647 0.126 0.043 123 14.5 postcentral 1736 1194 3053 2.412 0.456 0.153 0.048 38 3.6 posteriorcingulate 8885 5548 16047 2.577 0.655 0.143 0.096 208 37.3 precentral 7980 5279 13554 2.465 0.498 0.152 0.056 139 16.7 precuneus 1512 1015 2753 2.396 0.456 0.146 0.055 34 3.8 rostralanteriorcingulate 11811 7743 20151 2.360 0.510 0.145 0.051 204 23.0 rostralmiddlefrontal 13663 9135 29822 2.828 0.638 0.143 0.066 293 29.6 superiorfrontal 10030 6452 14881 2.152 0.474 0.140 0.080 165 17.9 superiorparietal 7358 4778 15341 2.879 0.661 0.126 0.052 121 18.1 superiortemporal 8212 5456 14698 2.515 0.471 0.129 0.039 109 12.8 supramarginal 432 267 894 2.514 0.558 0.170 0.067 11 1.2 frontalpole 882 618 3363 4.077 0.637 0.184 0.199 55 6.7 temporalpole 1079 657 1675 2.311 0.514 0.139 0.053 15 2.5 transversetemporal 3896 2502 7514 3.066 0.747 0.134 0.062 87 10.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Apr 15 02:01:04 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 63 labels changed using aseg relabeling using gibbs priors... 000: 11587 changed, 171356 examined... 001: 2776 changed, 43856 examined... 002: 845 changed, 14190 examined... 003: 400 changed, 4733 examined... 004: 214 changed, 2257 examined... 005: 127 changed, 1254 examined... 006: 50 changed, 701 examined... 007: 24 changed, 283 examined... 008: 17 changed, 149 examined... 009: 6 changed, 78 examined... 010: 2 changed, 42 examined... 011: 0 changed, 11 examined... 20 labels changed using aseg 000: 345 total segments, 262 labels (3141 vertices) changed 001: 106 total segments, 25 labels (110 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... 1212 vertices marked for relabeling... 1212 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Apr 15 02:02:18 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1870 1254 2801 2.187 0.495 0.146 0.055 28 3.8 G_and_S_frontomargin 2042 1347 3158 2.215 0.550 0.146 0.048 57 3.9 G_and_S_occipital_inf 1303 768 2007 2.225 0.474 0.148 0.075 36 3.8 G_and_S_paracentral 1960 1294 3935 2.671 0.502 0.137 0.045 35 3.6 G_and_S_subcentral 917 598 1790 2.434 0.495 0.160 0.057 19 2.2 G_and_S_transv_frontopol 2760 1878 5108 2.584 0.491 0.134 0.039 37 4.6 G_and_S_cingul-Ant 1782 1226 3388 2.688 0.549 0.134 0.033 25 2.4 G_and_S_cingul-Mid-Ant 1328 931 2353 2.478 0.443 0.120 0.030 13 1.7 G_and_S_cingul-Mid-Post 745 514 1730 2.742 0.501 0.181 0.091 26 2.3 G_cingul-Post-dorsal 453 307 660 2.200 0.917 0.208 0.148 24 1.9 G_cingul-Post-ventral 2295 1449 3112 1.854 0.515 0.168 0.066 42 6.4 G_cuneus 1629 1060 3872 2.823 0.464 0.140 0.045 27 2.9 G_front_inf-Opercular 514 328 1204 2.643 0.440 0.169 0.057 12 1.3 G_front_inf-Orbital 1275 836 3126 2.763 0.467 0.145 0.044 21 2.2 G_front_inf-Triangul 6399 4044 13117 2.555 0.573 0.147 0.054 124 13.6 G_front_middle 9725 6414 23503 2.978 0.627 0.155 0.085 267 27.1 G_front_sup 589 371 1256 3.110 0.662 0.140 0.062 12 1.4 G_Ins_lg_and_S_cent_ins 964 600 2664 3.681 0.680 0.159 0.084 34 3.5 G_insular_short 2972 1939 7248 3.006 0.716 0.169 0.102 87 12.8 G_occipital_middle 1892 1162 2618 2.000 0.512 0.145 0.051 30 4.4 G_occipital_sup 2549 1634 5361 2.639 0.526 0.153 0.065 61 6.9 G_oc-temp_lat-fusifor 3703 2376 5075 1.921 0.664 0.177 0.076 80 11.9 G_oc-temp_med-Lingual 1687 1082 3747 2.765 0.808 0.118 0.044 20 3.3 G_oc-temp_med-Parahip 3347 2160 7086 2.631 0.632 0.174 0.107 224 14.5 G_orbital 3746 2442 8346 2.684 0.490 0.148 0.052 76 8.0 G_pariet_inf-Angular 4262 2767 8724 2.606 0.495 0.135 0.044 69 7.4 G_pariet_inf-Supramar 3925 2487 7122 2.346 0.465 0.146 0.136 83 7.3 G_parietal_sup 3083 1782 4880 2.192 0.565 0.130 0.051 66 7.4 G_postcentral 3855 2208 8171 2.733 0.745 0.147 0.120 110 26.1 G_precentral 3963 2627 7987 2.498 0.507 0.164 0.069 91 9.7 G_precuneus 1332 823 2551 2.438 0.745 0.165 0.085 40 4.4 G_rectus 568 344 880 2.422 0.825 0.172 0.312 115 7.9 G_subcallosal 848 496 1378 2.285 0.557 0.126 0.039 11 1.4 G_temp_sup-G_T_transv 2771 1764 7976 3.309 0.787 0.154 0.091 81 13.5 G_temp_sup-Lateral 734 513 1807 3.317 0.643 0.116 0.039 7 1.1 G_temp_sup-Plan_polar 1605 1038 2859 2.640 0.519 0.123 0.037 22 2.5 G_temp_sup-Plan_tempo 3794 2450 8849 2.787 0.697 0.147 0.063 97 9.7 G_temporal_inf 3810 2447 11206 3.308 0.669 0.151 0.055 80 8.2 G_temporal_middle 435 292 550 2.045 0.435 0.103 0.020 2 0.4 Lat_Fis-ant-Horizont 351 248 515 2.234 0.336 0.101 0.020 2 0.3 Lat_Fis-ant-Vertical 1947 1298 2630 2.442 0.461 0.129 0.042 21 3.4 Lat_Fis-post 2778 1684 3551 1.966 0.594 0.165 0.069 52 7.8 Pole_occipital 2453 1710 8908 3.966 0.809 0.189 0.140 104 13.0 Pole_temporal 3089 2033 3635 1.979 0.642 0.147 0.070 53 8.2 S_calcarine 3594 2398 4294 1.915 0.690 0.133 0.085 63 7.8 S_central 1066 720 1568 2.296 0.412 0.127 0.035 11 1.5 S_cingul-Marginalis 532 354 838 2.813 0.502 0.118 0.031 3 0.7 S_circular_insula_ant 1520 1002 2341 2.796 0.492 0.094 0.022 7 1.4 S_circular_insula_inf 1948 1289 2779 2.513 0.405 0.117 0.044 24 4.0 S_circular_insula_sup 1390 935 2644 2.758 0.553 0.117 0.040 17 2.3 S_collat_transv_ant 321 233 568 2.498 0.371 0.130 0.030 3 0.3 S_collat_transv_post 3821 2482 5870 2.372 0.460 0.138 0.047 57 6.5 S_front_inf 1762 1205 2538 2.310 0.412 0.127 0.035 17 2.3 S_front_middle 2919 1981 4449 2.345 0.452 0.119 0.031 24 3.8 S_front_sup 767 535 1082 2.387 0.294 0.108 0.022 4 0.8 S_interm_prim-Jensen 3658 2397 4463 2.057 0.388 0.128 0.042 45 5.3 S_intrapariet_and_P_trans 1645 1100 2172 2.232 0.436 0.140 0.043 18 2.8 S_oc_middle_and_Lunatus 1825 1188 2231 2.031 0.487 0.133 0.049 55 2.9 S_oc_sup_and_transversal 776 514 1046 2.314 0.432 0.099 0.020 4 0.7 S_occipital_ant 1280 836 1695 2.501 0.366 0.133 0.039 15 2.0 S_oc-temp_lat 3237 2240 4790 2.257 0.471 0.134 0.064 68 6.0 S_oc-temp_med_and_Lingual 571 378 799 2.278 0.402 0.136 0.039 6 0.9 S_orbital_lateral 1354 919 1845 2.148 0.758 0.128 0.050 18 2.5 S_orbital_med-olfact 1634 1113 2593 2.393 0.534 0.143 0.048 22 3.1 S_orbital-H_Shaped 2444 1588 3167 2.338 0.549 0.136 0.039 27 4.0 S_parieto_occipital 1361 817 1383 2.134 0.577 0.162 0.242 249 3.6 S_pericallosal 3262 2190 4335 2.227 0.412 0.125 0.035 31 4.6 S_postcentral 1984 1343 3044 2.562 0.312 0.119 0.032 18 2.5 S_precentral-inf-part 1475 1004 2026 2.379 0.445 0.119 0.029 11 1.8 S_precentral-sup-part 822 569 1137 2.184 0.523 0.153 0.047 15 1.6 S_suborbital 2123 1419 3248 2.437 0.368 0.145 0.047 28 3.9 S_subparietal 2273 1529 3187 2.452 0.406 0.114 0.032 21 2.7 S_temporal_inf 6356 4278 10297 2.540 0.438 0.115 0.029 56 7.7 S_temporal_sup 376 249 480 2.347 0.410 0.106 0.033 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Apr 15 02:02:41 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1340 labels changed using aseg relabeling using gibbs priors... 000: 3424 changed, 171356 examined... 001: 784 changed, 14119 examined... 002: 213 changed, 4300 examined... 003: 99 changed, 1233 examined... 004: 48 changed, 582 examined... 005: 20 changed, 279 examined... 006: 13 changed, 109 examined... 007: 7 changed, 81 examined... 008: 3 changed, 41 examined... 009: 2 changed, 21 examined... 010: 0 changed, 14 examined... 217 labels changed using aseg 000: 73 total segments, 40 labels (286 vertices) changed 001: 34 total segments, 1 labels (3 vertices) changed 002: 33 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... 856 vertices marked for relabeling... 856 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 6 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Apr 15 02:03:47 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1932 1286 3528 2.675 0.579 0.145 0.036 32 2.8 caudalanteriorcingulate 4756 3068 9004 2.626 0.509 0.128 0.042 55 7.8 caudalmiddlefrontal 3644 2343 4951 2.007 0.533 0.152 0.053 55 8.0 cuneus 810 530 2221 3.260 0.720 0.138 0.049 9 1.7 entorhinal 5784 3841 10989 2.610 0.509 0.137 0.050 98 11.6 fusiform 8760 5763 15964 2.497 0.498 0.135 0.043 131 15.2 inferiorparietal 6883 4547 14652 2.775 0.723 0.138 0.056 137 14.9 inferiortemporal 2026 1339 3343 2.500 0.752 0.169 0.204 266 5.2 isthmuscingulate 9430 6005 15100 2.316 0.739 0.154 0.070 237 26.4 lateraloccipital 5424 3568 9601 2.480 0.658 0.159 0.086 248 18.7 lateralorbitofrontal 5829 3891 8148 1.987 0.603 0.164 0.063 105 15.4 lingual 2844 1839 4670 2.288 0.743 0.147 0.061 61 6.9 medialorbitofrontal 7670 5066 18984 3.103 0.826 0.142 0.051 132 16.9 middletemporal 1501 957 2577 2.395 0.648 0.118 0.088 49 3.0 parahippocampal 2285 1427 3525 2.350 0.513 0.122 0.052 35 5.7 paracentral 2322 1527 4450 2.604 0.456 0.131 0.039 30 3.6 parsopercularis 1200 797 2386 2.483 0.503 0.149 0.054 22 2.5 parsorbitalis 3060 2006 5609 2.479 0.480 0.134 0.039 41 4.9 parstriangularis 2517 1612 2592 1.705 0.434 0.150 0.085 47 8.0 pericalcarine 8562 5426 12756 2.169 0.633 0.127 0.043 132 15.8 postcentral 1987 1357 3443 2.398 0.450 0.151 0.047 43 4.0 posteriorcingulate 8828 5513 15894 2.577 0.655 0.143 0.097 208 37.2 precentral 7624 5061 13293 2.479 0.487 0.155 0.057 138 16.4 precuneus 2157 1431 3634 2.408 0.476 0.153 0.119 147 11.6 rostralanteriorcingulate 8717 5683 15311 2.378 0.498 0.144 0.049 150 16.8 rostralmiddlefrontal 15244 10199 32690 2.770 0.660 0.147 0.067 328 33.7 superiorfrontal 8065 5168 12025 2.163 0.469 0.140 0.090 139 14.6 superiorparietal 9787 6412 21384 2.968 0.739 0.130 0.063 197 27.2 superiortemporal 7984 5298 14180 2.495 0.476 0.131 0.040 108 12.6 supramarginal 1067 648 1666 2.308 0.516 0.138 0.051 14 2.4 transversetemporal 3446 2222 6784 3.050 0.727 0.130 0.058 70 8.8 insula #-------------------------------------------- #@# Tessellate rh Fri Apr 15 02:04:07 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 12 (out of 342363: 0.003505) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 13 vertices, 18 faces slice 30: 3524 vertices, 3726 faces slice 40: 12191 vertices, 12543 faces slice 50: 24263 vertices, 24721 faces slice 60: 37970 vertices, 38423 faces slice 70: 50740 vertices, 51184 faces slice 80: 63449 vertices, 63848 faces slice 90: 76677 vertices, 77126 faces slice 100: 89742 vertices, 90186 faces slice 110: 102644 vertices, 103108 faces slice 120: 115076 vertices, 115525 faces slice 130: 125990 vertices, 126381 faces slice 140: 136268 vertices, 136653 faces slice 150: 145281 vertices, 145651 faces slice 160: 152748 vertices, 153015 faces slice 170: 159047 vertices, 159278 faces slice 180: 164986 vertices, 165220 faces slice 190: 169066 vertices, 169243 faces slice 200: 170526 vertices, 170568 faces slice 210: 170526 vertices, 170568 faces slice 220: 170526 vertices, 170568 faces slice 230: 170526 vertices, 170568 faces slice 240: 170526 vertices, 170568 faces slice 250: 170526 vertices, 170568 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... 170526 voxel in cpt #1: X=-42 [v=170526,e=511704,f=341136] located at (31.911310, -29.600290, 25.253704) For the whole surface: X=-42 [v=170526,e=511704,f=341136] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Apr 15 02:04:16 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 15 02:04:22 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts avg radius = 50.9 mm, total surface area = 89667 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri Apr 15 02:05:15 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.53 (0.00-->5.96) (max @ vno 131939 --> 131940) face area 0.02 +- 0.03 (-0.22-->0.64) scaling brain by 0.282... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.624, avgs=0 005/300: dt: 0.9000, rms radial error=176.369, avgs=0 010/300: dt: 0.9000, rms radial error=175.812, avgs=0 015/300: dt: 0.9000, rms radial error=175.082, avgs=0 020/300: dt: 0.9000, rms radial error=174.249, avgs=0 025/300: dt: 0.9000, rms radial error=173.358, avgs=0 030/300: dt: 0.9000, rms radial error=172.436, avgs=0 035/300: dt: 0.9000, rms radial error=171.497, avgs=0 040/300: dt: 0.9000, rms radial error=170.551, avgs=0 045/300: dt: 0.9000, rms radial error=169.603, avgs=0 050/300: dt: 0.9000, rms radial error=168.656, avgs=0 055/300: dt: 0.9000, rms radial error=167.711, avgs=0 060/300: dt: 0.9000, rms radial error=166.771, avgs=0 065/300: dt: 0.9000, rms radial error=165.834, avgs=0 070/300: dt: 0.9000, rms radial error=164.903, avgs=0 075/300: dt: 0.9000, rms radial error=163.977, avgs=0 080/300: dt: 0.9000, rms radial error=163.056, avgs=0 085/300: dt: 0.9000, rms radial error=162.140, avgs=0 090/300: dt: 0.9000, rms radial error=161.229, avgs=0 095/300: dt: 0.9000, rms radial error=160.323, avgs=0 100/300: dt: 0.9000, rms radial error=159.422, avgs=0 105/300: dt: 0.9000, rms radial error=158.526, avgs=0 110/300: dt: 0.9000, rms radial error=157.637, avgs=0 115/300: dt: 0.9000, rms radial error=156.752, avgs=0 120/300: dt: 0.9000, rms radial error=155.872, avgs=0 125/300: dt: 0.9000, rms radial error=154.997, avgs=0 130/300: dt: 0.9000, rms radial error=154.127, avgs=0 135/300: dt: 0.9000, rms radial error=153.262, avgs=0 140/300: dt: 0.9000, rms radial error=152.401, avgs=0 145/300: dt: 0.9000, rms radial error=151.545, avgs=0 150/300: dt: 0.9000, rms radial error=150.694, avgs=0 155/300: dt: 0.9000, rms radial error=149.848, avgs=0 160/300: dt: 0.9000, rms radial error=149.006, avgs=0 165/300: dt: 0.9000, rms radial error=148.169, avgs=0 170/300: dt: 0.9000, rms radial error=147.336, avgs=0 175/300: dt: 0.9000, rms radial error=146.509, avgs=0 180/300: dt: 0.9000, rms radial error=145.685, avgs=0 185/300: dt: 0.9000, rms radial error=144.866, avgs=0 190/300: dt: 0.9000, rms radial error=144.052, avgs=0 195/300: dt: 0.9000, rms radial error=143.242, avgs=0 200/300: dt: 0.9000, rms radial error=142.436, avgs=0 205/300: dt: 0.9000, rms radial error=141.635, avgs=0 210/300: dt: 0.9000, rms radial error=140.839, avgs=0 215/300: dt: 0.9000, rms radial error=140.047, avgs=0 220/300: dt: 0.9000, rms radial error=139.259, avgs=0 225/300: dt: 0.9000, rms radial error=138.475, avgs=0 230/300: dt: 0.9000, rms radial error=137.696, avgs=0 235/300: dt: 0.9000, rms radial error=136.921, avgs=0 240/300: dt: 0.9000, rms radial error=136.150, avgs=0 245/300: dt: 0.9000, rms radial error=135.384, avgs=0 250/300: dt: 0.9000, rms radial error=134.622, avgs=0 255/300: dt: 0.9000, rms radial error=133.865, avgs=0 260/300: dt: 0.9000, rms radial error=133.111, avgs=0 265/300: dt: 0.9000, rms radial error=132.362, avgs=0 270/300: dt: 0.9000, rms radial error=131.617, avgs=0 275/300: dt: 0.9000, rms radial error=130.876, avgs=0 280/300: dt: 0.9000, rms radial error=130.139, avgs=0 285/300: dt: 0.9000, rms radial error=129.406, avgs=0 290/300: dt: 0.9000, rms radial error=128.678, avgs=0 295/300: dt: 0.9000, rms radial error=127.953, avgs=0 300/300: dt: 0.9000, rms radial error=127.233, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20572.36 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3675.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 418.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00583 epoch 4 (K=640.0), pass 1, starting sse = 29.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/16 = 0.01234 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Apr 15 02:12:13 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-42 (nv=170526, nf=341136, ne=511704, g=22) 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 11 iterations marking ambiguous vertices... 3486 ambiguous faces found in tessellation segmenting defects... 35 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 35 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4051 (-4.7025) -vertex loglikelihood: -6.1688 (-3.0844) -normal dot loglikelihood: -3.6423 (-3.6423) -quad curv loglikelihood: -6.4289 (-3.2144) Total Loglikelihood : -25.6451 CORRECTING DEFECT 0 (vertices=10, convex hull=34) After retessellation of defect 0, euler #=-32 (168360,504125,335733) : difference with theory (-32) = 0 CORRECTING DEFECT 1 (vertices=41, convex hull=52) After retessellation of defect 1, euler #=-31 (168364,504158,335763) : difference with theory (-31) = 0 CORRECTING DEFECT 2 (vertices=20, convex hull=40) After retessellation of defect 2, euler #=-30 (168370,504189,335789) : difference with theory (-30) = 0 CORRECTING DEFECT 3 (vertices=97, convex hull=83) After retessellation of defect 3, euler #=-29 (168394,504293,335870) : difference with theory (-29) = 0 CORRECTING DEFECT 4 (vertices=237, convex hull=138) After retessellation of defect 4, euler #=-28 (168447,504520,336045) : difference with theory (-28) = 0 CORRECTING DEFECT 5 (vertices=89, convex hull=85) After retessellation of defect 5, euler #=-27 (168456,504586,336103) : difference with theory (-27) = 0 CORRECTING DEFECT 6 (vertices=106, convex hull=118) After retessellation of defect 6, euler #=-26 (168513,504814,336275) : difference with theory (-26) = 0 CORRECTING DEFECT 7 (vertices=11, convex hull=26) After retessellation of defect 7, euler #=-25 (168515,504826,336286) : difference with theory (-25) = 0 CORRECTING DEFECT 8 (vertices=6, convex hull=28) After retessellation of defect 8, euler #=-24 (168518,504843,336301) : difference with theory (-24) = 0 CORRECTING DEFECT 9 (vertices=15, convex hull=24) After retessellation of defect 9, euler #=-23 (168523,504867,336321) : difference with theory (-23) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=39) After retessellation of defect 10, euler #=-22 (168533,504908,336353) : difference with theory (-22) = 0 CORRECTING DEFECT 11 (vertices=19, convex hull=61) After retessellation of defect 11, euler #=-21 (168541,504956,336394) : difference with theory (-21) = 0 CORRECTING DEFECT 12 (vertices=20, convex hull=43) After retessellation of defect 12, euler #=-20 (168551,505001,336430) : difference with theory (-20) = 0 CORRECTING DEFECT 13 (vertices=6, convex hull=21) After retessellation of defect 13, euler #=-19 (168554,505017,336444) : difference with theory (-19) = 0 CORRECTING DEFECT 14 (vertices=53, convex hull=69) After retessellation of defect 14, euler #=-18 (168577,505113,336518) : difference with theory (-18) = 0 CORRECTING DEFECT 15 (vertices=616, convex hull=389) After retessellation of defect 15, euler #=-17 (168607,505407,336783) : difference with theory (-17) = 0 CORRECTING DEFECT 16 (vertices=59, convex hull=87) After retessellation of defect 16, euler #=-16 (168639,505540,336885) : difference with theory (-16) = 0 CORRECTING DEFECT 17 (vertices=6, convex hull=14) After retessellation of defect 17, euler #=-15 (168640,505545,336890) : difference with theory (-15) = 0 CORRECTING DEFECT 18 (vertices=19, convex hull=40) After retessellation of defect 18, euler #=-14 (168646,505580,336920) : difference with theory (-14) = 0 CORRECTING DEFECT 19 (vertices=12, convex hull=27) After retessellation of defect 19, euler #=-13 (168648,505594,336933) : difference with theory (-13) = 0 CORRECTING DEFECT 20 (vertices=82, convex hull=98) After retessellation of defect 20, euler #=-12 (168688,505763,337063) : difference with theory (-12) = 0 CORRECTING DEFECT 21 (vertices=10, convex hull=22) After retessellation of defect 21, euler #=-11 (168693,505787,337083) : difference with theory (-11) = 0 CORRECTING DEFECT 22 (vertices=19, convex hull=23) After retessellation of defect 22, euler #=-10 (168694,505799,337095) : difference with theory (-10) = 0 CORRECTING DEFECT 23 (vertices=60, convex hull=51) After retessellation of defect 23, euler #=-9 (168705,505849,337135) : difference with theory (-9) = 0 CORRECTING DEFECT 24 (vertices=27, convex hull=33) After retessellation of defect 24, euler #=-8 (168714,505889,337167) : difference with theory (-8) = 0 CORRECTING DEFECT 25 (vertices=40, convex hull=59) After retessellation of defect 25, euler #=-7 (168726,505949,337216) : difference with theory (-7) = 0 CORRECTING DEFECT 26 (vertices=64, convex hull=96) After retessellation of defect 26, euler #=-6 (168768,506119,337345) : difference with theory (-6) = 0 CORRECTING DEFECT 27 (vertices=54, convex hull=41) Warning - incorrect dp selected!!!!(-107.906325 >= -107.906333 ) After retessellation of defect 27, euler #=-5 (168771,506145,337369) : difference with theory (-5) = 0 CORRECTING DEFECT 28 (vertices=20, convex hull=54) After retessellation of defect 28, euler #=-4 (168783,506200,337413) : difference with theory (-4) = 0 CORRECTING DEFECT 29 (vertices=82, convex hull=127) After retessellation of defect 29, euler #=-3 (168819,506362,337540) : difference with theory (-3) = 0 CORRECTING DEFECT 30 (vertices=63, convex hull=79) After retessellation of defect 30, euler #=-2 (168847,506479,337630) : difference with theory (-2) = 0 CORRECTING DEFECT 31 (vertices=26, convex hull=24) After retessellation of defect 31, euler #=-1 (168850,506498,337647) : difference with theory (-1) = 0 CORRECTING DEFECT 32 (vertices=45, convex hull=40) After retessellation of defect 32, euler #=0 (168853,506522,337669) : difference with theory (0) = 0 CORRECTING DEFECT 33 (vertices=64, convex hull=48) After retessellation of defect 33, euler #=1 (168862,506569,337708) : difference with theory (1) = 0 CORRECTING DEFECT 34 (vertices=40, convex hull=30) After retessellation of defect 34, euler #=2 (168865,506589,337726) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->14.99) (max @ vno 26513 --> 46149) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->14.99) (max @ vno 26513 --> 46149) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 156 mutations (36.8%), 268 crossovers (63.2%), 219 vertices were eliminated building final representation... 1661 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=168865, nf=337726, ne=506589, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.1 minutes 0 defective edges removing intersecting faces 000: 276 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 168865 - 506589 + 337726 = 2 --> 0 holes F =2V-4: 337726 = 337730-4 (0) 2E=3F: 1013178 = 1013178 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 36 intersecting 001: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Apr 15 02:38:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs nmr01002 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.48) (max @ vno 26513 --> 46149) face area 0.28 +- 0.12 (0.00-->2.54) mean absolute distance = 0.68 +- 0.86 4735 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.6, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.6, 50 (50) missing vertices, mean dist 0.2 [0.6 (%38.0)->0.7 (%62.0))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.12-->4.24) (max @ vno 26513 --> 46149) face area 0.28 +- 0.13 (0.00-->3.45) mean absolute distance = 0.35 +- 0.57 4083 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6300162.5, rms=10.02 001: dt: 0.5000, sse=7173680.5, rms=7.042 (0.000%) 002: dt: 0.5000, sse=7687577.0, rms=5.299 (0.000%) 003: dt: 0.5000, sse=8081307.5, rms=4.299 (0.000%) 004: dt: 0.5000, sse=8352765.5, rms=3.694 (0.000%) 005: dt: 0.5000, sse=8495561.0, rms=3.434 (0.000%) 006: dt: 0.5000, sse=8577874.0, rms=3.249 (0.000%) rms = 3.22, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8611141.0, rms=3.220 (0.000%) 008: dt: 0.2500, sse=5273892.0, rms=2.143 (0.000%) 009: dt: 0.2500, sse=4828339.0, rms=1.864 (0.000%) 010: dt: 0.2500, sse=4629230.5, rms=1.792 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=4568882.5, rms=1.747 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=4488233.0, rms=1.705 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.5, 32 (10) missing vertices, mean dist -0.2 [0.4 (%72.7)->0.3 (%27.3))] %82 local maxima, %13 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 (0.07-->4.32) (max @ vno 168592 --> 103991) face area 0.35 +- 0.16 (0.00-->4.07) mean absolute distance = 0.26 +- 0.38 4559 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5205534.5, rms=4.51 013: dt: 0.5000, sse=5670849.0, rms=2.921 (0.000%) rms = 2.97, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=5272301.5, rms=2.329 (0.000%) 015: dt: 0.2500, sse=5071698.0, rms=1.848 (0.000%) 016: dt: 0.2500, sse=4974119.5, rms=1.633 (0.000%) 017: dt: 0.2500, sse=4903126.5, rms=1.547 (0.000%) 018: dt: 0.2500, sse=4876580.0, rms=1.495 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4856404.5, rms=1.465 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4807552.5, rms=1.432 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.8, 34 (7) missing vertices, mean dist -0.1 [0.3 (%73.2)->0.2 (%26.8))] %89 local maxima, % 6 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-->4.57) (max @ vno 168592 --> 103991) face area 0.34 +- 0.16 (0.00-->3.81) mean absolute distance = 0.21 +- 0.31 4419 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5059002.5, rms=3.27 021: dt: 0.5000, sse=5411036.5, rms=2.515 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5082968.0, rms=1.775 (0.000%) 023: dt: 0.2500, sse=4967961.0, rms=1.394 (0.000%) 024: dt: 0.2500, sse=4949765.5, rms=1.292 (0.000%) rms = 1.29, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4920753.5, rms=1.289 (0.000%) rms = 1.26, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4875638.0, rms=1.259 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=88.7, 46 (6) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))] %91 local maxima, % 4 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4885641.5, rms=1.57 rms = 1.65, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4974423.5, rms=1.162 (0.000%) 028: dt: 0.2500, sse=5163577.5, rms=0.962 (0.000%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.96, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5163709.5, rms=0.961 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 8 non-cortical segments detected only using segment with 2687 vertices erasing segment 1 (vno[0] = 124014) erasing segment 2 (vno[0] = 124963) erasing segment 3 (vno[0] = 125180) erasing segment 4 (vno[0] = 127064) erasing segment 5 (vno[0] = 133083) erasing segment 6 (vno[0] = 134078) erasing segment 7 (vno[0] = 135061) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->4.63) (max @ vno 168592 --> 103991) face area 0.33 +- 0.15 (0.00-->3.79) refinement took 6.6 minutes #-------------------------------------------- #@# Smooth2 rh Fri Apr 15 02:45:04 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 15 02:45:09 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.1 mm, total surface area = 101491 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=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 210 vertices thresholded to be in k1 ~ [-0.20 1.10], k2 ~ [-0.10 0.08] total integrated curvature = 0.533*4pi (6.692) --> 0 handles ICI = 1.9, FI = 14.2, variation=235.996 146 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 130 vertices thresholded to be in [-0.11 0.26] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.014, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Fri Apr 15 02:47:43 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm nmr01002 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 [ nmr01002/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 [ 325 ] Gb_filter = 0 WARN: S lookup min: -0.319846 WARN: S explicit min: 0.000000 vertex = 156 #-------------------------------------------- #@# Sphere rh Fri Apr 15 02:47:49 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.264... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.43 pass 1: epoch 2 of 3 starting distance error %19.39 unfolding complete - removing small folds... starting distance error %19.33 removing remaining folds... final distance error %19.35 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.28 hours #-------------------------------------------- #@# Surf Reg rh Fri Apr 15 04:04:41 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.576 curvature mean = 0.011, std = 0.935 curvature mean = 0.025, std = 0.834 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 0.00) sse = 412741.9, tmin=2.9066 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 388588.1, tmin=4.3681 d=8.00 min @ (0.00, 0.00, 2.00) sse = 385907.6, tmin=5.8407 d=4.00 min @ (0.00, -1.00, 0.00) sse = 385111.8, tmin=7.3244 d=2.00 min @ (0.50, 0.50, 0.00) sse = 384947.2, tmin=8.8157 d=1.00 min @ (-0.25, -0.25, -0.25) sse = 384741.0, tmin=10.2993 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 11.80 min curvature mean = -0.009, std = 0.934 curvature mean = 0.012, std = 0.924 curvature mean = -0.014, std = 0.940 curvature mean = 0.006, std = 0.961 curvature mean = -0.017, std = 0.936 curvature mean = 0.002, std = 0.980 2 Reading smoothwm curvature mean = -0.022, std = 0.281 curvature mean = 0.004, std = 0.069 curvature mean = 0.062, std = 0.335 curvature mean = 0.005, std = 0.082 curvature mean = 0.032, std = 0.527 curvature mean = 0.005, std = 0.088 curvature mean = 0.015, std = 0.678 curvature mean = 0.006, std = 0.090 curvature mean = 0.005, std = 0.794 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... #-------------------------------------------- #@# Jacobian white rh Fri Apr 15 04:48:18 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri Apr 15 04:48:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Apr 15 04:48:23 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 1295 labels changed using aseg relabeling using gibbs priors... 000: 3641 changed, 168865 examined... 001: 893 changed, 15183 examined... 002: 242 changed, 4975 examined... 003: 91 changed, 1435 examined... 004: 38 changed, 578 examined... 005: 11 changed, 224 examined... 006: 10 changed, 70 examined... 007: 4 changed, 65 examined... 008: 3 changed, 21 examined... 009: 1 changed, 16 examined... 010: 0 changed, 7 examined... 246 labels changed using aseg 000: 117 total segments, 77 labels (560 vertices) changed 001: 44 total segments, 5 labels (26 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1573 vertices marked for relabeling... 1573 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 5 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Apr 15 04:49:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs nmr01002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.6, 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.48) (max @ vno 26513 --> 46149) face area 0.28 +- 0.12 (0.00-->2.54) mean absolute distance = 0.68 +- 0.86 4752 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 2 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 18 points - only 0.00% unknown deleting segment 5 with 153 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 8 points - only 0.00% unknown mean border=82.6, 50 (50) missing vertices, mean dist 0.2 [0.6 (%38.0)->0.7 (%62.0))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.12-->4.24) (max @ vno 26513 --> 46149) face area 0.28 +- 0.13 (0.00-->3.45) mean absolute distance = 0.35 +- 0.57 4086 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6304564.0, rms=10.01 001: dt: 0.5000, sse=7178592.0, rms=7.041 (0.000%) 002: dt: 0.5000, sse=7692854.5, rms=5.298 (0.000%) 003: dt: 0.5000, sse=8086409.0, rms=4.298 (0.000%) 004: dt: 0.5000, sse=8359135.0, rms=3.692 (0.000%) 005: dt: 0.5000, sse=8499774.0, rms=3.433 (0.000%) 006: dt: 0.5000, sse=8586377.0, rms=3.247 (0.000%) rms = 3.22, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8617859.0, rms=3.218 (0.000%) 008: dt: 0.2500, sse=5276536.0, rms=2.142 (0.000%) 009: dt: 0.2500, sse=4830540.5, rms=1.863 (0.000%) 010: dt: 0.2500, sse=4631314.0, rms=1.791 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=4571175.0, rms=1.747 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=4490900.0, rms=1.704 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 114 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 12 with 11 points - only 9.09% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown mean border=85.5, 34 (10) missing vertices, mean dist -0.2 [0.4 (%72.7)->0.3 (%27.3))] %82 local maxima, %13 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 +- 0.24 (0.07-->4.32) (max @ vno 168592 --> 103991) face area 0.35 +- 0.16 (0.00-->4.07) mean absolute distance = 0.26 +- 0.38 4547 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5210715.5, rms=4.51 013: dt: 0.5000, sse=5675945.5, rms=2.921 (0.000%) rms = 2.97, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=5277596.5, rms=2.329 (0.000%) 015: dt: 0.2500, sse=5077107.5, rms=1.848 (0.000%) 016: dt: 0.2500, sse=4979189.0, rms=1.633 (0.000%) 017: dt: 0.2500, sse=4909217.5, rms=1.548 (0.000%) 018: dt: 0.2500, sse=4882906.5, rms=1.495 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4861846.0, rms=1.465 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4813557.0, rms=1.432 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 12 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 115 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 11 points - only 9.09% unknown deleting segment 10 with 12 points - only 0.00% unknown deleting segment 11 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown mean border=87.8, 38 (7) missing vertices, mean dist -0.1 [0.3 (%73.2)->0.2 (%26.8))] %89 local maxima, % 6 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 +- 0.24 (0.06-->4.57) (max @ vno 168592 --> 103991) face area 0.34 +- 0.16 (0.00-->3.81) mean absolute distance = 0.21 +- 0.31 4449 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5066705.5, rms=3.26 021: dt: 0.5000, sse=5421312.0, rms=2.514 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5093088.5, rms=1.774 (0.000%) 023: dt: 0.2500, sse=4978004.5, rms=1.394 (0.000%) 024: dt: 0.2500, sse=4959796.0, rms=1.292 (0.000%) rms = 1.29, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4929614.0, rms=1.289 (0.000%) rms = 1.26, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4884721.0, rms=1.260 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 28 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 3 with 126 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 17 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 25 points - only 40.00% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown deleting segment 10 with 17 points - only 0.00% unknown deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown mean border=88.7, 54 (6) missing vertices, mean dist -0.0 [0.2 (%58.5)->0.2 (%41.5))] %91 local maxima, % 4 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=4897774.5, rms=1.57 rms = 1.65, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4987285.0, rms=1.163 (0.000%) 028: dt: 0.2500, sse=5176380.5, rms=0.963 (0.000%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.96, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5176652.0, rms=0.961 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=61.2, 64 (64) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.6 (%100.0))] %16 local maxima, %42 large gradients and %37 min vals, 2526 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=27924414.0, rms=27.61 001: dt: 0.5000, sse=21379140.0, rms=23.652 (0.000%) 002: dt: 0.5000, sse=16586613.0, rms=20.311 (0.000%) 003: dt: 0.5000, sse=13197604.0, rms=17.564 (0.000%) 004: dt: 0.5000, sse=10976794.0, rms=15.323 (0.000%) 005: dt: 0.5000, sse=9503393.0, rms=13.494 (0.000%) 006: dt: 0.5000, sse=8536710.0, rms=11.984 (0.000%) 007: dt: 0.5000, sse=7909714.5, rms=10.611 (0.000%) 008: dt: 0.5000, sse=7442511.5, rms=9.342 (0.000%) 009: dt: 0.5000, sse=7185441.5, rms=8.149 (0.000%) 010: dt: 0.5000, sse=7018510.5, rms=7.059 (0.000%) 011: dt: 0.5000, sse=6999067.5, rms=6.083 (0.000%) 012: dt: 0.5000, sse=7031842.0, rms=5.301 (0.000%) 013: dt: 0.5000, sse=7147703.5, rms=4.708 (0.000%) 014: dt: 0.5000, sse=7256258.5, rms=4.300 (0.000%) 015: dt: 0.5000, sse=7353236.5, rms=4.008 (0.000%) 016: dt: 0.5000, sse=7410511.5, rms=3.809 (0.000%) 017: dt: 0.5000, sse=7476431.0, rms=3.659 (0.000%) 018: dt: 0.5000, sse=7482636.0, rms=3.575 (0.000%) 019: dt: 0.5000, sse=7516985.0, rms=3.508 (0.000%) rms = 3.49, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7532981.5, rms=3.488 (0.000%) 021: dt: 0.2500, sse=5308735.5, rms=2.823 (0.000%) 022: dt: 0.2500, sse=5099026.0, rms=2.648 (0.000%) rms = 2.63, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4993250.0, rms=2.628 (0.000%) 024: dt: 0.1250, sse=4736734.5, rms=2.502 (0.000%) rms = 2.49, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4708788.5, rms=2.489 (0.000%) positioning took 3.3 minutes mean border=59.4, 1581 (10) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.6 (%51.9))] %33 local maxima, %33 large gradients and %29 min vals, 825 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=5350936.5, rms=4.27 026: dt: 0.5000, sse=5656366.0, rms=3.619 (0.000%) 027: dt: 0.5000, sse=7304990.5, rms=3.530 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6051787.5, rms=2.914 (0.000%) 029: dt: 0.2500, sse=5527534.0, rms=2.665 (0.000%) rms = 2.63, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5495017.5, rms=2.629 (0.000%) 031: dt: 0.1250, sse=5242021.5, rms=2.467 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5220781.0, rms=2.440 (0.000%) positioning took 1.0 minutes mean border=58.0, 1945 (7) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))] %47 local maxima, %19 large gradients and %29 min vals, 961 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=5387064.0, rms=3.24 rms = 3.29, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5206942.5, rms=2.850 (0.000%) 034: dt: 0.2500, sse=5227989.0, rms=2.588 (0.000%) 035: dt: 0.2500, sse=5441715.0, rms=2.509 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=5515412.5, rms=2.501 (0.000%) 037: dt: 0.1250, sse=5351953.0, rms=2.382 (0.000%) rms = 2.36, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5362943.5, rms=2.359 (0.000%) positioning took 0.9 minutes mean border=57.3, 3732 (7) missing vertices, mean dist 0.0 [0.2 (%44.9)->0.3 (%55.1))] %50 local maxima, %15 large gradients and %29 min vals, 828 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5396470.0, rms=2.57 rms = 2.96, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5303164.5, rms=2.412 (0.000%) 040: dt: 0.2500, sse=5523613.5, rms=2.347 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5599773.0, rms=2.335 (0.000%) 042: dt: 0.1250, sse=5495246.0, rms=2.255 (0.000%) rms = 2.24, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=5523807.5, rms=2.239 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area.pial vertex spacing 0.99 +- 0.41 (0.05-->6.37) (max @ vno 96747 --> 97918) face area 0.39 +- 0.29 (0.00-->6.17) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 168865 vertices processed 25000 of 168865 vertices processed 50000 of 168865 vertices processed 75000 of 168865 vertices processed 100000 of 168865 vertices processed 125000 of 168865 vertices processed 150000 of 168865 vertices processed 0 of 168865 vertices processed 25000 of 168865 vertices processed 50000 of 168865 vertices processed 75000 of 168865 vertices processed 100000 of 168865 vertices processed 125000 of 168865 vertices processed 150000 of 168865 vertices processed thickness calculation complete, 1219:1935 truncations. 35976 vertices at 0 distance 111005 vertices at 1 distance 103484 vertices at 2 distance 47819 vertices at 3 distance 16845 vertices at 4 distance 5363 vertices at 5 distance 1687 vertices at 6 distance 500 vertices at 7 distance 221 vertices at 8 distance 126 vertices at 9 distance 84 vertices at 10 distance 52 vertices at 11 distance 21 vertices at 12 distance 28 vertices at 13 distance 23 vertices at 14 distance 18 vertices at 15 distance 16 vertices at 16 distance 17 vertices at 17 distance 12 vertices at 18 distance 10 vertices at 19 distance 11 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness positioning took 13.4 minutes #-------------------------------------------- #@# Surf Volume rh Fri Apr 15 05:02:52 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Fri Apr 15 05:02:52 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts pctsurfcon --s nmr01002 --rh-only Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts/pctsurfcon.log Fri Apr 15 05:02:52 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.wm.mgh --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 92286 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.wm.mgh Dim: 168865 1 1 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.gm.mgh --projfrac 0.3 --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 109914 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.gm.mgh Dim: 168865 1 1 mri_concat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.wm.mgh /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.20984/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh --annot nmr01002 rh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh --annot nmr01002 rh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh Vertex Area is 0.655251 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1750 1206.567 2 2002 caudalanteriorcingulate 1201 829.977 3 2003 caudalmiddlefrontal 4291 2853.787 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2761 1792.352 6 2006 entorhinal 598 425.724 7 2007 fusiform 5922 3901.324 8 2008 inferiorparietal 11042 7231.893 9 2009 inferiortemporal 5787 3863.295 10 2010 isthmuscingulate 1633 1055.423 11 2011 lateraloccipital 7382 4752.286 12 2012 lateralorbitofrontal 4254 2888.645 13 2013 lingual 6087 3959.214 14 2014 medialorbitofrontal 3031 2066.835 15 2015 middletemporal 6198 4111.585 16 2016 parahippocampal 1269 839.644 17 2017 paracentral 2349 1509.890 18 2018 parsopercularis 2891 1922.346 19 2019 parsorbitalis 1430 949.284 20 2020 parstriangularis 3073 2004.613 21 2021 pericalcarine 2569 1693.402 22 2022 postcentral 7027 4396.992 23 2023 posteriorcingulate 2107 1410.709 24 2024 precentral 9360 5623.655 25 2025 precuneus 9040 5958.036 26 2026 rostralanteriorcingulate 1144 764.358 27 2027 rostralmiddlefrontal 10960 7246.514 28 2028 superiorfrontal 12380 8407.577 29 2029 superiorparietal 10533 6744.130 30 2030 superiortemporal 7070 4643.735 31 2031 supramarginal 7271 4783.464 32 2032 frontalpole 502 336.103 33 2033 temporalpole 810 535.557 34 2034 transversetemporal 862 528.355 35 2035 insula 4035 2710.273 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Apr 15 05:03:01 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1750 1207 3016 2.518 0.460 0.105 0.022 14 1.6 bankssts 1201 830 1952 2.263 0.775 0.150 0.040 20 2.0 caudalanteriorcingulate 4291 2854 8990 2.650 0.611 0.130 0.038 54 6.9 caudalmiddlefrontal 2761 1792 3399 1.773 0.424 0.150 0.059 50 6.6 cuneus 598 426 1877 3.455 0.838 0.145 0.048 6 1.2 entorhinal 5922 3901 12290 2.746 0.588 0.134 0.047 88 9.9 fusiform 11042 7232 19240 2.481 0.514 0.139 0.045 182 19.6 inferiorparietal 5787 3863 13135 2.965 0.732 0.141 0.051 83 11.5 inferiortemporal 1633 1055 2587 2.337 0.741 0.160 0.074 35 4.9 isthmuscingulate 7382 4752 11963 2.313 0.601 0.148 0.048 113 14.4 lateraloccipital 4254 2889 7495 2.344 0.692 0.164 0.099 111 18.4 lateralorbitofrontal 6087 3959 8149 2.022 0.653 0.153 0.066 115 16.4 lingual 3031 2067 5842 2.333 0.722 0.159 0.093 119 8.7 medialorbitofrontal 6198 4112 14751 3.024 0.712 0.143 0.044 103 10.7 middletemporal 1269 840 2352 2.529 0.555 0.125 0.058 25 3.3 parahippocampal 2349 1510 3831 2.466 0.547 0.119 0.039 28 4.3 paracentral 2891 1922 5889 2.758 0.595 0.146 0.054 144 5.6 parsopercularis 1430 949 3754 3.083 0.795 0.176 0.071 32 4.3 parsorbitalis 3073 2005 5973 2.572 0.671 0.140 0.050 48 6.3 parstriangularis 2569 1693 2463 1.528 0.415 0.145 0.047 41 4.7 pericalcarine 7027 4397 10225 2.096 0.656 0.130 0.324 211 19.6 postcentral 2107 1411 3375 2.297 0.698 0.153 0.060 44 4.3 posteriorcingulate 9360 5624 15872 2.589 0.604 0.114 0.047 177 17.9 precentral 9040 5958 14238 2.337 0.537 0.146 0.060 278 25.9 precuneus 1144 764 2032 2.532 0.589 0.145 0.050 19 2.0 rostralanteriorcingulate 10960 7247 19643 2.326 0.642 0.155 0.061 222 26.5 rostralmiddlefrontal 12380 8408 28751 2.808 0.822 0.143 0.056 316 26.9 superiorfrontal 10533 6744 16255 2.217 0.587 0.136 0.049 199 22.1 superiorparietal 7070 4644 14591 2.848 0.575 0.135 0.050 103 12.2 superiortemporal 7271 4783 13492 2.639 0.564 0.139 0.041 103 12.1 supramarginal 502 336 969 2.311 0.706 0.161 0.056 10 1.2 frontalpole 810 536 3004 4.229 0.692 0.160 0.086 16 2.5 temporalpole 862 528 1489 2.432 0.374 0.117 0.031 11 1.1 transversetemporal 4035 2710 7758 2.919 0.718 0.142 0.074 87 10.7 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Apr 15 05:03:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 32 labels changed using aseg relabeling using gibbs priors... 000: 11797 changed, 168865 examined... 001: 2784 changed, 44860 examined... 002: 916 changed, 14179 examined... 003: 379 changed, 5038 examined... 004: 167 changed, 2141 examined... 005: 111 changed, 995 examined... 006: 53 changed, 637 examined... 007: 26 changed, 299 examined... 008: 15 changed, 151 examined... 009: 11 changed, 86 examined... 010: 3 changed, 55 examined... 011: 1 changed, 21 examined... 012: 0 changed, 9 examined... 24 labels changed using aseg 000: 374 total segments, 286 labels (4103 vertices) changed 001: 124 total segments, 37 labels (205 vertices) changed 002: 90 total segments, 3 labels (6 vertices) changed 003: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 167 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 891 vertices marked for relabeling... 891 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Apr 15 05:04:35 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1396 950 2306 2.086 0.647 0.155 0.070 34 3.2 G_and_S_frontomargin 1690 1161 3519 2.773 0.613 0.154 0.050 26 3.4 G_and_S_occipital_inf 1623 938 2660 2.396 0.615 0.116 0.046 24 3.8 G_and_S_paracentral 1570 1030 2993 2.658 0.449 0.144 0.053 31 3.8 G_and_S_subcentral 1849 1217 3172 2.280 0.599 0.159 0.063 42 4.8 G_and_S_transv_frontopol 3125 2125 5810 2.437 0.744 0.141 0.043 44 5.7 G_and_S_cingul-Ant 1497 1058 3425 2.934 0.910 0.139 0.045 20 2.8 G_and_S_cingul-Mid-Ant 1552 1075 2732 2.513 0.433 0.136 0.042 23 2.2 G_and_S_cingul-Mid-Post 732 451 1443 2.839 0.525 0.185 0.093 20 2.4 G_cingul-Post-dorsal 306 187 616 2.570 0.533 0.165 0.077 7 0.6 G_cingul-Post-ventral 2639 1739 3224 1.705 0.414 0.151 0.054 46 5.8 G_cuneus 1754 1152 4481 2.941 0.616 0.166 0.069 140 4.3 G_front_inf-Opercular 417 277 1138 3.104 0.687 0.167 0.068 9 1.0 G_front_inf-Orbital 1565 1004 3594 2.755 0.590 0.151 0.055 31 3.6 G_front_inf-Triangul 5666 3710 13378 2.663 0.655 0.159 0.060 123 14.5 G_front_middle 8040 5393 20354 2.909 0.741 0.154 0.061 260 19.8 G_front_sup 665 455 1614 3.386 0.591 0.161 0.101 18 2.1 G_Ins_lg_and_S_cent_ins 895 567 2266 3.122 0.714 0.169 0.078 24 2.8 G_insular_short 2831 1781 5550 2.616 0.503 0.151 0.060 76 6.3 G_occipital_middle 2220 1398 3326 2.103 0.528 0.144 0.050 37 4.4 G_occipital_sup 1841 1161 4343 2.940 0.525 0.148 0.073 42 3.8 G_oc-temp_lat-fusifor 3643 2293 5064 1.945 0.676 0.167 0.088 101 13.3 G_oc-temp_med-Lingual 1375 920 3502 3.077 0.706 0.133 0.047 17 2.4 G_oc-temp_med-Parahip 3465 2314 8526 2.890 0.805 0.192 0.142 137 20.8 G_orbital 3521 2256 7199 2.557 0.503 0.151 0.053 70 7.4 G_pariet_inf-Angular 4134 2689 9251 2.811 0.534 0.155 0.046 77 8.0 G_pariet_inf-Supramar 3300 2090 6053 2.375 0.595 0.141 0.052 61 7.2 G_parietal_sup 2728 1558 4216 2.164 0.592 0.144 0.780 159 13.3 G_postcentral 3925 2042 8066 2.955 0.566 0.111 0.064 124 9.3 G_precentral 4435 2814 7907 2.416 0.539 0.153 0.077 221 18.1 G_precuneus 757 529 2027 2.630 0.676 0.179 0.191 25 2.9 G_rectus 466 316 876 2.634 0.593 0.146 0.115 62 2.0 G_subcallosal 690 424 1348 2.521 0.372 0.128 0.036 11 1.0 G_temp_sup-G_T_transv 2468 1557 6499 3.034 0.511 0.143 0.044 43 4.7 G_temp_sup-Lateral 620 425 1716 3.906 0.885 0.134 0.043 8 1.1 G_temp_sup-Plan_polar 1334 886 2486 2.734 0.516 0.128 0.088 18 2.3 G_temp_sup-Plan_tempo 3351 2182 8682 3.111 0.792 0.151 0.060 59 8.0 G_temporal_inf 3706 2417 10077 3.219 0.673 0.153 0.051 74 7.3 G_temporal_middle 577 373 706 2.105 0.387 0.092 0.019 3 0.5 Lat_Fis-ant-Horizont 388 258 501 2.492 0.378 0.134 0.047 4 0.7 Lat_Fis-ant-Vertical 1867 1244 2556 2.576 0.511 0.135 0.043 22 3.2 Lat_Fis-post 4008 2413 5250 1.997 0.550 0.151 0.057 66 9.3 Pole_occipital 2608 1727 8596 3.658 0.720 0.160 0.072 49 7.1 Pole_temporal 3354 2257 3744 1.859 0.676 0.147 0.045 49 6.4 S_calcarine 3168 2127 3318 1.760 0.543 0.112 0.033 24 4.6 S_central 1301 884 1831 2.161 0.381 0.103 0.023 9 1.3 S_cingul-Marginalis 729 472 1098 2.583 0.495 0.128 0.051 8 1.2 S_circular_insula_ant 1331 912 2116 2.711 0.487 0.096 0.020 6 1.2 S_circular_insula_inf 1843 1257 2691 2.443 0.397 0.107 0.025 10 2.0 S_circular_insula_sup 1241 858 2232 2.614 0.500 0.103 0.020 7 1.1 S_collat_transv_ant 928 618 1323 2.310 0.561 0.157 0.048 14 2.0 S_collat_transv_post 1984 1352 3018 2.332 0.398 0.130 0.037 21 2.8 S_front_inf 2722 1788 3786 2.042 0.574 0.142 0.050 42 5.6 S_front_middle 4004 2707 7211 2.503 0.761 0.129 0.052 65 7.5 S_front_sup 665 428 944 2.368 0.519 0.137 0.045 7 1.1 S_interm_prim-Jensen 4139 2726 5486 2.149 0.583 0.133 0.047 85 9.5 S_intrapariet_and_P_trans 976 679 1255 2.135 0.451 0.127 0.029 8 1.2 S_oc_middle_and_Lunatus 1978 1331 2645 2.162 0.421 0.123 0.036 25 2.3 S_oc_sup_and_transversal 451 303 923 2.471 0.592 0.116 0.031 6 0.6 S_occipital_ant 1381 945 2066 2.430 0.378 0.137 0.040 18 2.2 S_oc-temp_lat 2516 1752 3849 2.407 0.346 0.111 0.026 17 2.8 S_oc-temp_med_and_Lingual 464 323 818 2.506 0.721 0.172 0.073 8 1.5 S_orbital_lateral 859 618 1150 1.931 0.764 0.112 0.037 7 1.5 S_orbital_med-olfact 1474 1019 2160 2.007 0.543 0.149 0.050 23 2.9 S_orbital-H_Shaped 3015 2028 3814 2.130 0.524 0.134 0.043 36 5.3 S_parieto_occipital 1819 1171 1591 1.758 0.628 0.150 0.059 35 4.4 S_pericallosal 2671 1808 3410 2.160 0.412 0.120 0.032 24 3.4 S_postcentral 2101 1397 3070 2.456 0.447 0.114 0.028 17 2.5 S_precentral-inf-part 1771 1190 2573 2.428 0.407 0.120 0.030 15 2.2 S_precentral-sup-part 343 235 488 2.241 0.808 0.121 0.026 2 0.4 S_suborbital 1952 1310 3260 2.544 0.481 0.149 0.051 31 3.6 S_subparietal 1290 873 1961 2.603 0.622 0.112 0.025 9 1.4 S_temporal_inf 8511 5755 13183 2.480 0.462 0.122 0.030 87 10.6 S_temporal_sup 399 271 579 2.395 0.398 0.127 0.035 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Apr 15 05:04:57 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1576 labels changed using aseg relabeling using gibbs priors... 000: 3186 changed, 168865 examined... 001: 741 changed, 13565 examined... 002: 211 changed, 4106 examined... 003: 94 changed, 1272 examined... 004: 49 changed, 543 examined... 005: 37 changed, 303 examined... 006: 24 changed, 210 examined... 007: 18 changed, 145 examined... 008: 14 changed, 104 examined... 009: 5 changed, 76 examined... 010: 2 changed, 33 examined... 011: 0 changed, 10 examined... 347 labels changed using aseg 000: 70 total segments, 37 labels (207 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 651 vertices marked for relabeling... 651 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 4 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Apr 15 05:06:02 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1304 897 2139 2.338 0.841 0.154 0.045 22 2.6 caudalanteriorcingulate 4566 3019 9414 2.649 0.599 0.132 0.039 59 7.6 caudalmiddlefrontal 3509 2312 4258 1.777 0.417 0.147 0.055 58 7.7 cuneus 550 395 1672 3.360 0.810 0.145 0.045 6 1.0 entorhinal 5007 3320 9882 2.678 0.517 0.131 0.046 73 7.9 fusiform 10472 6855 18248 2.490 0.517 0.140 0.045 176 18.8 inferiorparietal 6741 4469 15952 3.020 0.762 0.144 0.055 102 14.2 inferiortemporal 1639 1060 2584 2.328 0.733 0.160 0.074 35 4.8 isthmuscingulate 7719 4974 12380 2.295 0.606 0.147 0.047 117 15.1 lateraloccipital 5050 3434 9439 2.379 0.760 0.172 0.109 160 22.6 lateralorbitofrontal 6134 3996 8262 2.023 0.652 0.153 0.066 117 16.5 lingual 2403 1652 4830 2.393 0.725 0.155 0.102 106 7.2 medialorbitofrontal 7247 4840 16420 2.925 0.702 0.139 0.041 111 11.9 middletemporal 1261 829 2329 2.538 0.553 0.123 0.055 25 3.2 parahippocampal 2392 1544 3978 2.473 0.549 0.119 0.039 29 4.4 paracentral 2941 1961 5981 2.767 0.591 0.143 0.053 144 5.5 parsopercularis 1510 1005 3227 2.654 0.613 0.155 0.055 28 3.3 parsorbitalis 3064 1987 5976 2.581 0.666 0.143 0.051 49 6.4 parstriangularis 2549 1684 2434 1.525 0.411 0.145 0.047 40 4.7 pericalcarine 7562 4762 11052 2.111 0.650 0.129 0.304 216 20.4 postcentral 2167 1456 3510 2.312 0.691 0.153 0.060 44 4.4 posteriorcingulate 9077 5438 15506 2.599 0.604 0.114 0.047 175 17.7 precentral 9181 6016 14642 2.345 0.536 0.145 0.059 280 26.0 precuneus 1267 842 2224 2.481 0.599 0.150 0.050 22 2.3 rostralanteriorcingulate 6445 4296 12248 2.435 0.718 0.157 0.063 126 16.3 rostralmiddlefrontal 17114 11501 36458 2.630 0.816 0.144 0.055 407 37.4 superiorfrontal 9135 5818 14230 2.244 0.583 0.138 0.051 185 20.2 superiorparietal 9210 6086 19999 2.942 0.709 0.133 0.048 131 15.6 superiortemporal 6917 4526 12855 2.653 0.570 0.140 0.041 98 11.5 supramarginal 837 515 1416 2.412 0.368 0.114 0.030 11 1.0 transversetemporal 3649 2459 7097 2.945 0.637 0.138 0.062 58 8.5 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Fri Apr 15 05:06:21 EDT 2016 bbregister --s nmr01002 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz --lta /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta --init-fsl --T2 Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat.log Fri Apr 15 05:06:22 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts /usr/local/freesurfer/stable5_3_0/bin/bbregister --s nmr01002 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz --lta /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz... TR=5000.00, TE=387.00, TI=1800.00, flip angle=120.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii... fslregister --s nmr01002 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister --dof 6 --fsvol brainmask.mgz Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat.fslregister.log Fri Apr 15 05:06:24 EDT 2016 --s nmr01002 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ compute-0-68 Linux compute-0-68 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brainmask.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/refvol.fslregister.nii mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brainmask.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brainmask.mgz... TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 5.21541e-08) j_ras = (-2.98023e-08, 0, -1) k_ras = (0, 1, 0) writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) keeping frame 0 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii... Mov determinant is -0.726471 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts tkregister2_cmdl --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/reg0.21206.dat --regheader --fslregout /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat.fsl.mat0 --s nmr01002 --noedit tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii reg file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/reg0.21206.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.898 0.000 0.000 115.000; 0.000 0.000 0.900 -86.400; 0.000 -0.898 0.000 115.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.000 1.000 0.000 11.157; -0.995 -0.000 0.099 0.050; 0.099 0.000 0.995 -1.860; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.000 1.000 0.000 11.157; -0.995 -0.000 0.099 0.050; 0.099 0.000 0.995 -1.860; 0.000 0.000 0.000 1.000; Determinant 1 subject = nmr01002 RegMat --------------------------- 0.000 1.000 0.000 11.157; -0.995 -0.000 0.099 0.050; 0.099 0.000 0.995 -1.860; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.726471, ref det = -1 Fri Apr 15 05:06:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts flirt.fsl -ref /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/refvol.fslregister.nii -in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/current/etc/flirtsch/xyztrans.sch -init /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat.fsl.mat0 Fri Apr 15 05:09:17 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts flirt.fsl -ref /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/refvol.fslregister.nii -in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat.fsl.mat -init /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/stable5_3_0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s nmr01002 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --fslreg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl ---- FSL registration matrix -------- -0.000 0.094 0.996 30.836; 0.007 0.996 -0.094 17.075; -1.000 0.007 -0.001 231.295; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii reg file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii Tmov: -------------------- -0.898 0.000 0.000 115.000; 0.000 0.000 0.900 -86.400; 0.000 -0.898 0.000 115.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -0.726471, ref det = -1 ---- Input registration matrix (computed) -------- -0.000 1.000 0.007 10.927; -0.996 -0.001 0.094 -0.012; 0.094 -0.007 0.996 -3.832; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.000 1.000 0.007 10.927; -0.996 -0.001 0.094 -0.012; 0.094 -0.007 0.996 -3.832; 0.000 0.000 0.000 1.000; Determinant 1 subject = nmr01002 RegMat --------------------------- -0.000 1.000 0.007 10.927; -0.996 -0.001 0.094 -0.012; 0.094 -0.007 0.996 -3.832; 0.000 0.000 0.000 1.000; Started at Fri Apr 15 05:06:24 EDT 2016 Ended at Fri Apr 15 05:11:52 EDT 2016 fslregister Done To check results, run: tkregister2 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --surf orig mri_segreg --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --init-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --out-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_segreg --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --init-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat --out-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname compute-0-68 machine x86_64 user dwakeman movvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii regfile /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.init.dat subject nmr01002 dof 6 outregfile /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1461429696 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.000 1.000 0.007 10.927; -0.996 -0.001 0.094 -0.012; 0.094 -0.007 0.996 -3.832; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.005426 1 -25.0 -25.0 25.0 1.040429 2 -25.0 25.0 -25.0 0.987819 3 -25.0 25.0 25.0 1.018350 4 25.0 -25.0 -25.0 0.997998 5 25.0 -25.0 25.0 0.999170 6 25.0 25.0 -25.0 1.056937 7 25.0 25.0 25.0 0.989037 REL: 8 0.066894 8.095166 1.011896 rel = 0.0661079 Initial costs ---------------- Number of surface hits 3212 WM Intensity 162.0418 +/- 23.4678 Ctx Intensity 197.4004 +/- 23.1020 Pct Contrast 19.9316 +/- 10.8639 Cost 0.0669 RelCost 0.0661 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0432 1.0432 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0176 1.0176 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9741 0.9741 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9735 0.9735 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9107 0.9107 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8974 0.8974 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8971 0.8971 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.8389 0.8389 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.8344 0.8344 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8263 0.8263 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0669 0.0669 0.0 Brute Force -------------------------- Min cost was 0.066894 Number of iterations 729 Search time 2.590000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 -0.038 0.000 0.000 0.000 0.000 0.000 0.0667476502 9 -0.041 0.000 0.000 0.000 0.000 0.000 0.0667461350 11 -0.046 0.000 0.000 0.000 0.000 0.000 0.0667452176 12 -0.045 0.000 0.000 0.000 0.000 0.000 0.0667451799 21 -0.045 0.001 0.000 0.000 0.000 0.000 0.0667431430 25 -0.045 0.009 0.000 0.000 0.000 0.000 0.0667364638 27 -0.045 0.008 0.000 0.000 0.000 0.000 0.0667364446 36 -0.045 0.008 0.091 0.000 0.000 0.000 0.0642415868 38 -0.045 0.008 0.107 0.000 0.000 0.000 0.0641984412 39 -0.045 0.008 0.106 0.000 0.000 0.000 0.0641971309 40 -0.045 0.008 0.104 0.000 0.000 0.000 0.0641959004 50 -0.045 0.008 0.104 0.021 0.000 0.000 0.0641643185 52 -0.045 0.008 0.104 0.018 0.000 0.000 0.0641632244 63 -0.045 0.008 0.104 0.018 -0.003 0.000 0.0641627313 65 -0.045 0.008 0.104 0.018 -0.002 0.000 0.0641624556 72 -0.045 0.008 0.104 0.018 -0.002 0.069 0.0630067459 74 -0.045 0.008 0.104 0.018 -0.002 0.057 0.0628933545 76 -0.045 0.008 0.104 0.018 -0.002 0.055 0.0628851071 77 -0.045 0.008 0.104 0.018 -0.002 0.052 0.0628825203 87 -0.042 0.008 0.104 0.018 -0.002 0.052 0.0628563297 88 -0.017 0.008 0.104 0.018 -0.002 0.052 0.0627716306 93 -0.016 0.008 0.104 0.018 -0.002 0.052 0.0627714694 102 -0.016 0.027 0.104 0.018 -0.002 0.052 0.0627179140 103 -0.016 0.020 0.104 0.018 -0.002 0.052 0.0626931017 116 -0.016 0.019 0.101 0.018 -0.002 0.052 0.0626899796 127 -0.016 0.019 0.101 0.008 -0.002 0.052 0.0626676680 128 -0.016 0.019 0.101 0.005 -0.002 0.052 0.0626660310 138 -0.016 0.019 0.101 0.005 -0.004 0.052 0.0626657666 140 -0.016 0.019 0.101 0.005 -0.003 0.052 0.0626655943 147 -0.016 0.019 0.101 0.005 -0.003 0.070 0.0625781317 149 -0.016 0.019 0.101 0.005 -0.003 0.065 0.0625614157 150 -0.016 0.019 0.101 0.005 -0.003 0.064 0.0625613585 160 -0.015 0.019 0.101 0.005 -0.003 0.064 0.0625603964 162 -0.014 0.019 0.101 0.005 -0.003 0.064 0.0625599338 172 -0.014 0.027 0.101 0.005 -0.003 0.064 0.0625340472 173 -0.014 0.026 0.101 0.005 -0.003 0.064 0.0625338294 184 -0.014 0.026 0.100 0.005 -0.003 0.064 0.0625337218 194 -0.014 0.026 0.100 0.010 -0.003 0.064 0.0625329445 195 -0.014 0.026 0.100 0.008 -0.003 0.064 0.0625322480 213 -0.014 0.026 0.100 0.008 -0.003 0.072 0.0625225182 214 -0.014 0.026 0.100 0.008 -0.003 0.071 0.0625203620 215 -0.014 0.026 0.100 0.008 -0.003 0.069 0.0625186419 217 -0.012 0.033 0.098 0.011 -0.003 0.074 0.0624949854 220 -0.008 0.044 0.096 0.015 -0.003 0.082 0.0624800338 226 -0.008 0.044 0.096 0.015 -0.003 0.082 0.0624800336 233 -0.008 0.044 0.096 0.015 -0.003 0.082 0.0624799545 242 -0.006 0.044 0.096 0.015 -0.003 0.082 0.0624798814 252 -0.006 0.044 0.096 0.015 -0.003 0.083 0.0624795748 262 -0.006 0.044 0.101 0.015 -0.003 0.083 0.0624733138 263 -0.006 0.044 0.102 0.015 -0.003 0.083 0.0624733066 272 -0.006 0.044 0.102 0.019 -0.003 0.083 0.0624722572 273 -0.006 0.044 0.102 0.018 -0.003 0.083 0.0624721388 274 -0.006 0.044 0.102 0.017 -0.003 0.083 0.0624721234 285 -0.006 0.044 0.102 0.017 -0.006 0.083 0.0624711781 287 -0.006 0.044 0.102 0.017 -0.005 0.083 0.0624709799 288 -0.006 0.044 0.102 0.017 -0.004 0.083 0.0624707774 296 -0.006 0.044 0.102 0.018 -0.004 0.084 0.0624703237 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.999854 1 -25.0 -25.0 25.0 1.042848 2 -25.0 25.0 -25.0 0.986700 3 -25.0 25.0 25.0 1.017459 4 25.0 -25.0 -25.0 0.995549 5 25.0 -25.0 25.0 1.001350 6 25.0 25.0 -25.0 1.049018 7 25.0 25.0 25.0 0.991627 REL: 8 0.062470 8.084405 1.010551 rel = 0.0618181 Number of iterations 4 Min cost was 0.062470 Number of FunctionCalls 373 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.212000 sec Parameters at optimum (transmm) -0.00634 0.04431 0.10150 Parameters at optimum (rotdeg) 0.01759 -0.00434 0.08361 Final costs ---------------- Number of surface hits 3212 WM Intensity 162.0138 +/- 23.4316 Ctx Intensity 197.4158 +/- 23.1430 Pct Contrast 19.9494 +/- 10.8638 Cost 0.0625 RelCost 0.0661 Reg at min cost was 0.001 1.000 0.007 10.921; -0.996 0.001 0.094 0.049; 0.094 -0.007 0.996 -3.730; 0.000 0.000 0.000 1.000; Writing optimal reg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat, type = 14 Original Reg -0.000 1.000 0.007 10.927; -0.996 -0.001 0.094 -0.012; 0.094 -0.007 0.996 -3.832; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.001 -0.000 0.000 0.006; 0.000 -0.001 0.000 -0.061; 0.000 -0.000 -0.000 -0.102; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.135321 Computing change in rh position Surface RMS Diff (mm) 0.126364 0.191367 mri_segreg done mri_segreg --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --init-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat --out-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_segreg --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii --init-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat --out-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname compute-0-68 machine x86_64 user dwakeman movvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/template.nii regfile /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/tmp.bbregister.21170/bbr.pass1.dat subject nmr01002 dof 6 outregfile /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1461262985 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.001 1.000 0.007 10.921; -0.996 0.001 0.094 0.049; 0.094 -0.007 0.996 -3.730; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.000320 1 -25.0 -25.0 25.0 1.007749 2 -25.0 25.0 -25.0 1.002020 3 -25.0 25.0 25.0 1.018172 4 25.0 -25.0 -25.0 1.003640 5 25.0 -25.0 25.0 1.014478 6 25.0 25.0 -25.0 1.023230 7 25.0 25.0 25.0 0.995313 REL: 8 0.063529 8.064922 1.008115 rel = 0.063018 Initial costs ---------------- Number of surface hits 320764 WM Intensity 161.6949 +/- 23.3644 Ctx Intensity 197.3450 +/- 23.0012 Pct Contrast 20.1232 +/- 11.1205 Cost 0.0635 RelCost 0.0630 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0692 0.0692 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0688 0.0688 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0680 0.0680 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0670 0.0670 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0669 0.0669 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0657 0.0657 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0650 0.0650 0.0 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0647 0.0647 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0635 0.0635 0.0 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.0635 0.0635 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0625 0.0625 0.0 Brute Force -------------------------- Min cost was 0.062470 Number of iterations 729 Search time 2.294000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 8 -0.009 0.000 0.000 0.000 0.000 0.000 0.0635205394 9 -0.008 0.000 0.000 0.000 0.000 0.000 0.0635204994 17 -0.008 -0.020 0.000 0.000 0.000 0.000 0.0634115196 18 -0.008 -0.035 0.000 0.000 0.000 0.000 0.0633915275 19 -0.008 -0.033 0.000 0.000 0.000 0.000 0.0633911802 27 -0.008 -0.033 -0.017 0.000 0.000 0.000 0.0633361864 28 -0.008 -0.033 -0.022 0.000 0.000 0.000 0.0633361771 29 -0.008 -0.033 -0.019 0.000 0.000 0.000 0.0633350855 38 -0.008 -0.033 -0.019 0.003 0.000 0.000 0.0633335183 39 -0.008 -0.033 -0.019 0.004 0.000 0.000 0.0633329895 40 -0.008 -0.033 -0.019 0.005 0.000 0.000 0.0633329312 48 -0.008 -0.033 -0.019 0.005 -0.001 0.000 0.0633290433 49 -0.008 -0.033 -0.019 0.005 -0.012 0.000 0.0633086118 60 -0.008 -0.033 -0.019 0.005 -0.012 0.001 0.0633084966 70 0.000 -0.033 -0.019 0.005 -0.012 0.001 0.0632998506 80 0.000 -0.032 -0.019 0.005 -0.012 0.001 0.0632993729 81 0.000 -0.031 -0.019 0.005 -0.012 0.001 0.0632993635 90 0.000 -0.031 -0.018 0.005 -0.012 0.001 0.0632991515 99 0.000 -0.031 -0.018 0.007 -0.012 0.001 0.0632987688 108 0.000 -0.031 -0.018 0.007 -0.016 0.001 0.0632963027 118 0.000 -0.031 -0.018 0.007 -0.016 0.002 0.0632961998 126 0.004 -0.030 -0.018 0.008 -0.017 0.002 0.0632954165 127 0.003 -0.030 -0.018 0.008 -0.017 0.002 0.0632953495 128 0.003 -0.030 -0.018 0.008 -0.017 0.002 0.0632953465 133 0.003 -0.030 -0.018 0.008 -0.017 0.002 0.0632953199 135 0.003 -0.030 -0.018 0.008 -0.017 0.002 0.0632953137 163 0.003 -0.030 -0.017 0.008 -0.017 0.002 0.0632951933 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.000117 1 -25.0 -25.0 25.0 1.007301 2 -25.0 25.0 -25.0 1.002088 3 -25.0 25.0 25.0 1.018394 4 25.0 -25.0 -25.0 1.003985 5 25.0 -25.0 25.0 1.014726 6 25.0 25.0 -25.0 1.023942 7 25.0 25.0 25.0 0.995230 REL: 8 0.063295 8.065783 1.008223 rel = 0.062779 Number of iterations 3 Min cost was 0.063295 Number of FunctionCalls 258 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 35.821000 sec Parameters at optimum (transmm) 0.00307 -0.02977 -0.01719 Parameters at optimum (rotdeg) 0.00785 -0.01696 0.00230 Final costs ---------------- Number of surface hits 320764 WM Intensity 161.7041 +/- 23.3518 Ctx Intensity 197.3361 +/- 22.9994 Pct Contrast 20.1121 +/- 11.1066 Cost 0.0633 RelCost 0.0630 Reg at min cost was 0.001 1.000 0.007 10.925; -0.996 0.001 0.093 0.020; 0.093 -0.007 0.996 -3.744; 0.000 0.000 0.000 1.000; Writing optimal reg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat, type = 14 Original Reg 0.001 1.000 0.007 10.921; -0.996 0.001 0.094 0.049; 0.094 -0.007 0.996 -3.730; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.000 0.000 -0.004; 0.000 -0.000 0.000 0.029; 0.000 -0.000 -0.000 0.014; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.041041 Computing change in rh position Surface RMS Diff (mm) 0.043058 0.060159 mri_segreg done tkregister2_cmdl --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat --noedit --ltaout /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz reg file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.001 1.000 0.007 10.925; -0.996 0.001 0.093 0.020; 0.093 -0.007 0.996 -3.744; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz Ttarg: -------------------- -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; INFO: loading movable /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz Tmov: -------------------- -0.898 0.000 0.000 115.000; 0.000 0.000 0.900 -86.400; 0.000 -0.898 0.000 115.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.001 1.000 0.007 10.925; -0.996 0.001 0.093 0.020; 0.093 -0.007 0.996 -3.744; 0.000 0.000 0.000 1.000; Determinant 1 subject = nmr01002 RegMat --------------------------- 0.001 1.000 0.007 10.925; -0.996 0.001 0.093 0.020; 0.093 -0.007 0.996 -3.744; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 0.001 -0.006 -0.041; -0.001 1.000 -0.007 0.060; 0.006 0.007 1.000 1.685; 0.000 0.000 0.000 1.000; transformed matrix: 0.001 0.084 0.896 30.709; 0.006 0.894 -0.084 17.177; -0.898 0.006 0.001 231.212; 0.000 0.000 0.000 1.000; Cleaning up Started at Fri Apr 15 05:06:22 EDT 2016 Ended at Fri Apr 15 05:13:05 EDT 2016 BBR-Run-Time-Sec 403 bbregister Done To check results, run: tkregister2 --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz --reg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.dat --surf mri_convert -at /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta -rl /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz mri_convert -at /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta -rl /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig/FLAIRraw.mgz... TR=5000.00, TE=387.00, TI=1800.00, flip angle=120.00 i_ras = (0, -1, 0) j_ras = (-0.0993197, 0, -0.995056) k_ras = (-0.995056, 0, 0.0993197) INFO: Reading transformation from file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta... Reading transform with LTAreadEx() reading extra input line subject nmr01002 reading extra input line fscale 0.150000 reading template info from volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz... INFO: Applying transformation from file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/transforms/FLAIRraw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 0.001 -0.006 -0.041; -0.001 1.000 -0.007 0.060; 0.006 0.007 1.000 1.685; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz... mri_normalize -aseg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz -sigma 4 -surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white identity.nofile -surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white identity.nofile /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz using segmentation for initial intensity normalization using Gaussian smoothing of bias field, sigma=4.000 reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz... computing distance transform computing distance transform computing nonmaximum suppression 20673 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field writing normalized volume to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/FLAIR.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts cp -v /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.woFLAIR.pial `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial' -> `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR nmr01002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->3.56) (max @ vno 74575 --> 75800) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 308 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown deleting segment 7 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 23 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown deleting segment 11 with 77 points - only 0.00% unknown 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.25 (0.02-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5273678.0, rms=0.00 rms = 0.86, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5273678.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 77 points - only 0.00% unknown 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 0.88 +- 0.25 (0.02-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5273678.0, rms=0.00 rms = 0.86, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5273678.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 77 points - only 0.00% unknown 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 0.88 +- 0.25 (0.02-->3.56) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.53) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5273678.0, rms=0.00 rms = 0.86, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5273678.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 77 points - only 0.00% unknown 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=5273678.0, rms=0.00 rms = 0.86, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5273678.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [100.70 185.30], gm=143.00+-14.10, and vertices in regions > 135.9 17262 surface locations found to contain inconsistent values (17226 in, 36 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=542654.4, rms=0.20 001: dt: 0.5000, sse=507908.4, rms=0.196 (0.000%) 002: dt: 0.5000, sse=480970.3, rms=0.185 (0.000%) 003: dt: 0.5000, sse=464360.5, rms=0.175 (0.000%) 004: dt: 0.5000, sse=451477.7, rms=0.166 (0.000%) 005: dt: 0.5000, sse=441296.8, rms=0.158 (0.000%) 006: dt: 0.5000, sse=433187.2, rms=0.150 (0.000%) 007: dt: 0.5000, sse=426681.2, rms=0.143 (0.000%) 008: dt: 0.5000, sse=421161.3, rms=0.136 (0.000%) 009: dt: 0.5000, sse=416156.2, rms=0.131 (0.000%) 010: dt: 0.5000, sse=412044.0, rms=0.125 (0.000%) 011: dt: 0.5000, sse=408146.1, rms=0.121 (0.000%) 012: dt: 0.5000, sse=404887.3, rms=0.116 (0.000%) 013: dt: 0.5000, sse=401703.0, rms=0.113 (0.000%) 014: dt: 0.5000, sse=398903.2, rms=0.109 (0.000%) 015: dt: 0.5000, sse=396464.3, rms=0.106 (0.000%) 016: dt: 0.5000, sse=394086.9, rms=0.104 (0.000%) 017: dt: 0.5000, sse=391918.9, rms=0.101 (0.000%) 018: dt: 0.5000, sse=390017.9, rms=0.099 (0.000%) 019: dt: 0.5000, sse=387838.0, rms=0.097 (0.000%) 020: dt: 0.5000, sse=386145.2, rms=0.096 (0.000%) 021: dt: 0.5000, sse=384512.3, rms=0.095 (0.000%) 022: dt: 0.5000, sse=382929.7, rms=0.094 (0.000%) 023: dt: 0.5000, sse=381613.8, rms=0.093 (0.000%) 024: dt: 0.5000, sse=380177.2, rms=0.092 (0.000%) 025: dt: 0.5000, sse=378882.1, rms=0.091 (0.000%) 026: dt: 0.5000, sse=377472.4, rms=0.091 (0.000%) 027: dt: 0.5000, sse=376403.3, rms=0.090 (0.000%) 028: dt: 0.5000, sse=375387.2, rms=0.090 (0.000%) 029: dt: 0.5000, sse=374160.4, rms=0.090 (0.000%) 030: dt: 0.5000, sse=373169.6, rms=0.090 (0.000%) positioning took 4.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [98.60 181.40], gm=140.00+-13.80, and vertices in regions > 133.1 2368 surface locations found to contain inconsistent values (2268 in, 100 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=37233.8, rms=0.05 031: dt: 0.5000, sse=37100.0, rms=0.051 (0.000%) 032: dt: 0.5000, sse=37054.6, rms=0.048 (0.000%) 033: dt: 0.5000, sse=37041.4, rms=0.045 (0.000%) 034: dt: 0.5000, sse=37049.3, rms=0.043 (0.000%) 035: dt: 0.5000, sse=37075.3, rms=0.041 (0.000%) 036: dt: 0.5000, sse=37077.5, rms=0.039 (0.000%) 037: dt: 0.5000, sse=37096.2, rms=0.038 (0.000%) 038: dt: 0.5000, sse=37129.3, rms=0.036 (0.000%) 039: dt: 0.5000, sse=37144.9, rms=0.035 (0.000%) 040: dt: 0.5000, sse=37166.5, rms=0.033 (0.000%) 041: dt: 0.5000, sse=37173.2, rms=0.032 (0.000%) 042: dt: 0.5000, sse=37191.3, rms=0.031 (0.000%) 043: dt: 0.5000, sse=37213.9, rms=0.030 (0.000%) 044: dt: 0.5000, sse=37256.4, rms=0.029 (0.000%) 045: dt: 0.5000, sse=37282.2, rms=0.027 (0.000%) 046: dt: 0.5000, sse=37301.8, rms=0.026 (0.000%) 047: dt: 0.5000, sse=37312.1, rms=0.026 (0.000%) 048: dt: 0.5000, sse=37355.0, rms=0.025 (0.000%) 049: dt: 0.5000, sse=37386.1, rms=0.024 (0.000%) 050: dt: 0.5000, sse=37417.2, rms=0.023 (0.000%) 051: dt: 0.5000, sse=37430.0, rms=0.023 (0.000%) 052: dt: 0.5000, sse=37458.7, rms=0.022 (0.000%) 053: dt: 0.5000, sse=37471.9, rms=0.021 (0.000%) 054: dt: 0.5000, sse=37526.7, rms=0.021 (0.000%) 055: dt: 0.5000, sse=37532.8, rms=0.021 (0.000%) 056: dt: 0.5000, sse=37571.0, rms=0.020 (0.000%) 057: dt: 0.5000, sse=37584.3, rms=0.020 (0.000%) 058: dt: 0.5000, sse=37611.0, rms=0.020 (0.000%) 059: dt: 0.5000, sse=37649.1, rms=0.019 (0.000%) 060: dt: 0.5000, sse=37661.8, rms=0.019 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [98.60 181.40], gm=140.00+-13.80, and vertices in regions > 133.1 496 surface locations found to contain inconsistent values (397 in, 99 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3817.4, rms=0.02 061: dt: 0.5000, sse=3820.9, rms=0.019 (0.000%) 062: dt: 0.5000, sse=3819.6, rms=0.018 (0.000%) 063: dt: 0.5000, sse=3820.9, rms=0.017 (0.000%) 064: dt: 0.5000, sse=3821.4, rms=0.016 (0.000%) 065: dt: 0.5000, sse=3821.2, rms=0.016 (0.000%) 066: dt: 0.5000, sse=3821.8, rms=0.015 (0.000%) 067: dt: 0.5000, sse=3820.4, rms=0.015 (0.000%) 068: dt: 0.5000, sse=3823.1, rms=0.015 (0.000%) 069: dt: 0.5000, sse=3822.7, rms=0.015 (0.000%) 070: dt: 0.5000, sse=3822.7, rms=0.015 (0.000%) 071: dt: 0.5000, sse=3822.9, rms=0.014 (0.000%) 072: dt: 0.5000, sse=3824.6, rms=0.014 (0.000%) 073: dt: 0.5000, sse=3824.5, rms=0.014 (0.000%) 074: dt: 0.5000, sse=3824.7, rms=0.014 (0.000%) 075: dt: 0.5000, sse=3827.8, rms=0.014 (0.000%) 076: dt: 0.5000, sse=3825.8, rms=0.014 (0.000%) 077: dt: 0.5000, sse=3826.8, rms=0.014 (0.000%) 078: dt: 0.5000, sse=3830.5, rms=0.014 (0.000%) 079: dt: 0.5000, sse=3831.3, rms=0.014 (0.000%) 080: dt: 0.5000, sse=3833.5, rms=0.014 (0.000%) 081: dt: 0.5000, sse=3832.8, rms=0.014 (0.000%) 082: dt: 0.5000, sse=3833.9, rms=0.014 (0.000%) 083: dt: 0.5000, sse=3835.4, rms=0.014 (0.000%) 084: dt: 0.5000, sse=3838.4, rms=0.014 (0.000%) 085: dt: 0.5000, sse=3838.3, rms=0.014 (0.000%) 086: dt: 0.5000, sse=3843.9, rms=0.014 (0.000%) 087: dt: 0.5000, sse=3845.5, rms=0.014 (0.000%) 088: dt: 0.5000, sse=3845.1, rms=0.014 (0.000%) 089: dt: 0.5000, sse=3849.3, rms=0.015 (0.000%) 090: dt: 0.5000, sse=3850.6, rms=0.015 (0.000%) positioning took 3.7 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [95.00 185.00], gm=140.00+-15.00, and vertices in regions > 132.5 84 surface locations found to contain inconsistent values (31 in, 53 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=395.1, rms=0.01 091: dt: 0.5000, sse=397.8, rms=0.010 (0.000%) 092: dt: 0.5000, sse=396.4, rms=0.009 (0.000%) 093: dt: 0.5000, sse=395.1, rms=0.009 (0.000%) 094: dt: 0.5000, sse=394.4, rms=0.009 (0.000%) 095: dt: 0.5000, sse=395.7, rms=0.009 (0.000%) 096: dt: 0.5000, sse=395.2, rms=0.009 (0.000%) 097: dt: 0.5000, sse=395.3, rms=0.009 (0.000%) 098: dt: 0.5000, sse=395.1, rms=0.009 (0.000%) 099: dt: 0.5000, sse=396.1, rms=0.009 (0.000%) 100: dt: 0.5000, sse=396.5, rms=0.009 (0.000%) 101: dt: 0.5000, sse=395.8, rms=0.009 (0.000%) 102: dt: 0.5000, sse=395.8, rms=0.009 (0.000%) 103: dt: 0.5000, sse=396.5, rms=0.009 (0.000%) 104: dt: 0.5000, sse=397.3, rms=0.009 (0.000%) 105: dt: 0.5000, sse=397.9, rms=0.010 (0.000%) 106: dt: 0.5000, sse=397.6, rms=0.009 (0.000%) 107: dt: 0.5000, sse=398.4, rms=0.010 (0.000%) 108: dt: 0.5000, sse=397.8, rms=0.009 (0.000%) 109: dt: 0.5000, sse=397.3, rms=0.009 (0.000%) 110: dt: 0.5000, sse=397.9, rms=0.009 (0.000%) 111: dt: 0.5000, sse=397.8, rms=0.009 (0.000%) 112: dt: 0.5000, sse=397.9, rms=0.009 (0.000%) 113: dt: 0.5000, sse=397.6, rms=0.009 (0.000%) 114: dt: 0.5000, sse=398.1, rms=0.009 (0.000%) 115: dt: 0.5000, sse=397.6, rms=0.009 (0.000%) 116: dt: 0.5000, sse=397.2, rms=0.009 (0.000%) 117: dt: 0.5000, sse=397.0, rms=0.009 (0.000%) 118: dt: 0.5000, sse=396.6, rms=0.009 (0.000%) 119: dt: 0.5000, sse=396.2, rms=0.009 (0.000%) 120: dt: 0.5000, sse=396.9, rms=0.009 (0.000%) positioning took 3.6 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area.pial vertex spacing 0.96 +- 0.40 (0.06-->6.36) (max @ vno 117187 --> 117166) face area 0.37 +- 0.28 (0.00-->6.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1050:1175 truncations. 37348 vertices at 0 distance 113730 vertices at 1 distance 106743 vertices at 2 distance 47333 vertices at 3 distance 16253 vertices at 4 distance 5235 vertices at 5 distance 1697 vertices at 6 distance 584 vertices at 7 distance 213 vertices at 8 distance 97 vertices at 9 distance 66 vertices at 10 distance 43 vertices at 11 distance 33 vertices at 12 distance 32 vertices at 13 distance 26 vertices at 14 distance 15 vertices at 15 distance 11 vertices at 16 distance 13 vertices at 17 distance 14 vertices at 18 distance 11 vertices at 19 distance 5 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness positioning took 18.6 minutes /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts cp -v /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.woFLAIR.pial `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial' -> `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR nmr01002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 315982 voxels (1.88%) border gray 350174 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.6, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.05-->4.63) (max @ vno 103991 --> 168592) face area 0.33 +- 0.15 (0.00-->3.77) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 20 points - only 0.00% unknown deleting segment 5 with 14 points - only 0.00% unknown deleting segment 6 with 152 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.05-->4.63) (max @ vno 168592 --> 103991) face area 0.33 +- 0.15 (0.00-->3.77) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5140865.5, rms=0.00 rms = 1.09, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5140865.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 20 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 152 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown 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 0.89 +- 0.25 (0.05-->4.63) (max @ vno 168592 --> 103991) face area 0.33 +- 0.15 (0.00-->3.77) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5140865.5, rms=0.00 rms = 1.10, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5140865.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 20 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 152 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown 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 (0.05-->4.63) (max @ vno 168592 --> 103991) face area 0.33 +- 0.15 (0.00-->3.77) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5140865.5, rms=0.00 rms = 1.09, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5140865.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 20 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 152 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown 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=5140865.5, rms=0.00 rms = 1.10, time step reduction 1 of 3 to 0.250... rms = 0.27, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5140865.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.30 174.70], gm=142.00+-10.90, and vertices in regions > 136.5 26597 surface locations found to contain inconsistent values (26294 in, 303 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=551162.9, rms=0.27 001: dt: 0.5000, sse=515990.3, rms=0.259 (0.000%) 002: dt: 0.5000, sse=487874.2, rms=0.245 (0.000%) 003: dt: 0.5000, sse=470645.4, rms=0.232 (0.000%) 004: dt: 0.5000, sse=456823.7, rms=0.220 (0.000%) 005: dt: 0.5000, sse=446112.9, rms=0.209 (0.000%) 006: dt: 0.5000, sse=437759.6, rms=0.199 (0.000%) 007: dt: 0.5000, sse=430879.1, rms=0.189 (0.000%) 008: dt: 0.5000, sse=425124.6, rms=0.181 (0.000%) 009: dt: 0.5000, sse=420034.9, rms=0.173 (0.000%) 010: dt: 0.5000, sse=415692.9, rms=0.166 (0.000%) 011: dt: 0.5000, sse=411708.9, rms=0.159 (0.000%) 012: dt: 0.5000, sse=408053.9, rms=0.153 (0.000%) 013: dt: 0.5000, sse=404853.2, rms=0.148 (0.000%) 014: dt: 0.5000, sse=401674.9, rms=0.143 (0.000%) 015: dt: 0.5000, sse=398892.4, rms=0.139 (0.000%) 016: dt: 0.5000, sse=396371.2, rms=0.135 (0.000%) 017: dt: 0.5000, sse=394069.3, rms=0.131 (0.000%) 018: dt: 0.5000, sse=391870.6, rms=0.128 (0.000%) 019: dt: 0.5000, sse=390084.7, rms=0.125 (0.000%) 020: dt: 0.5000, sse=387966.9, rms=0.123 (0.000%) 021: dt: 0.5000, sse=386123.8, rms=0.121 (0.000%) 022: dt: 0.5000, sse=384519.2, rms=0.119 (0.000%) 023: dt: 0.5000, sse=382875.4, rms=0.117 (0.000%) 024: dt: 0.5000, sse=381628.4, rms=0.116 (0.000%) 025: dt: 0.5000, sse=380003.4, rms=0.114 (0.000%) 026: dt: 0.5000, sse=378728.0, rms=0.113 (0.000%) 027: dt: 0.5000, sse=377685.0, rms=0.112 (0.000%) 028: dt: 0.5000, sse=376480.8, rms=0.112 (0.000%) 029: dt: 0.5000, sse=375367.2, rms=0.111 (0.000%) 030: dt: 0.5000, sse=374344.8, rms=0.110 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [108.70 175.30], gm=142.00+-11.10, and vertices in regions > 136.4 6317 surface locations found to contain inconsistent values (6038 in, 279 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=37951.4, rms=0.09 031: dt: 0.5000, sse=37767.9, rms=0.085 (0.000%) 032: dt: 0.5000, sse=37815.8, rms=0.080 (0.000%) 033: dt: 0.5000, sse=37928.2, rms=0.076 (0.000%) 034: dt: 0.5000, sse=38027.3, rms=0.073 (0.000%) 035: dt: 0.5000, sse=38112.1, rms=0.070 (0.000%) 036: dt: 0.5000, sse=38181.5, rms=0.067 (0.000%) 037: dt: 0.5000, sse=38247.7, rms=0.065 (0.000%) 038: dt: 0.5000, sse=38292.1, rms=0.062 (0.000%) 039: dt: 0.5000, sse=38345.3, rms=0.060 (0.000%) 040: dt: 0.5000, sse=38396.5, rms=0.058 (0.000%) 041: dt: 0.5000, sse=38449.3, rms=0.056 (0.000%) 042: dt: 0.5000, sse=38490.0, rms=0.054 (0.000%) 043: dt: 0.5000, sse=38529.2, rms=0.052 (0.000%) 044: dt: 0.5000, sse=38571.9, rms=0.050 (0.000%) 045: dt: 0.5000, sse=38614.5, rms=0.049 (0.000%) 046: dt: 0.5000, sse=38657.7, rms=0.047 (0.000%) 047: dt: 0.5000, sse=38699.2, rms=0.046 (0.000%) 048: dt: 0.5000, sse=38754.0, rms=0.045 (0.000%) 049: dt: 0.5000, sse=38789.1, rms=0.043 (0.000%) 050: dt: 0.5000, sse=38820.4, rms=0.042 (0.000%) 051: dt: 0.5000, sse=38858.4, rms=0.041 (0.000%) 052: dt: 0.5000, sse=38897.7, rms=0.040 (0.000%) 053: dt: 0.5000, sse=38944.8, rms=0.039 (0.000%) 054: dt: 0.5000, sse=38985.8, rms=0.038 (0.000%) 055: dt: 0.5000, sse=39020.7, rms=0.037 (0.000%) 056: dt: 0.5000, sse=39052.4, rms=0.036 (0.000%) 057: dt: 0.5000, sse=39095.3, rms=0.035 (0.000%) 058: dt: 0.5000, sse=39128.9, rms=0.034 (0.000%) 059: dt: 0.5000, sse=39161.8, rms=0.033 (0.000%) 060: dt: 0.5000, sse=39192.9, rms=0.033 (0.000%) positioning took 3.6 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.00 175.00], gm=142.00+-11.00, and vertices in regions > 136.5 2212 surface locations found to contain inconsistent values (1950 in, 262 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4213.7, rms=0.04 061: dt: 0.5000, sse=4207.2, rms=0.043 (0.000%) 062: dt: 0.5000, sse=4196.6, rms=0.041 (0.000%) 063: dt: 0.5000, sse=4192.5, rms=0.040 (0.000%) 064: dt: 0.5000, sse=4186.2, rms=0.039 (0.000%) 065: dt: 0.5000, sse=4183.8, rms=0.038 (0.000%) 066: dt: 0.5000, sse=4179.3, rms=0.037 (0.000%) 067: dt: 0.5000, sse=4171.6, rms=0.036 (0.000%) 068: dt: 0.5000, sse=4168.0, rms=0.035 (0.000%) 069: dt: 0.5000, sse=4162.5, rms=0.034 (0.000%) 070: dt: 0.5000, sse=4156.7, rms=0.034 (0.000%) 071: dt: 0.5000, sse=4152.9, rms=0.033 (0.000%) 072: dt: 0.5000, sse=4155.9, rms=0.032 (0.000%) 073: dt: 0.5000, sse=4155.6, rms=0.032 (0.000%) 074: dt: 0.5000, sse=4153.5, rms=0.031 (0.000%) 075: dt: 0.5000, sse=4150.1, rms=0.030 (0.000%) 076: dt: 0.5000, sse=4151.0, rms=0.030 (0.000%) 077: dt: 0.5000, sse=4148.3, rms=0.029 (0.000%) 078: dt: 0.5000, sse=4146.8, rms=0.029 (0.000%) 079: dt: 0.5000, sse=4144.4, rms=0.028 (0.000%) 080: dt: 0.5000, sse=4146.8, rms=0.028 (0.000%) 081: dt: 0.5000, sse=4146.9, rms=0.028 (0.000%) 082: dt: 0.5000, sse=4145.5, rms=0.027 (0.000%) 083: dt: 0.5000, sse=4144.6, rms=0.027 (0.000%) 084: dt: 0.5000, sse=4147.0, rms=0.027 (0.000%) 085: dt: 0.5000, sse=4148.1, rms=0.026 (0.000%) 086: dt: 0.5000, sse=4148.6, rms=0.026 (0.000%) 087: dt: 0.5000, sse=4147.2, rms=0.026 (0.000%) 088: dt: 0.5000, sse=4153.7, rms=0.026 (0.000%) 089: dt: 0.5000, sse=4152.8, rms=0.025 (0.000%) 090: dt: 0.5000, sse=4151.4, rms=0.025 (0.000%) positioning took 3.5 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.00 175.00], gm=142.00+-11.00, and vertices in regions > 136.5 552 surface locations found to contain inconsistent values (295 in, 257 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=541.6, rms=0.03 091: dt: 0.5000, sse=541.4, rms=0.029 (0.000%) 092: dt: 0.5000, sse=535.7, rms=0.028 (0.000%) 093: dt: 0.5000, sse=534.7, rms=0.028 (0.000%) 094: dt: 0.5000, sse=529.0, rms=0.028 (0.000%) 095: dt: 0.5000, sse=524.4, rms=0.027 (0.000%) 096: dt: 0.5000, sse=522.4, rms=0.027 (0.000%) 097: dt: 0.5000, sse=517.8, rms=0.026 (0.000%) 098: dt: 0.5000, sse=518.6, rms=0.026 (0.000%) 099: dt: 0.5000, sse=517.0, rms=0.026 (0.000%) 100: dt: 0.5000, sse=516.1, rms=0.026 (0.000%) 101: dt: 0.5000, sse=514.9, rms=0.026 (0.000%) 102: dt: 0.5000, sse=513.3, rms=0.026 (0.000%) 103: dt: 0.5000, sse=508.2, rms=0.025 (0.000%) 104: dt: 0.5000, sse=507.3, rms=0.025 (0.000%) 105: dt: 0.5000, sse=505.4, rms=0.025 (0.000%) 106: dt: 0.5000, sse=503.8, rms=0.024 (0.000%) 107: dt: 0.5000, sse=506.0, rms=0.025 (0.000%) 108: dt: 0.5000, sse=507.1, rms=0.025 (0.000%) 109: dt: 0.5000, sse=507.2, rms=0.025 (0.000%) 110: dt: 0.5000, sse=506.4, rms=0.025 (0.000%) 111: dt: 0.5000, sse=502.5, rms=0.024 (0.000%) 112: dt: 0.5000, sse=499.4, rms=0.024 (0.000%) 113: dt: 0.5000, sse=499.1, rms=0.024 (0.000%) 114: dt: 0.5000, sse=497.8, rms=0.023 (0.000%) 115: dt: 0.5000, sse=501.0, rms=0.024 (0.000%) 116: dt: 0.5000, sse=500.5, rms=0.024 (0.000%) 117: dt: 0.5000, sse=498.4, rms=0.023 (0.000%) 118: dt: 0.5000, sse=498.1, rms=0.023 (0.000%) 119: dt: 0.5000, sse=498.1, rms=0.023 (0.000%) 120: dt: 0.5000, sse=494.6, rms=0.023 (0.000%) positioning took 3.5 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area.pial vertex spacing 0.97 +- 0.40 (0.03-->6.33) (max @ vno 96747 --> 97918) face area 0.37 +- 0.28 (0.00-->6.17) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 168865 vertices processed 25000 of 168865 vertices processed 50000 of 168865 vertices processed 75000 of 168865 vertices processed 100000 of 168865 vertices processed 125000 of 168865 vertices processed 150000 of 168865 vertices processed 0 of 168865 vertices processed 25000 of 168865 vertices processed 50000 of 168865 vertices processed 75000 of 168865 vertices processed 100000 of 168865 vertices processed 125000 of 168865 vertices processed 150000 of 168865 vertices processed thickness calculation complete, 860:1348 truncations. 39398 vertices at 0 distance 114467 vertices at 1 distance 101595 vertices at 2 distance 45247 vertices at 3 distance 15426 vertices at 4 distance 4876 vertices at 5 distance 1488 vertices at 6 distance 478 vertices at 7 distance 194 vertices at 8 distance 83 vertices at 9 distance 67 vertices at 10 distance 41 vertices at 11 distance 22 vertices at 12 distance 12 vertices at 13 distance 6 vertices at 14 distance 13 vertices at 15 distance 6 vertices at 16 distance 10 vertices at 17 distance 9 vertices at 18 distance 9 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness positioning took 18.0 minutes #-------------------------------------------- #@# Surf Volume lh Fri Apr 15 05:51:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 ] #-------------------------------------------- #@# Surf Volume rh Fri Apr 15 05:51:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 ] #-------------------------------------------- #@# Cortical ribbon mask Fri Apr 15 05:51:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon nmr01002 SUBJECTS_DIR is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 49 writing volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Apr 15 06:13:07 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002 sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Computing euler number orig.nofix lheno = -38, rheno = -42 orig.nofix lhholes = 20, rhholes = 22 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 284049.774 283798.000 diff= 251.8 pctdiff= 0.089 rhCtxGM: 274473.844 274248.000 diff= 225.8 pctdiff= 0.082 lhCtxWM: 291343.508 292033.000 diff= -689.5 pctdiff=-0.237 rhCtxWM: 290128.337 290026.000 diff= 102.3 pctdiff= 0.035 SubCortGMVol 65073.000 SupraTentVol 1244498.463 (1243431.000) diff=1067.463 pctdiff=0.086 SupraTentVolNotVent 1206725.463 (1205658.000) diff=1067.463 pctdiff=0.088 BrainSegVol 1390111.000 (1387644.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1349077.000 (1348645.463) diff=431.537 pctdiff=0.032 BrainSegVolNotVent 1349077.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 19118 19118.055 4 5 Left-Inf-Lat-Vent 520 520.060 5 7 Left-Cerebellum-White-Matter 19700 19699.701 6 8 Left-Cerebellum-Cortex 53472 53472.230 7 10 Left-Thalamus-Proper 8963 8962.595 8 11 Left-Caudate 3573 3573.187 9 12 Left-Putamen 6421 6421.121 10 13 Left-Pallidum 1439 1438.815 11 14 3rd-Ventricle 722 721.945 12 15 4th-Ventricle 1958 1957.972 13 16 Brain-Stem 27112 27112.328 14 17 Left-Hippocampus 4400 4400.408 15 18 Left-Amygdala 1787 1786.623 16 24 CSF 902 902.354 17 26 Left-Accumbens-area 573 573.266 18 28 Left-VentralDC 4634 4634.012 19 30 Left-vessel 220 219.571 20 31 Left-choroid-plexus 1494 1493.786 23 43 Right-Lateral-Ventricle 14433 14432.729 24 44 Right-Inf-Lat-Vent 502 502.259 25 46 Right-Cerebellum-White-Matter 18732 18731.957 26 47 Right-Cerebellum-Cortex 53362 53361.777 27 49 Right-Thalamus-Proper 7901 7900.568 28 50 Right-Caudate 3964 3964.413 29 51 Right-Putamen 5970 5970.317 30 52 Right-Pallidum 1727 1727.467 31 53 Right-Hippocampus 5094 5093.581 32 54 Right-Amygdala 1979 1978.811 33 58 Right-Accumbens-area 715 714.996 34 60 Right-VentralDC 4636 4636.441 35 62 Right-vessel 265 264.728 36 63 Right-choroid-plexus 1793 1792.552 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1813 1813.132 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 39 39.252 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 275 274.977 45 251 CC_Posterior 1374 1374.238 46 252 CC_Mid_Posterior 547 546.627 47 253 CC_Central 503 502.871 48 254 CC_Mid_Anterior 605 604.529 49 255 CC_Anterior 1351 1351.204 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Apr 15 06:14:48 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --volmask SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 556334 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 556334 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Apr 15 06:17:50 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/ribbon.mgz Loading filled from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9211 vertices from left hemi Ripped 10246 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 1135623 Used brute-force search on 535 voxels Fixing Parahip LH WM Found 32 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 3.000000 4 k 2.000000 5 k 2.000000 6 k 1.000000 7 k 2.000000 8 k 4.000000 9 k 4.000000 10 k 1.000000 11 k 1.000000 12 k 2.000000 13 k 2.000000 14 k 8.000000 15 k 4.000000 16 k 1.000000 17 k 1.000000 18 k 1.000000 19 k 1.000000 20 k 8.000000 21 k 6.000000 22 k 59.000000 23 k 2.000000 24 k 1960.000000 25 k 1.000000 26 k 2.000000 27 k 39.000000 28 k 1.000000 29 k 1.000000 30 k 1.000000 31 k 2.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 2130.000000 2 k 2.000000 3 k 31.000000 4 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject nmr01002 --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject nmr01002 --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-68 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 284049.774 283798.000 diff= 251.8 pctdiff= 0.089 rhCtxGM: 274473.844 274248.000 diff= 225.8 pctdiff= 0.082 lhCtxWM: 291343.508 292033.000 diff= -689.5 pctdiff=-0.237 rhCtxWM: 290128.337 290026.000 diff= 102.3 pctdiff= 0.035 SubCortGMVol 65073.000 SupraTentVol 1244498.463 (1243431.000) diff=1067.463 pctdiff=0.086 SupraTentVolNotVent 1206725.463 (1205658.000) diff=1067.463 pctdiff=0.088 BrainSegVol 1390111.000 (1387644.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1349077.000 (1348645.463) diff=431.537 pctdiff=0.032 BrainSegVolNotVent 1349077.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2707 2707.135 2 3002 wm-lh-caudalanteriorcingulate 3227 3227.328 3 3003 wm-lh-caudalmiddlefrontal 8958 8957.563 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2690 2690.155 6 3006 wm-lh-entorhinal 1067 1067.396 7 3007 wm-lh-fusiform 8907 8907.357 8 3008 wm-lh-inferiorparietal 12492 12491.797 9 3009 wm-lh-inferiortemporal 8521 8520.816 10 3010 wm-lh-isthmuscingulate 5473 5472.681 11 3011 wm-lh-lateraloccipital 12286 12286.009 12 3012 wm-lh-lateralorbitofrontal 7889 7888.796 13 3013 wm-lh-lingual 6813 6813.062 14 3014 wm-lh-medialorbitofrontal 5224 5224.340 15 3015 wm-lh-middletemporal 7885 7884.745 16 3016 wm-lh-parahippocampal 1980 1980.247 17 3017 wm-lh-paracentral 3571 3570.669 18 3018 wm-lh-parsopercularis 4201 4201.498 19 3019 wm-lh-parsorbitalis 1162 1161.759 20 3020 wm-lh-parstriangularis 3976 3976.273 21 3021 wm-lh-pericalcarine 3099 3098.679 22 3022 wm-lh-postcentral 9464 9463.994 23 3023 wm-lh-posteriorcingulate 4939 4938.779 24 3024 wm-lh-precentral 15056 15056.108 25 3025 wm-lh-precuneus 13331 13331.155 26 3026 wm-lh-rostralanteriorcingulate 3320 3320.030 27 3027 wm-lh-rostralmiddlefrontal 17385 17385.475 28 3028 wm-lh-superiorfrontal 22848 22848.000 29 3029 wm-lh-superiorparietal 14927 14926.674 30 3030 wm-lh-superiortemporal 10687 10687.067 31 3031 wm-lh-supramarginal 12755 12755.275 32 3032 wm-lh-frontalpole 328 327.865 33 3033 wm-lh-temporalpole 1018 1017.645 34 3034 wm-lh-transversetemporal 967 967.264 35 3035 wm-lh-insula 10554 10554.033 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 3042 3041.703 120 4002 wm-rh-caudalanteriorcingulate 3347 3347.264 121 4003 wm-rh-caudalmiddlefrontal 6903 6902.730 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2611 2611.135 124 4006 wm-rh-entorhinal 980 980.215 125 4007 wm-rh-fusiform 7629 7629.008 126 4008 wm-rh-inferiorparietal 17160 17159.871 127 4009 wm-rh-inferiortemporal 8354 8353.673 128 4010 wm-rh-isthmuscingulate 3847 3846.690 129 4011 wm-rh-lateraloccipital 8804 8804.213 130 4012 wm-rh-lateralorbitofrontal 7846 7846.441 131 4013 wm-rh-lingual 7308 7307.788 132 4014 wm-rh-medialorbitofrontal 3635 3634.554 133 4015 wm-rh-middletemporal 7206 7205.760 134 4016 wm-rh-parahippocampal 2176 2175.640 135 4017 wm-rh-paracentral 4894 4893.625 136 4018 wm-rh-parsopercularis 5101 5100.810 137 4019 wm-rh-parsorbitalis 1925 1924.939 138 4020 wm-rh-parstriangularis 4863 4863.343 139 4021 wm-rh-pericalcarine 3428 3428.135 140 4022 wm-rh-postcentral 8353 8353.469 141 4023 wm-rh-posteriorcingulate 5216 5216.463 142 4024 wm-rh-precentral 15790 15790.184 143 4025 wm-rh-precuneus 14998 14997.646 144 4026 wm-rh-rostralanteriorcingulate 3053 3052.658 145 4027 wm-rh-rostralmiddlefrontal 15977 15977.303 146 4028 wm-rh-superiorfrontal 21372 21372.105 147 4029 wm-rh-superiorparietal 14411 14410.916 148 4030 wm-rh-superiortemporal 9657 9656.847 149 4031 wm-rh-supramarginal 11727 11726.648 150 4032 wm-rh-frontalpole 480 479.953 151 4033 wm-rh-temporalpole 912 911.827 152 4034 wm-rh-transversetemporal 762 762.182 153 4035 wm-rh-insula 10913 10913.490 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 41731 41730.516 237 5002 Right-UnsegmentedWhiteMatter 42788 42787.953 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label #-------------------------------------------- #@# BA Labels lh Fri Apr 15 06:25:42 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.label --trgsubject nmr01002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 603 Checking for and removing duplicates Writing label file ./lh.BA1.label 4732 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.label --trgsubject nmr01002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 789 Checking for and removing duplicates Writing label file ./lh.BA2.label 8698 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.label --trgsubject nmr01002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 488 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4565 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.label --trgsubject nmr01002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 841 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6824 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.label --trgsubject nmr01002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 944 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6728 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.label --trgsubject nmr01002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 665 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.label --trgsubject nmr01002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 3060 Checking for and removing duplicates Writing label file ./lh.BA6.label 16649 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.label --trgsubject nmr01002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 710 Checking for and removing duplicates Writing label file ./lh.BA44.label 4891 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.label --trgsubject nmr01002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 1655 Checking for and removing duplicates Writing label file ./lh.BA45.label 5077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.label --trgsubject nmr01002 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 2300 Checking for and removing duplicates Writing label file ./lh.V1.label 6941 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.label --trgsubject nmr01002 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 4452 Checking for and removing duplicates Writing label file ./lh.V2.label 12566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.label --trgsubject nmr01002 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 697 Checking for and removing duplicates Writing label file ./lh.MT.label 2715 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.perirhinal.label --trgsubject nmr01002 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 308 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1507 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 231 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2304 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1574 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2643 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1745 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1596 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8631 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 327 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2239 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 529 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1680 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.thresh.label --trgsubject nmr01002 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1661 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 5066 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.thresh.label --trgsubject nmr01002 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1934 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5268 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.thresh.label --trgsubject nmr01002 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 678 mri_label2label: Done mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-68 machine x86_64 user dwakeman subject nmr01002 hemi lh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 120608 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.BA.annot mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-68 machine x86_64 user dwakeman subject nmr01002 hemi lh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 142403 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab nmr01002 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/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 1436 748 2193 2.201 0.425 0.140 0.067 45 3.9 BA1 4256 2797 6316 2.305 0.458 0.126 0.038 46 6.8 BA2 1175 782 1246 1.938 0.574 0.135 0.050 13 2.0 BA3a 3010 1932 3753 1.873 0.662 0.118 0.038 42 4.7 BA3b 1743 952 2918 2.611 0.618 0.139 0.180 56 19.8 BA4a 1431 932 2161 2.282 0.629 0.156 0.161 48 4.9 BA4p 12294 7950 24871 2.702 0.584 0.140 0.066 270 28.6 BA6 2782 1847 5165 2.610 0.376 0.130 0.038 36 4.2 BA44 4216 2798 8005 2.556 0.451 0.146 0.047 68 7.9 BA45 4443 2847 4710 1.657 0.483 0.155 0.071 81 13.4 V1 10176 6523 12861 1.961 0.517 0.164 0.064 183 26.2 V2 2417 1615 4405 2.712 0.688 0.150 0.098 88 9.9 MT 1369 907 2951 2.727 0.846 0.138 0.105 50 3.7 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab nmr01002 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 982 460 1373 2.168 0.407 0.137 0.065 23 2.8 BA1 1692 1121 2757 2.289 0.472 0.122 0.037 30 3.0 BA2 873 578 805 1.813 0.503 0.147 0.049 10 1.7 BA3a 1860 1225 1847 1.527 0.403 0.108 0.033 17 2.6 BA3b 1687 931 2793 2.600 0.619 0.137 0.179 49 19.2 BA4a 1180 788 1779 2.283 0.626 0.175 0.201 51 4.8 BA4p 6951 4373 13059 2.594 0.585 0.135 0.076 181 18.3 BA6 1812 1205 3484 2.614 0.356 0.137 0.041 28 3.1 BA44 1577 1036 3348 2.606 0.416 0.143 0.045 25 2.8 BA45 4739 3041 5055 1.650 0.490 0.156 0.072 88 14.7 V1 4954 3151 5766 1.837 0.486 0.170 0.074 98 14.2 V2 646 446 1305 2.905 0.687 0.137 0.041 8 0.9 MT #-------------------------------------------- #@# BA Labels rh Fri Apr 15 06:30:13 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.label --trgsubject nmr01002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 521 Checking for and removing duplicates Writing label file ./rh.BA1.label 4483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.label --trgsubject nmr01002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 705 Checking for and removing duplicates Writing label file ./rh.BA2.label 7392 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.label --trgsubject nmr01002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.label --trgsubject nmr01002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.label --trgsubject nmr01002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 894 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.label --trgsubject nmr01002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 553 Checking for and removing duplicates Writing label file ./rh.BA4p.label 5026 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.label --trgsubject nmr01002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 2196 Checking for and removing duplicates Writing label file ./rh.BA6.label 14452 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.label --trgsubject nmr01002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 1606 Checking for and removing duplicates Writing label file ./rh.BA44.label 8518 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.label --trgsubject nmr01002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 1806 Checking for and removing duplicates Writing label file ./rh.BA45.label 7161 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.label --trgsubject nmr01002 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 2542 Checking for and removing duplicates Writing label file ./rh.V1.label 7269 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.label --trgsubject nmr01002 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 4398 Checking for and removing duplicates Writing label file ./rh.V2.label 12414 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.label --trgsubject nmr01002 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 168865 Number of reverse mapping hits = 431 Checking for and removing duplicates Writing label file ./rh.MT.label 2363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.perirhinal.label --trgsubject nmr01002 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 277 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 1029 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1024 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 164 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2852 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1729 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 311 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2494 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 301 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1689 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1590 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 1238 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 382 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1394 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 527 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1705 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.thresh.label --trgsubject nmr01002 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 1705 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4937 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.thresh.label --trgsubject nmr01002 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 2192 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.thresh.label --trgsubject nmr01002 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 168865 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 316 mri_label2label: Done mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-68 machine x86_64 user dwakeman subject nmr01002 hemi rh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 120601 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.BA.annot mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-68 machine x86_64 user dwakeman subject nmr01002 hemi rh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 141637 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab nmr01002 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/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 583 1625 2.124 0.393 0.144 0.059 21 2.8 BA1 3489 2316 4907 2.158 0.414 0.124 0.077 74 10.8 BA2 991 665 839 1.715 0.464 0.154 0.044 12 1.8 BA3a 2365 1455 2617 1.650 0.601 0.123 0.817 107 5.4 BA3b 2086 1134 3515 2.674 0.509 0.113 0.086 99 6.9 BA4a 1353 866 1857 2.194 0.412 0.103 0.040 11 2.5 BA4p 9313 5891 19050 2.795 0.630 0.130 0.046 238 17.4 BA6 4659 3103 8523 2.636 0.497 0.135 0.047 168 8.9 BA44 5189 3395 9497 2.520 0.526 0.145 0.050 84 10.3 BA45 4961 3133 4802 1.545 0.458 0.148 0.065 88 12.5 V1 9945 6465 12435 1.983 0.576 0.156 0.056 178 23.1 V2 1937 1309 3317 2.521 0.599 0.136 0.041 26 3.0 MT 899 599 2297 3.226 0.920 0.148 0.079 15 2.7 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab nmr01002 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 757 366 963 1.958 0.389 0.139 0.058 13 1.7 BA1 1961 1324 2822 2.087 0.390 0.111 0.030 16 2.3 BA2 878 592 687 1.692 0.414 0.157 0.045 10 1.7 BA3a 1917 1204 1869 1.517 0.539 0.120 0.996 101 4.6 BA3b 1309 690 2129 2.682 0.519 0.121 0.110 84 5.3 BA4a 1100 730 1532 2.200 0.415 0.100 0.031 7 1.3 BA4p 6081 3727 11655 2.753 0.539 0.126 0.043 80 10.9 BA6 1264 855 2778 2.900 0.530 0.153 0.061 28 2.8 BA44 1617 1033 3243 2.673 0.512 0.153 0.059 123 3.5 BA45 4682 2983 4510 1.537 0.450 0.147 0.065 80 11.6 V1 5403 3430 6191 1.823 0.543 0.161 0.063 116 14.7 V2 259 159 470 2.413 0.413 0.138 0.037 4 0.4 MT /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Apr 15 06:34:41 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o nmr01002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject nmr01002. processing subject lh.EC_average... reading output surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1235 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label nmr01002 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 438 270 1018 2.648 0.776 0.115 0.039 4 0.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Apr 15 06:35:00 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o nmr01002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject nmr01002. processing subject rh.EC_average... reading output surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1073 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label nmr01002 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 355 230 887 3.086 0.826 0.138 0.052 4 0.7 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Apr 14 20:03:48 EDT 2016 Ended at Fri Apr 15 06:35:18 EDT 2016 #@#%# recon-all-run-time-hours 10.525 recon-all -s nmr01002 finished without error at Fri Apr 15 06:35:18 EDT 2016 New invocation of recon-all Fri Apr 15 16:21:00 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 subjid nmr01002 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux compute-0-75 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 58720256 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 1608616 31268636 4 99124 487364 -/+ buffers/cache: 1022128 31855124 Swap: 67108860 90720 67018140 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:02-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:04-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 8 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:07-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:08-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:09-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:09-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:10-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:10-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:11-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:11-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:12-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:13-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:13-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:14-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:14-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:15-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:15-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:16-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:16-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:17-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:19-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:20-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:20-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:21-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/15-20:21:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: dwakeman Machine: compute-0-75 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Fri Apr 15 16:21:26 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2917 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 40 seconds. #-------------------------------------------- #@# Mask BFS Fri Apr 15 16:25:08 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1879483 voxels in mask (pct= 11.20) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Apr 15 16:25:10 EDT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-75 machine x86_64 user dwakeman 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 927 values in range Counting number of voxels Found 927 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-75 machine x86_64 user dwakeman input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 0 deletes, 927 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 (105.0): 104.7 +- 6.5 [80.0 --> 125.0] GM (73.0) : 71.8 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.4 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5521 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6051 filled 337 bright non-wm voxels segmented. 3333 diagonally connected voxels added... white matter segmentation took 1.8 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 0.61 minutes reading wm segmentation from wm.seg.mgz... 219 voxels added to wm to prevent paths from MTL structures to cortex 2739 additional wm voxels added 0 additional wm voxels added SEG EDIT: 76008 voxels turned on, 58347 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+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 32 found - 32 modified | TOTAL: 58 pass 2 (xy-): 0 found - 32 modified | TOTAL: 58 pass 1 (yz+): 33 found - 33 modified | TOTAL: 91 pass 2 (yz+): 0 found - 33 modified | TOTAL: 91 pass 1 (yz-): 16 found - 16 modified | TOTAL: 107 pass 2 (yz-): 0 found - 16 modified | TOTAL: 107 pass 1 (xz+): 22 found - 22 modified | TOTAL: 129 pass 2 (xz+): 0 found - 22 modified | TOTAL: 129 pass 1 (xz-): 18 found - 18 modified | TOTAL: 147 pass 2 (xz-): 0 found - 18 modified | TOTAL: 147 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 18 found - 18 modified | TOTAL: 31 pass 2 (+++): 0 found - 18 modified | TOTAL: 31 pass 1 (+++): 12 found - 12 modified | TOTAL: 43 pass 2 (+++): 0 found - 12 modified | TOTAL: 43 pass 1 (+++): 15 found - 15 modified | TOTAL: 58 pass 2 (+++): 0 found - 15 modified | TOTAL: 58 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 84 found - 84 modified | TOTAL: 208 pass 2 (+-): 0 found - 84 modified | TOTAL: 208 pass 1 (--): 91 found - 91 modified | TOTAL: 299 pass 2 (--): 0 found - 91 modified | TOTAL: 299 pass 1 (-+): 104 found - 104 modified | TOTAL: 403 pass 2 (-+): 0 found - 104 modified | TOTAL: 403 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 626 (out of 717426: 0.087256) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 927 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Fri Apr 15 16:27:51 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3639 (min = 350, max = 1400), aspect = 1.41 (min = 0.10, max = 0.75) need search nearby using seed (127, 121, 155), TAL = (1.0, 27.0, 7.0) talairach voxel to voxel transform 0.961 0.080 -0.079 3.033; -0.109 0.873 -0.240 41.374; 0.072 0.194 1.050 -41.403; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 121, 155) --> (1.0, 27.0, 7.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (1.00, 27.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 7.00) SRC: (105.25, 97.89, 152.56) search lh wm seed point around talairach space (-17.00, 27.00, 7.00), SRC: (139.85, 93.96, 155.14) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Apr 15 16:28:40 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 19 (out of 347268: 0.005471) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 2944 vertices, 3132 faces slice 40: 10921 vertices, 11278 faces slice 50: 22273 vertices, 22668 faces slice 60: 34740 vertices, 35181 faces slice 70: 47149 vertices, 47532 faces slice 80: 59678 vertices, 60114 faces slice 90: 72395 vertices, 72851 faces slice 100: 85976 vertices, 86438 faces slice 110: 98341 vertices, 98802 faces slice 120: 111100 vertices, 111556 faces slice 130: 123616 vertices, 124049 faces slice 140: 134919 vertices, 135312 faces slice 150: 144969 vertices, 145304 faces slice 160: 153120 vertices, 153436 faces slice 170: 160115 vertices, 160371 faces slice 180: 166375 vertices, 166591 faces slice 190: 171266 vertices, 171444 faces slice 200: 172828 vertices, 172866 faces slice 210: 172828 vertices, 172866 faces slice 220: 172828 vertices, 172866 faces slice 230: 172828 vertices, 172866 faces slice 240: 172828 vertices, 172866 faces slice 250: 172828 vertices, 172866 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... 172828 voxel in cpt #1: X=-38 [v=172828,e=518598,f=345732] located at (-23.818184, -26.572702, 31.230940) For the whole surface: X=-38 [v=172828,e=518598,f=345732] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Apr 15 16:28:49 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Apr 15 16:28:55 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts avg radius = 51.0 mm, total surface area = 90513 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Apr 15 16:29:49 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.54 (0.00-->6.55) (max @ vno 129289 --> 130308) face area 0.02 +- 0.03 (-0.09-->0.52) scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.808, avgs=0 005/300: dt: 0.9000, rms radial error=176.547, avgs=0 010/300: dt: 0.9000, rms radial error=175.989, avgs=0 015/300: dt: 0.9000, rms radial error=175.257, avgs=0 020/300: dt: 0.9000, rms radial error=174.425, avgs=0 025/300: dt: 0.9000, rms radial error=173.535, avgs=0 030/300: dt: 0.9000, rms radial error=172.613, avgs=0 035/300: dt: 0.9000, rms radial error=171.674, avgs=0 040/300: dt: 0.9000, rms radial error=170.728, avgs=0 045/300: dt: 0.9000, rms radial error=169.779, avgs=0 050/300: dt: 0.9000, rms radial error=168.830, avgs=0 055/300: dt: 0.9000, rms radial error=167.885, avgs=0 060/300: dt: 0.9000, rms radial error=166.943, avgs=0 065/300: dt: 0.9000, rms radial error=166.005, avgs=0 070/300: dt: 0.9000, rms radial error=165.073, avgs=0 075/300: dt: 0.9000, rms radial error=164.145, avgs=0 080/300: dt: 0.9000, rms radial error=163.222, avgs=0 085/300: dt: 0.9000, rms radial error=162.304, avgs=0 090/300: dt: 0.9000, rms radial error=161.392, avgs=0 095/300: dt: 0.9000, rms radial error=160.484, avgs=0 100/300: dt: 0.9000, rms radial error=159.581, avgs=0 105/300: dt: 0.9000, rms radial error=158.683, avgs=0 110/300: dt: 0.9000, rms radial error=157.790, avgs=0 115/300: dt: 0.9000, rms radial error=156.902, avgs=0 120/300: dt: 0.9000, rms radial error=156.019, avgs=0 125/300: dt: 0.9000, rms radial error=155.140, avgs=0 130/300: dt: 0.9000, rms radial error=154.267, avgs=0 135/300: dt: 0.9000, rms radial error=153.398, avgs=0 140/300: dt: 0.9000, rms radial error=152.534, avgs=0 145/300: dt: 0.9000, rms radial error=151.675, avgs=0 150/300: dt: 0.9000, rms radial error=150.820, avgs=0 155/300: dt: 0.9000, rms radial error=149.971, avgs=0 160/300: dt: 0.9000, rms radial error=149.125, avgs=0 165/300: dt: 0.9000, rms radial error=148.285, avgs=0 170/300: dt: 0.9000, rms radial error=147.449, avgs=0 175/300: dt: 0.9000, rms radial error=146.618, avgs=0 180/300: dt: 0.9000, rms radial error=145.791, avgs=0 185/300: dt: 0.9000, rms radial error=144.969, avgs=0 190/300: dt: 0.9000, rms radial error=144.152, avgs=0 195/300: dt: 0.9000, rms radial error=143.339, avgs=0 200/300: dt: 0.9000, rms radial error=142.530, avgs=0 205/300: dt: 0.9000, rms radial error=141.726, avgs=0 210/300: dt: 0.9000, rms radial error=140.927, avgs=0 215/300: dt: 0.9000, rms radial error=140.132, avgs=0 220/300: dt: 0.9000, rms radial error=139.341, avgs=0 225/300: dt: 0.9000, rms radial error=138.555, avgs=0 230/300: dt: 0.9000, rms radial error=137.773, avgs=0 235/300: dt: 0.9000, rms radial error=136.996, avgs=0 240/300: dt: 0.9000, rms radial error=136.223, avgs=0 245/300: dt: 0.9000, rms radial error=135.454, avgs=0 250/300: dt: 0.9000, rms radial error=134.690, avgs=0 255/300: dt: 0.9000, rms radial error=133.930, avgs=0 260/300: dt: 0.9000, rms radial error=133.174, avgs=0 265/300: dt: 0.9000, rms radial error=132.422, avgs=0 270/300: dt: 0.9000, rms radial error=131.675, avgs=0 275/300: dt: 0.9000, rms radial error=130.932, avgs=0 280/300: dt: 0.9000, rms radial error=130.193, avgs=0 285/300: dt: 0.9000, rms radial error=129.458, avgs=0 290/300: dt: 0.9000, rms radial error=128.727, avgs=0 295/300: dt: 0.9000, rms radial error=128.001, avgs=0 300/300: dt: 0.9000, rms radial error=127.278, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20908.40 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 = 3769.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 431.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00517 epoch 4 (K=640.0), pass 1, starting sse = 25.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/17 = 0.01369 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Apr 15 16:36:56 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=172828, nf=345732, ne=518598, g=20) 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... 3174 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3257 (-4.6629) -vertex loglikelihood: -6.1497 (-3.0749) -normal dot loglikelihood: -3.6182 (-3.6182) -quad curv loglikelihood: -6.3064 (-3.1532) Total Loglikelihood : -25.4000 CORRECTING DEFECT 0 (vertices=18, convex hull=22) After retessellation of defect 0, euler #=-22 (170915,512130,341193) : difference with theory (-23) = -1 CORRECTING DEFECT 1 (vertices=27, convex hull=75) After retessellation of defect 1, euler #=-21 (170927,512198,341250) : difference with theory (-22) = -1 CORRECTING DEFECT 2 (vertices=69, convex hull=64) After retessellation of defect 2, euler #=-20 (170936,512254,341298) : difference with theory (-21) = -1 CORRECTING DEFECT 3 (vertices=26, convex hull=32) After retessellation of defect 3, euler #=-19 (170940,512276,341317) : difference with theory (-20) = -1 CORRECTING DEFECT 4 (vertices=22, convex hull=61) After retessellation of defect 4, euler #=-18 (170952,512336,341366) : difference with theory (-19) = -1 CORRECTING DEFECT 5 (vertices=80, convex hull=86) After retessellation of defect 5, euler #=-17 (170964,512403,341422) : difference with theory (-18) = -1 CORRECTING DEFECT 6 (vertices=26, convex hull=69) After retessellation of defect 6, euler #=-16 (170979,512475,341480) : difference with theory (-17) = -1 CORRECTING DEFECT 7 (vertices=819, convex hull=349) After retessellation of defect 7, euler #=-16 (171193,513301,342092) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=25, convex hull=31) After retessellation of defect 8, euler #=-15 (171197,513322,342110) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=34) After retessellation of defect 9, euler #=-14 (171202,513350,342134) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=50, convex hull=26) After retessellation of defect 10, euler #=-13 (171207,513374,342154) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-12 (171214,513405,342179) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=363, convex hull=95) After retessellation of defect 12, euler #=-11 (171237,513513,342265) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=10, convex hull=23) After retessellation of defect 13, euler #=-10 (171239,513523,342274) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=9, convex hull=25) After retessellation of defect 14, euler #=-9 (171242,513540,342289) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=79, convex hull=67) After retessellation of defect 15, euler #=-8 (171258,513622,342356) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=32) After retessellation of defect 16, euler #=-7 (171264,513648,342377) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=19) After retessellation of defect 17, euler #=-6 (171265,513657,342386) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=51) After retessellation of defect 18, euler #=-5 (171280,513717,342432) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=76) After retessellation of defect 19, euler #=-4 (171303,513814,342507) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=42, convex hull=50) After retessellation of defect 20, euler #=-3 (171318,513876,342555) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=69) After retessellation of defect 21, euler #=-2 (171329,513934,342603) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=41, convex hull=76) After retessellation of defect 22, euler #=-1 (171350,514030,342679) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=16, convex hull=27) After retessellation of defect 23, euler #=0 (171354,514050,342696) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=8, convex hull=18) After retessellation of defect 24, euler #=1 (171355,514057,342703) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=15, convex hull=15) After retessellation of defect 25, euler #=2 (171356,514062,342708) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (33.6%), 160 crossovers (66.4%), 94 vertices were eliminated building final representation... 1472 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=171356, nf=342708, ne=514062, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.8 minutes 0 defective edges removing intersecting faces 000: 141 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 171356 - 514062 + 342708 = 2 --> 0 holes F =2V-4: 342708 = 342712-4 (0) 2E=3F: 1028124 = 1028124 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Apr 15 16:54:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs nmr01002 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.0 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.4 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4846 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=81.7, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.8)->0.8 (%65.2))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.10-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.56 4106 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6549240.5, rms=10.18 001: dt: 0.5000, sse=7446538.0, rms=7.192 (0.000%) 002: dt: 0.5000, sse=7916716.0, rms=5.428 (0.000%) 003: dt: 0.5000, sse=8368161.5, rms=4.396 (0.000%) 004: dt: 0.5000, sse=8619471.0, rms=3.764 (0.000%) 005: dt: 0.5000, sse=8796283.0, rms=3.473 (0.000%) 006: dt: 0.5000, sse=8840013.0, rms=3.279 (0.000%) 007: dt: 0.5000, sse=8901644.0, rms=3.226 (0.000%) 008: dt: 0.5000, sse=8858166.0, rms=3.144 (0.000%) rms = 3.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6120095.0, rms=2.322 (0.000%) 010: dt: 0.2500, sse=5105572.0, rms=1.911 (0.000%) 011: dt: 0.2500, sse=4843470.0, rms=1.816 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4746325.0, rms=1.782 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4664403.5, rms=1.740 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=84.9, 94 (24) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.49) mean absolute distance = 0.26 +- 0.38 4758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5489852.5, rms=4.84 014: dt: 0.5000, sse=5833355.0, rms=3.049 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6453838.0, rms=3.020 (0.000%) 016: dt: 0.2500, sse=5449253.5, rms=1.841 (0.000%) 017: dt: 0.2500, sse=5276166.0, rms=1.594 (0.000%) 018: dt: 0.2500, sse=5121221.5, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5089623.0, rms=1.483 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5007341.5, rms=1.449 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.5, 123 (17) missing vertices, mean dist -0.1 [0.3 (%75.0)->0.2 (%25.0))] %90 local maxima, % 5 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 +- 0.24 (0.10-->3.61) (max @ vno 75800 --> 74575) face area 0.33 +- 0.16 (0.00-->2.66) mean absolute distance = 0.20 +- 0.31 4377 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5289322.5, rms=3.43 021: dt: 0.5000, sse=5521510.5, rms=2.554 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5187069.5, rms=1.786 (0.000%) 023: dt: 0.2500, sse=5094396.0, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5085621.0, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=5034150.0, rms=1.313 (0.000%) rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4994697.5, rms=1.278 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.3, 112 (14) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))] %92 local maxima, % 3 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5009834.5, rms=1.61 rms = 1.70, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5100041.0, rms=1.186 (0.000%) 028: dt: 0.2500, sse=5288887.0, rms=0.981 (0.000%) rms = 1.00, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5287264.5, rms=0.979 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 2139 vertices erasing segment 1 (vno[0] = 84151) erasing segment 2 (vno[0] = 95362) erasing segment 3 (vno[0] = 101746) erasing segment 4 (vno[0] = 105209) erasing segment 5 (vno[0] = 110214) erasing segment 6 (vno[0] = 111310) erasing segment 7 (vno[0] = 118503) erasing segment 8 (vno[0] = 123094) erasing segment 9 (vno[0] = 123467) erasing segment 10 (vno[0] = 124283) erasing segment 11 (vno[0] = 124325) erasing segment 12 (vno[0] = 124399) erasing segment 13 (vno[0] = 126884) erasing segment 14 (vno[0] = 127923) erasing segment 15 (vno[0] = 129142) erasing segment 16 (vno[0] = 129145) erasing segment 17 (vno[0] = 171209) erasing segment 18 (vno[0] = 171260) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area vertex spacing 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.61) refinement took 6.7 minutes #-------------------------------------------- #@# Smooth2 lh Fri Apr 15 17:01:36 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri Apr 15 17:01:42 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.2 mm, total surface area = 102557 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.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=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 244 vertices thresholded to be in k1 ~ [-0.30 0.46], k2 ~ [-0.09 0.08] total integrated curvature = 0.470*4pi (5.901) --> 1 handles ICI = 1.7, FI = 12.0, variation=201.479 159 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 160 vertices thresholded to be in [-0.12 0.20] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Fri Apr 15 17:04:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm nmr01002 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 [ nmr01002/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 [ 277 ] Gb_filter = 0 WARN: S lookup min: -0.445948 WARN: S explicit min: 0.000000 vertex = 560 #-------------------------------------------- #@# Sphere lh Fri Apr 15 17:04:28 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.262... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.51 pass 1: epoch 2 of 3 starting distance error %19.49 unfolding complete - removing small folds... starting distance error %19.44 removing remaining folds... final distance error %19.46 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.08 hours #-------------------------------------------- #@# Surf Reg lh Fri Apr 15 18:09:19 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.582 curvature mean = 0.022, std = 0.940 curvature mean = 0.025, std = 0.831 Starting MRISrigidBodyAlignGlobal() d=16.00 min @ (4.00, 0.00, 0.00) sse = 320951.7, tmin=4.4295 d=8.00 min @ (0.00, 0.00, -2.00) sse = 317732.4, tmin=5.9291 d=4.00 min @ (0.00, 0.00, 1.00) sse = 317547.9, tmin=7.4469 d=2.00 min @ (0.00, 0.00, -0.50) sse = 317254.2, tmin=8.9776 d=0.50 min @ (0.00, 0.12, 0.12) sse = 317232.8, tmin=11.9971 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 12.00 min curvature mean = -0.016, std = 0.930 curvature mean = 0.011, std = 0.921 curvature mean = -0.024, std = 0.934 curvature mean = 0.006, std = 0.962 curvature mean = -0.029, std = 0.930 curvature mean = 0.001, std = 0.982 2 Reading smoothwm curvature mean = -0.023, std = 0.290 curvature mean = 0.001, std = 0.065 curvature mean = 0.064, std = 0.314 curvature mean = 0.002, std = 0.077 curvature mean = 0.031, std = 0.509 curvature mean = 0.002, std = 0.082 curvature mean = 0.016, std = 0.659 curvature mean = 0.002, std = 0.084 curvature mean = 0.005, std = 0.774 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... #-------------------------------------------- #@# Jacobian white lh Fri Apr 15 18:51:22 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Apr 15 18:51:26 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Apr 15 18:51:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 1383 labels changed using aseg relabeling using gibbs priors... 000: 3706 changed, 171356 examined... 001: 825 changed, 15612 examined... 002: 207 changed, 4577 examined... 003: 79 changed, 1255 examined... 004: 32 changed, 448 examined... 005: 15 changed, 186 examined... 006: 8 changed, 95 examined... 007: 1 changed, 45 examined... 008: 0 changed, 5 examined... 273 labels changed using aseg 000: 132 total segments, 78 labels (425 vertices) changed 001: 56 total segments, 5 labels (7 vertices) changed 002: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2152 vertices marked for relabeling... 2152 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 6 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Apr 15 18:52:35 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs nmr01002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.0 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.4 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.1 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4875 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 2 with 390 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 24 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown deleting segment 7 with 77 points - only 0.00% unknown mean border=81.6, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.9)->0.8 (%65.1))] %75 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.10-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.56 4108 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6559968.5, rms=10.17 001: dt: 0.5000, sse=7461793.5, rms=7.186 (0.000%) 002: dt: 0.5000, sse=7937244.5, rms=5.423 (0.000%) 003: dt: 0.5000, sse=8385862.0, rms=4.393 (0.000%) 004: dt: 0.5000, sse=8643414.0, rms=3.762 (0.000%) 005: dt: 0.5000, sse=8818178.0, rms=3.472 (0.000%) 006: dt: 0.5000, sse=8865095.0, rms=3.278 (0.000%) 007: dt: 0.5000, sse=8923952.0, rms=3.225 (0.000%) 008: dt: 0.5000, sse=8884310.0, rms=3.142 (0.000%) rms = 3.14, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6135491.5, rms=2.321 (0.000%) 010: dt: 0.2500, sse=5116798.5, rms=1.910 (0.000%) 011: dt: 0.2500, sse=4854582.5, rms=1.815 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4756534.0, rms=1.782 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4674707.0, rms=1.740 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 3 with 301 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 30 points - only 20.00% unknown deleting segment 9 with 19 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 92 points - only 0.00% unknown mean border=84.9, 107 (30) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.49) mean absolute distance = 0.26 +- 0.38 4767 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5504108.0, rms=4.84 014: dt: 0.5000, sse=5845735.5, rms=3.046 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6470790.5, rms=3.018 (0.000%) 016: dt: 0.2500, sse=5463383.5, rms=1.840 (0.000%) 017: dt: 0.2500, sse=5290663.0, rms=1.594 (0.000%) 018: dt: 0.2500, sse=5134967.0, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5103492.0, rms=1.482 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5020638.5, rms=1.449 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 2 with 326 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 30 points - only 20.00% unknown deleting segment 8 with 29 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 87 points - only 0.00% unknown mean border=87.5, 135 (21) missing vertices, mean dist -0.1 [0.3 (%75.1)->0.2 (%24.9))] %91 local maxima, % 5 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 +- 0.24 (0.06-->3.57) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.57) mean absolute distance = 0.20 +- 0.31 4633 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5303339.0, rms=3.43 021: dt: 0.5000, sse=5533845.0, rms=2.552 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5199737.5, rms=1.785 (0.000%) 023: dt: 0.2500, sse=5108356.5, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5098355.5, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5064211.5, rms=1.295 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 332 points - only 0.00% unknown deleting segment 2 with 43 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 30 points - only 20.00% unknown deleting segment 6 with 32 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 88 points - only 0.00% unknown mean border=88.3, 124 (16) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))] %93 local maxima, % 3 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=5080916.5, rms=1.63 rms = 1.76, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5126339.0, rms=1.205 (0.000%) 027: dt: 0.2500, sse=5308216.0, rms=0.995 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5302311.5, rms=0.991 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.5, 176 (176) missing vertices, mean dist 1.6 [0.2 (%0.0)->2.7 (%100.0))] %17 local maxima, %43 large gradients and %37 min vals, 2149 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=28917232.0, rms=27.88 001: dt: 0.5000, sse=22017664.0, rms=23.801 (0.000%) 002: dt: 0.5000, sse=16958370.0, rms=20.344 (0.000%) 003: dt: 0.5000, sse=13337680.0, rms=17.481 (0.000%) 004: dt: 0.5000, sse=10896594.0, rms=15.127 (0.000%) 005: dt: 0.5000, sse=9322017.0, rms=13.216 (0.000%) 006: dt: 0.5000, sse=8387903.5, rms=11.663 (0.000%) 007: dt: 0.5000, sse=7858582.5, rms=10.307 (0.000%) 008: dt: 0.5000, sse=7568910.5, rms=9.093 (0.000%) 009: dt: 0.5000, sse=7347558.5, rms=7.967 (0.000%) 010: dt: 0.5000, sse=7285092.0, rms=6.954 (0.000%) 011: dt: 0.5000, sse=7234676.5, rms=6.077 (0.000%) 012: dt: 0.5000, sse=7420736.0, rms=5.395 (0.000%) 013: dt: 0.5000, sse=7505157.0, rms=4.878 (0.000%) 014: dt: 0.5000, sse=7659759.0, rms=4.500 (0.000%) 015: dt: 0.5000, sse=7684337.5, rms=4.240 (0.000%) 016: dt: 0.5000, sse=7806904.5, rms=4.042 (0.000%) 017: dt: 0.5000, sse=7778638.5, rms=3.921 (0.000%) 018: dt: 0.5000, sse=7875842.0, rms=3.804 (0.000%) 019: dt: 0.5000, sse=7823162.5, rms=3.724 (0.000%) 020: dt: 0.5000, sse=7883691.5, rms=3.648 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=7825071.5, rms=3.611 (0.000%) 022: dt: 0.2500, sse=5402979.5, rms=2.902 (0.000%) 023: dt: 0.2500, sse=5162961.0, rms=2.708 (0.000%) rms = 2.68, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5037293.0, rms=2.678 (0.000%) 025: dt: 0.1250, sse=4796873.5, rms=2.565 (0.000%) rms = 2.55, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4765548.5, rms=2.550 (0.000%) positioning took 3.4 minutes mean border=58.4, 1621 (18) missing vertices, mean dist 0.1 [0.2 (%47.5)->0.5 (%52.5))] %35 local maxima, %31 large gradients and %29 min vals, 998 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=5437133.0, rms=4.41 027: dt: 0.5000, sse=5766396.0, rms=3.591 (0.000%) rms = 3.60, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5355303.5, rms=3.043 (0.000%) 029: dt: 0.2500, sse=5461536.5, rms=2.789 (0.000%) 030: dt: 0.2500, sse=5380913.5, rms=2.679 (0.000%) 031: dt: 0.2500, sse=5433374.0, rms=2.624 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5421596.0, rms=2.586 (0.000%) 033: dt: 0.1250, sse=5232463.0, rms=2.460 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5222861.0, rms=2.434 (0.000%) positioning took 1.1 minutes mean border=56.9, 2034 (14) missing vertices, mean dist 0.1 [0.2 (%39.2)->0.3 (%60.8))] %50 local maxima, %17 large gradients and %29 min vals, 981 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=5396368.0, rms=3.26 rms = 3.38, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5198584.5, rms=2.816 (0.000%) 036: dt: 0.2500, sse=5243725.5, rms=2.561 (0.000%) 037: dt: 0.2500, sse=5459089.0, rms=2.488 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5532462.5, rms=2.475 (0.000%) 039: dt: 0.1250, sse=5370675.5, rms=2.368 (0.000%) rms = 2.35, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5383979.5, rms=2.348 (0.000%) positioning took 0.9 minutes mean border=56.2, 3823 (7) missing vertices, mean dist 0.0 [0.2 (%45.0)->0.3 (%55.0))] %52 local maxima, %13 large gradients and %28 min vals, 839 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5422611.5, rms=2.59 rms = 3.02, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5321467.0, rms=2.426 (0.000%) 042: dt: 0.2500, sse=5546384.5, rms=2.374 (0.000%) rms = 2.37, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=5630089.0, rms=2.365 (0.000%) 044: dt: 0.1250, sse=5511681.0, rms=2.282 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=5533756.5, rms=2.265 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.07-->6.29) (max @ vno 117187 --> 117166) face area 0.38 +- 0.29 (0.00-->6.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1331:1807 truncations. 35410 vertices at 0 distance 111759 vertices at 1 distance 107633 vertices at 2 distance 48758 vertices at 3 distance 17113 vertices at 4 distance 5456 vertices at 5 distance 1864 vertices at 6 distance 631 vertices at 7 distance 222 vertices at 8 distance 137 vertices at 9 distance 97 vertices at 10 distance 50 vertices at 11 distance 37 vertices at 12 distance 45 vertices at 13 distance 37 vertices at 14 distance 24 vertices at 15 distance 17 vertices at 16 distance 18 vertices at 17 distance 19 vertices at 18 distance 13 vertices at 19 distance 6 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness positioning took 13.8 minutes #-------------------------------------------- #@# Surf Volume lh Fri Apr 15 19:06:25 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Fri Apr 15 19:06:26 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts pctsurfcon --s nmr01002 --lh-only Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts/pctsurfcon.log Fri Apr 15 19:06:26 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-75 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.wm.mgh --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 92943 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.wm.mgh Dim: 171356 1 1 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.gm.mgh --projfrac 0.3 --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 110866 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.gm.mgh Dim: 171356 1 1 mri_concat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.wm.mgh /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.10333/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh --annot nmr01002 lh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh --annot nmr01002 lh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-75 machine x86_64 user dwakeman UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.w-g.pct.mgh Vertex Area is 0.652869 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1622 1084.128 2 1002 caudalanteriorcingulate 1290 866.706 3 1003 caudalmiddlefrontal 4633 2977.096 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2539 1613.013 6 1006 entorhinal 848 557.549 7 1007 fusiform 6472 4305.900 8 1008 inferiorparietal 9079 5986.337 9 1009 inferiortemporal 6819 4491.680 10 1010 isthmuscingulate 1988 1312.351 11 1011 lateraloccipital 9085 5787.125 12 1012 lateralorbitofrontal 4805 3177.072 13 1013 lingual 5914 3932.342 14 1014 medialorbitofrontal 3563 2312.425 15 1015 middletemporal 5824 3819.678 16 1016 parahippocampal 1512 963.338 17 1017 paracentral 1887 1166.398 18 1018 parsopercularis 2563 1692.679 19 1019 parsorbitalis 1217 802.958 20 1020 parstriangularis 2484 1635.439 21 1021 pericalcarine 2476 1589.359 22 1022 postcentral 7760 4884.539 23 1023 posteriorcingulate 1782 1218.851 24 1024 precentral 8883 5533.357 25 1025 precuneus 8020 5306.536 26 1026 rostralanteriorcingulate 1563 1045.751 27 1027 rostralmiddlefrontal 11935 7815.872 28 1028 superiorfrontal 13621 9103.479 29 1029 superiorparietal 10006 6437.070 30 1030 superiortemporal 7452 4834.023 31 1031 supramarginal 8255 5487.222 32 1032 frontalpole 405 251.983 33 1033 temporalpole 892 624.247 34 1034 transversetemporal 1098 666.206 35 1035 insula 3851 2470.165 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Apr 15 19:06:37 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1622 1084 3089 2.819 0.619 0.113 0.027 14 1.7 bankssts 1290 867 2625 2.736 0.632 0.159 0.041 26 2.0 caudalanteriorcingulate 4633 2977 8661 2.623 0.509 0.127 0.043 54 7.7 caudalmiddlefrontal 2539 1613 3291 1.911 0.468 0.165 0.060 44 6.3 cuneus 848 558 2334 3.257 0.718 0.138 0.049 10 1.8 entorhinal 6472 4306 13070 2.694 0.587 0.143 0.054 115 13.2 fusiform 9079 5986 16594 2.493 0.499 0.136 0.043 134 16.0 inferiorparietal 6819 4492 14199 2.738 0.746 0.132 0.049 122 13.9 inferiortemporal 1988 1312 3257 2.453 0.773 0.169 0.245 465 5.5 isthmuscingulate 9085 5787 14552 2.322 0.731 0.154 0.071 240 27.3 lateraloccipital 4805 3177 8491 2.479 0.627 0.156 0.076 92 13.8 lateralorbitofrontal 5914 3932 8246 1.986 0.611 0.164 0.066 109 15.8 lingual 3563 2312 5710 2.303 0.730 0.154 0.091 254 13.2 medialorbitofrontal 5824 3820 14936 3.174 0.784 0.148 0.058 109 14.6 middletemporal 1512 963 2628 2.419 0.651 0.116 0.039 31 2.6 parahippocampal 1887 1166 2938 2.390 0.515 0.122 0.061 42 4.7 paracentral 2563 1693 4880 2.579 0.481 0.130 0.039 31 3.9 parsopercularis 1217 803 2566 2.550 0.489 0.163 0.062 28 3.0 parsorbitalis 2484 1635 4741 2.490 0.489 0.134 0.038 36 3.9 parstriangularis 2476 1589 2554 1.713 0.431 0.149 0.079 53 9.3 pericalcarine 7760 4885 11678 2.154 0.641 0.126 0.042 118 13.9 postcentral 1782 1219 3106 2.395 0.478 0.154 0.051 39 3.9 posteriorcingulate 8883 5533 16107 2.582 0.656 0.142 0.081 320 28.6 precentral 8020 5307 13617 2.464 0.496 0.152 0.059 136 16.9 precuneus 1563 1046 2839 2.442 0.464 0.142 0.059 32 3.6 rostralanteriorcingulate 11935 7816 20327 2.362 0.511 0.146 0.051 205 23.2 rostralmiddlefrontal 13621 9103 29771 2.829 0.635 0.143 0.072 451 30.0 superiorfrontal 10006 6437 14848 2.151 0.476 0.140 0.045 143 18.4 superiorparietal 7452 4834 15570 2.882 0.662 0.125 0.069 130 29.9 superiortemporal 8255 5487 14745 2.515 0.473 0.129 0.038 112 12.9 supramarginal 405 252 865 2.514 0.569 0.173 0.070 11 1.1 frontalpole 892 624 3397 4.067 0.643 0.183 0.132 82 5.3 temporalpole 1098 666 1695 2.308 0.507 0.140 0.051 15 2.5 transversetemporal 3851 2470 7443 3.079 0.761 0.134 0.082 96 10.0 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Apr 15 19:06:58 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 74 labels changed using aseg relabeling using gibbs priors... 000: 11382 changed, 171356 examined... 001: 2802 changed, 43764 examined... 002: 913 changed, 14543 examined... 003: 431 changed, 5132 examined... 004: 214 changed, 2394 examined... 005: 114 changed, 1163 examined... 006: 49 changed, 606 examined... 007: 29 changed, 261 examined... 008: 9 changed, 160 examined... 009: 7 changed, 54 examined... 010: 5 changed, 47 examined... 011: 3 changed, 28 examined... 012: 1 changed, 15 examined... 013: 0 changed, 5 examined... 23 labels changed using aseg 000: 349 total segments, 267 labels (3048 vertices) changed 001: 98 total segments, 16 labels (81 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 169 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1165 vertices marked for relabeling... 1165 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 15 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Apr 15 19:08:13 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1823 1226 2719 2.174 0.469 0.147 0.059 30 3.8 G_and_S_frontomargin 1865 1246 2881 2.173 0.539 0.142 0.069 111 7.0 G_and_S_occipital_inf 1316 777 2049 2.250 0.473 0.148 0.066 49 3.7 G_and_S_paracentral 2021 1339 4166 2.688 0.487 0.136 0.045 37 3.6 G_and_S_subcentral 929 609 1833 2.430 0.505 0.160 0.056 19 2.1 G_and_S_transv_frontopol 2622 1786 4872 2.593 0.478 0.131 0.035 32 3.8 G_and_S_cingul-Ant 1802 1235 3455 2.687 0.547 0.135 0.034 27 2.5 G_and_S_cingul-Mid-Ant 1308 915 2324 2.486 0.448 0.120 0.030 12 1.6 G_and_S_cingul-Mid-Post 726 502 1720 2.730 0.493 0.183 0.084 22 2.3 G_cingul-Post-dorsal 458 310 664 2.146 0.919 0.196 0.109 15 2.2 G_cingul-Post-ventral 2306 1462 3127 1.842 0.505 0.169 0.066 42 6.4 G_cuneus 1595 1031 3810 2.835 0.463 0.141 0.047 27 3.0 G_front_inf-Opercular 453 291 1105 2.675 0.444 0.173 0.058 11 1.1 G_front_inf-Orbital 1267 833 3104 2.760 0.471 0.147 0.043 23 2.2 G_front_inf-Triangul 6221 3935 12888 2.569 0.572 0.147 0.054 123 13.7 G_front_middle 9638 6356 23307 2.977 0.627 0.156 0.095 438 27.1 G_front_sup 591 368 1273 3.186 0.646 0.138 0.068 12 1.7 G_Ins_lg_and_S_cent_ins 938 587 2619 3.708 0.682 0.159 0.118 30 3.0 G_insular_short 2961 1930 7315 3.024 0.704 0.170 0.085 71 10.1 G_occipital_middle 1858 1140 2584 1.998 0.520 0.144 0.047 30 3.9 G_occipital_sup 2711 1734 5658 2.629 0.527 0.151 0.059 56 5.7 G_oc-temp_lat-fusifor 3945 2534 5418 1.913 0.646 0.177 0.080 88 12.7 G_oc-temp_med-Lingual 1712 1096 3961 2.823 0.827 0.121 0.045 22 3.4 G_oc-temp_med-Parahip 3310 2130 7037 2.651 0.641 0.171 0.092 85 10.7 G_orbital 3703 2411 8297 2.690 0.488 0.150 0.053 74 7.9 G_pariet_inf-Angular 4315 2803 8828 2.600 0.504 0.136 0.044 73 7.8 G_pariet_inf-Supramar 4009 2533 7285 2.356 0.460 0.146 0.050 66 7.9 G_parietal_sup 3092 1779 4886 2.192 0.556 0.131 0.049 61 6.7 G_postcentral 3899 2225 8241 2.739 0.735 0.143 0.084 87 14.0 G_precentral 3931 2610 7859 2.491 0.516 0.163 0.074 83 9.7 G_precuneus 1190 723 2176 2.298 0.674 0.169 0.092 45 4.5 G_rectus 791 497 1311 2.495 0.878 0.160 0.181 184 6.3 G_subcallosal 871 507 1409 2.277 0.554 0.128 0.041 11 1.5 G_temp_sup-G_T_transv 2806 1779 8035 3.315 0.786 0.152 0.141 93 25.1 G_temp_sup-Lateral 739 515 1792 3.295 0.635 0.113 0.035 6 1.0 G_temp_sup-Plan_polar 1554 1003 2776 2.652 0.503 0.124 0.036 22 2.3 G_temp_sup-Plan_tempo 3720 2384 8648 2.800 0.695 0.147 0.059 93 9.6 G_temporal_inf 3651 2327 10841 3.317 0.673 0.153 0.058 80 8.4 G_temporal_middle 456 306 586 2.051 0.436 0.102 0.021 3 0.4 Lat_Fis-ant-Horizont 341 244 512 2.256 0.337 0.103 0.019 2 0.3 Lat_Fis-ant-Vertical 1937 1289 2610 2.453 0.470 0.128 0.040 20 3.2 Lat_Fis-post 2791 1671 3512 1.965 0.592 0.164 0.077 53 8.1 Pole_occipital 2433 1705 8720 3.936 0.835 0.187 0.115 129 12.4 Pole_temporal 3078 2019 3619 1.983 0.634 0.146 0.066 60 9.6 S_calcarine 3587 2400 4228 1.899 0.690 0.135 0.086 185 11.2 S_central 1044 704 1517 2.288 0.415 0.127 0.035 11 1.5 S_cingul-Marginalis 544 362 859 2.791 0.488 0.120 0.032 4 0.8 S_circular_insula_ant 1502 996 2313 2.789 0.506 0.093 0.021 7 1.4 S_circular_insula_inf 1982 1311 2829 2.509 0.407 0.117 0.063 40 4.0 S_circular_insula_sup 1409 954 2662 2.738 0.538 0.114 0.034 14 1.8 S_collat_transv_ant 338 239 585 2.422 0.451 0.148 0.046 4 0.6 S_collat_transv_post 3993 2587 6174 2.365 0.468 0.138 0.048 54 6.8 S_front_inf 1805 1239 2589 2.309 0.416 0.128 0.034 18 2.4 S_front_middle 2964 2005 4539 2.361 0.455 0.120 0.031 26 3.8 S_front_sup 792 552 1128 2.402 0.301 0.107 0.022 4 0.8 S_interm_prim-Jensen 3729 2453 4614 2.053 0.388 0.129 0.039 43 5.6 S_intrapariet_and_P_trans 1677 1124 2202 2.237 0.428 0.143 0.045 20 3.0 S_oc_middle_and_Lunatus 1826 1182 2222 2.031 0.484 0.132 0.044 21 3.4 S_oc_sup_and_transversal 723 478 947 2.317 0.399 0.103 0.021 4 0.7 S_occipital_ant 1376 901 1869 2.491 0.366 0.134 0.044 16 2.2 S_oc-temp_lat 3146 2178 4713 2.305 0.476 0.130 0.040 49 5.3 S_oc-temp_med_and_Lingual 621 409 879 2.278 0.375 0.137 0.040 7 1.1 S_orbital_lateral 1326 903 1839 2.173 0.750 0.133 0.054 21 2.7 S_orbital_med-olfact 1668 1129 2628 2.376 0.519 0.148 0.062 27 4.3 S_orbital-H_Shaped 2408 1570 3132 2.332 0.550 0.136 0.038 26 3.8 S_parieto_occipital 1379 828 1417 2.116 0.593 0.161 0.322 461 3.7 S_pericallosal 3173 2123 4167 2.229 0.414 0.127 0.035 31 4.7 S_postcentral 1884 1270 2845 2.565 0.309 0.118 0.032 17 2.3 S_precentral-inf-part 1479 1006 2023 2.375 0.444 0.120 0.030 11 1.9 S_precentral-sup-part 924 635 1298 2.247 0.556 0.157 0.050 17 1.8 S_suborbital 2154 1433 3307 2.448 0.373 0.146 0.048 30 4.0 S_subparietal 2291 1554 3233 2.454 0.416 0.113 0.031 20 2.6 S_temporal_inf 6306 4252 10253 2.541 0.439 0.115 0.029 54 7.7 S_temporal_sup 410 274 527 2.330 0.410 0.106 0.032 2 0.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Apr 15 19:08:36 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1336 labels changed using aseg relabeling using gibbs priors... 000: 3397 changed, 171356 examined... 001: 798 changed, 14097 examined... 002: 203 changed, 4244 examined... 003: 91 changed, 1190 examined... 004: 41 changed, 521 examined... 005: 25 changed, 239 examined... 006: 10 changed, 142 examined... 007: 10 changed, 60 examined... 008: 8 changed, 55 examined... 009: 5 changed, 45 examined... 010: 4 changed, 35 examined... 011: 1 changed, 24 examined... 012: 0 changed, 7 examined... 228 labels changed using aseg 000: 66 total segments, 33 labels (273 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 892 vertices marked for relabeling... 892 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 6 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Apr 15 19:09:42 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab nmr01002 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1994 1326 3626 2.692 0.554 0.144 0.036 32 2.9 caudalanteriorcingulate 4725 3047 8951 2.628 0.509 0.128 0.044 56 8.1 caudalmiddlefrontal 3606 2317 4861 2.002 0.532 0.153 0.053 55 7.9 cuneus 844 552 2261 3.224 0.737 0.136 0.048 9 1.7 entorhinal 5898 3918 11321 2.611 0.526 0.138 0.048 94 10.3 fusiform 8779 5773 15973 2.496 0.496 0.136 0.043 130 15.3 inferiorparietal 6841 4523 14657 2.773 0.728 0.137 0.054 135 15.5 inferiortemporal 2006 1325 3286 2.453 0.768 0.168 0.243 465 5.6 isthmuscingulate 9262 5879 14800 2.311 0.737 0.154 0.070 243 27.8 lateraloccipital 5421 3563 9617 2.487 0.667 0.159 0.082 118 16.2 lateralorbitofrontal 5848 3897 8176 1.985 0.603 0.164 0.066 108 15.6 lingual 2815 1824 4622 2.282 0.736 0.149 0.064 70 7.2 medialorbitofrontal 7580 4987 18610 3.097 0.817 0.142 0.051 130 16.5 middletemporal 1514 968 2613 2.412 0.648 0.118 0.039 31 2.6 parahippocampal 2219 1382 3405 2.349 0.512 0.122 0.063 54 6.2 paracentral 2372 1559 4542 2.601 0.454 0.131 0.039 30 3.7 parsopercularis 1230 815 2424 2.464 0.516 0.148 0.053 22 2.5 parsorbitalis 3045 1994 5598 2.488 0.487 0.136 0.040 44 5.0 parstriangularis 2504 1605 2583 1.711 0.432 0.150 0.079 53 9.3 pericalcarine 8630 5468 12904 2.175 0.630 0.128 0.042 129 15.4 postcentral 2039 1385 3519 2.383 0.465 0.150 0.049 44 4.3 posteriorcingulate 8726 5437 15755 2.582 0.658 0.142 0.081 317 28.3 precentral 7615 5050 13262 2.476 0.488 0.155 0.060 134 16.5 precuneus 2140 1415 3633 2.426 0.487 0.152 0.102 212 9.2 rostralanteriorcingulate 8678 5654 15268 2.381 0.499 0.143 0.049 143 16.5 rostralmiddlefrontal 15311 10238 32771 2.763 0.661 0.148 0.071 484 33.7 superiorfrontal 8071 5167 12010 2.160 0.468 0.140 0.047 119 15.1 superiorparietal 9849 6458 21559 2.971 0.740 0.131 0.071 233 38.1 superiortemporal 8076 5359 14316 2.496 0.476 0.131 0.040 112 13.0 supramarginal 1080 656 1684 2.307 0.513 0.139 0.049 15 2.4 transversetemporal 3425 2210 6766 3.057 0.729 0.130 0.079 81 8.3 insula #-------------------------------------------- #@# Tessellate rh Fri Apr 15 19:10:03 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 12 (out of 343297: 0.003496) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 13 vertices, 18 faces slice 30: 3524 vertices, 3726 faces slice 40: 12191 vertices, 12543 faces slice 50: 24263 vertices, 24721 faces slice 60: 37970 vertices, 38423 faces slice 70: 50740 vertices, 51184 faces slice 80: 63449 vertices, 63848 faces slice 90: 76677 vertices, 77126 faces slice 100: 89742 vertices, 90186 faces slice 110: 102644 vertices, 103108 faces slice 120: 115080 vertices, 115532 faces slice 130: 126417 vertices, 126823 faces slice 140: 136806 vertices, 137193 faces slice 150: 145819 vertices, 146191 faces slice 160: 153286 vertices, 153555 faces slice 170: 159585 vertices, 159818 faces slice 180: 165524 vertices, 165760 faces slice 190: 169604 vertices, 169783 faces slice 200: 171064 vertices, 171108 faces slice 210: 171064 vertices, 171108 faces slice 220: 171064 vertices, 171108 faces slice 230: 171064 vertices, 171108 faces slice 240: 171064 vertices, 171108 faces slice 250: 171064 vertices, 171108 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... 171064 voxel in cpt #1: X=-44 [v=171064,e=513324,f=342216] located at (31.930441, -29.514544, 25.405790) For the whole surface: X=-44 [v=171064,e=513324,f=342216] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Apr 15 19:10:12 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 15 19:10:18 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts avg radius = 50.9 mm, total surface area = 89972 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri Apr 15 19:11:11 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.53 (0.00-->5.85) (max @ vno 73619 --> 74940) face area 0.02 +- 0.03 (-0.22-->0.64) scaling brain by 0.281... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.683, avgs=0 005/300: dt: 0.9000, rms radial error=176.428, avgs=0 010/300: dt: 0.9000, rms radial error=175.871, avgs=0 015/300: dt: 0.9000, rms radial error=175.139, avgs=0 020/300: dt: 0.9000, rms radial error=174.306, avgs=0 025/300: dt: 0.9000, rms radial error=173.414, avgs=0 030/300: dt: 0.9000, rms radial error=172.492, avgs=0 035/300: dt: 0.9000, rms radial error=171.553, avgs=0 040/300: dt: 0.9000, rms radial error=170.607, avgs=0 045/300: dt: 0.9000, rms radial error=169.658, avgs=0 050/300: dt: 0.9000, rms radial error=168.711, avgs=0 055/300: dt: 0.9000, rms radial error=167.766, avgs=0 060/300: dt: 0.9000, rms radial error=166.826, avgs=0 065/300: dt: 0.9000, rms radial error=165.889, avgs=0 070/300: dt: 0.9000, rms radial error=164.957, avgs=0 075/300: dt: 0.9000, rms radial error=164.031, avgs=0 080/300: dt: 0.9000, rms radial error=163.109, avgs=0 085/300: dt: 0.9000, rms radial error=162.193, avgs=0 090/300: dt: 0.9000, rms radial error=161.281, avgs=0 095/300: dt: 0.9000, rms radial error=160.375, avgs=0 100/300: dt: 0.9000, rms radial error=159.474, avgs=0 105/300: dt: 0.9000, rms radial error=158.578, avgs=0 110/300: dt: 0.9000, rms radial error=157.688, avgs=0 115/300: dt: 0.9000, rms radial error=156.803, avgs=0 120/300: dt: 0.9000, rms radial error=155.923, avgs=0 125/300: dt: 0.9000, rms radial error=155.047, avgs=0 130/300: dt: 0.9000, rms radial error=154.177, avgs=0 135/300: dt: 0.9000, rms radial error=153.311, avgs=0 140/300: dt: 0.9000, rms radial error=152.450, avgs=0 145/300: dt: 0.9000, rms radial error=151.594, avgs=0 150/300: dt: 0.9000, rms radial error=150.743, avgs=0 155/300: dt: 0.9000, rms radial error=149.896, avgs=0 160/300: dt: 0.9000, rms radial error=149.054, avgs=0 165/300: dt: 0.9000, rms radial error=148.216, avgs=0 170/300: dt: 0.9000, rms radial error=147.384, avgs=0 175/300: dt: 0.9000, rms radial error=146.555, avgs=0 180/300: dt: 0.9000, rms radial error=145.732, avgs=0 185/300: dt: 0.9000, rms radial error=144.913, avgs=0 190/300: dt: 0.9000, rms radial error=144.098, avgs=0 195/300: dt: 0.9000, rms radial error=143.288, avgs=0 200/300: dt: 0.9000, rms radial error=142.482, avgs=0 205/300: dt: 0.9000, rms radial error=141.681, avgs=0 210/300: dt: 0.9000, rms radial error=140.884, avgs=0 215/300: dt: 0.9000, rms radial error=140.091, avgs=0 220/300: dt: 0.9000, rms radial error=139.303, avgs=0 225/300: dt: 0.9000, rms radial error=138.519, avgs=0 230/300: dt: 0.9000, rms radial error=137.740, avgs=0 235/300: dt: 0.9000, rms radial error=136.964, avgs=0 240/300: dt: 0.9000, rms radial error=136.194, avgs=0 245/300: dt: 0.9000, rms radial error=135.427, avgs=0 250/300: dt: 0.9000, rms radial error=134.665, avgs=0 255/300: dt: 0.9000, rms radial error=133.907, avgs=0 260/300: dt: 0.9000, rms radial error=133.154, avgs=0 265/300: dt: 0.9000, rms radial error=132.404, avgs=0 270/300: dt: 0.9000, rms radial error=131.659, avgs=0 275/300: dt: 0.9000, rms radial error=130.918, avgs=0 280/300: dt: 0.9000, rms radial error=130.181, avgs=0 285/300: dt: 0.9000, rms radial error=129.448, avgs=0 290/300: dt: 0.9000, rms radial error=128.719, avgs=0 295/300: dt: 0.9000, rms radial error=127.994, avgs=0 300/300: dt: 0.9000, rms radial error=127.273, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20657.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3698.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 421.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00589 epoch 4 (K=640.0), pass 1, starting sse = 29.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/18 = 0.00983 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Apr 15 19:18:21 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=171064, nf=342216, ne=513324, 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... 3535 ambiguous faces found in tessellation segmenting defects... 36 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 36 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4088 (-4.7044) -vertex loglikelihood: -6.1950 (-3.0975) -normal dot loglikelihood: -3.6422 (-3.6422) -quad curv loglikelihood: -6.4380 (-3.2190) Total Loglikelihood : -25.6840 CORRECTING DEFECT 0 (vertices=10, convex hull=34) After retessellation of defect 0, euler #=-32 (168843,505537,336662) : difference with theory (-33) = -1 CORRECTING DEFECT 1 (vertices=38, convex hull=51) After retessellation of defect 1, euler #=-31 (168848,505574,336695) : difference with theory (-32) = -1 CORRECTING DEFECT 2 (vertices=29, convex hull=50) After retessellation of defect 2, euler #=-30 (168856,505617,336731) : difference with theory (-31) = -1 CORRECTING DEFECT 3 (vertices=107, convex hull=88) After retessellation of defect 3, euler #=-29 (168880,505725,336816) : difference with theory (-30) = -1 CORRECTING DEFECT 4 (vertices=247, convex hull=134) After retessellation of defect 4, euler #=-28 (168940,505972,337004) : difference with theory (-29) = -1 CORRECTING DEFECT 5 (vertices=91, convex hull=87) After retessellation of defect 5, euler #=-27 (168966,506090,337097) : difference with theory (-28) = -1 CORRECTING DEFECT 6 (vertices=90, convex hull=126) After retessellation of defect 6, euler #=-26 (168996,506235,337213) : difference with theory (-27) = -1 CORRECTING DEFECT 7 (vertices=11, convex hull=26) After retessellation of defect 7, euler #=-25 (168999,506250,337226) : difference with theory (-26) = -1 CORRECTING DEFECT 8 (vertices=6, convex hull=28) After retessellation of defect 8, euler #=-24 (169002,506267,337241) : difference with theory (-25) = -1 CORRECTING DEFECT 9 (vertices=14, convex hull=25) After retessellation of defect 9, euler #=-23 (169007,506293,337263) : difference with theory (-24) = -1 CORRECTING DEFECT 10 (vertices=26, convex hull=40) After retessellation of defect 10, euler #=-22 (169023,506353,337308) : difference with theory (-23) = -1 CORRECTING DEFECT 11 (vertices=24, convex hull=64) After retessellation of defect 11, euler #=-21 (169034,506411,337356) : difference with theory (-22) = -1 CORRECTING DEFECT 12 (vertices=20, convex hull=43) After retessellation of defect 12, euler #=-20 (169044,506456,337392) : difference with theory (-21) = -1 CORRECTING DEFECT 13 (vertices=6, convex hull=21) After retessellation of defect 13, euler #=-19 (169047,506472,337406) : difference with theory (-20) = -1 CORRECTING DEFECT 14 (vertices=54, convex hull=67) After retessellation of defect 14, euler #=-18 (169070,506568,337480) : difference with theory (-19) = -1 CORRECTING DEFECT 15 (vertices=609, convex hull=387) After retessellation of defect 15, euler #=-17 (169158,507041,337866) : difference with theory (-18) = -1 CORRECTING DEFECT 16 (vertices=60, convex hull=87) normal vector of length zero at vertex 170256 with 3 faces normal vector of length zero at vertex 170256 with 3 faces After retessellation of defect 16, euler #=-16 (169191,507177,337970) : difference with theory (-17) = -1 CORRECTING DEFECT 17 (vertices=6, convex hull=14) After retessellation of defect 17, euler #=-15 (169192,507182,337975) : difference with theory (-16) = -1 CORRECTING DEFECT 18 (vertices=28, convex hull=67) After retessellation of defect 18, euler #=-14 (169202,507239,338023) : difference with theory (-15) = -1 CORRECTING DEFECT 19 (vertices=29, convex hull=26) After retessellation of defect 19, euler #=-13 (169210,507270,338047) : difference with theory (-14) = -1 CORRECTING DEFECT 20 (vertices=11, convex hull=28) After retessellation of defect 20, euler #=-12 (169211,507281,338058) : difference with theory (-13) = -1 CORRECTING DEFECT 21 (vertices=88, convex hull=107) After retessellation of defect 21, euler #=-12 (169255,507468,338201) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=11, convex hull=24) After retessellation of defect 22, euler #=-11 (169260,507493,338222) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=15, convex hull=14) After retessellation of defect 23, euler #=-10 (169262,507501,338229) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=59, convex hull=50) After retessellation of defect 24, euler #=-9 (169273,507548,338266) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=27, convex hull=36) After retessellation of defect 25, euler #=-8 (169281,507585,338296) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=47, convex hull=66) After retessellation of defect 26, euler #=-7 (169308,507697,338382) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=71, convex hull=91) After retessellation of defect 27, euler #=-6 (169348,507860,338506) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=52, convex hull=43) After retessellation of defect 28, euler #=-5 (169352,507890,338533) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=54) After retessellation of defect 29, euler #=-4 (169361,507939,338574) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=82, convex hull=118) After retessellation of defect 30, euler #=-3 (169421,508169,338745) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=56, convex hull=76) After retessellation of defect 31, euler #=-2 (169443,508268,338823) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=26, convex hull=28) After retessellation of defect 32, euler #=-1 (169447,508290,338842) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=45, convex hull=33) After retessellation of defect 33, euler #=0 (169449,508311,338862) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=60, convex hull=48) After retessellation of defect 34, euler #=1 (169456,508353,338898) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=43, convex hull=31) After retessellation of defect 35, euler #=2 (169459,508371,338914) : 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-->12.85) (max @ vno 29126 --> 46123) 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-->12.85) (max @ vno 29126 --> 46123) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 146 mutations (35.9%), 261 crossovers (64.1%), 149 vertices were eliminated building final representation... 1605 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=169459, nf=338914, ne=508371, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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: 229 intersecting 001: 12 intersecting 002: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 169459 - 508371 + 338914 = 2 --> 0 holes F =2V-4: 338914 = 338918-4 (0) 2E=3F: 1016742 = 1016742 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 54 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Apr 15 19:43:59 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs nmr01002 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.69) (max @ vno 29126 --> 46123) face area 0.28 +- 0.12 (0.00-->2.46) mean absolute distance = 0.69 +- 0.90 4495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.5, 454 (454) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %74 local maxima, %22 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.06-->5.06) (max @ vno 106389 --> 106390) face area 0.28 +- 0.13 (0.00-->2.48) mean absolute distance = 0.35 +- 0.60 3929 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6338009.0, rms=10.07 001: dt: 0.5000, sse=7206390.0, rms=7.130 (0.000%) 002: dt: 0.5000, sse=7729556.0, rms=5.451 (0.000%) 003: dt: 0.5000, sse=8169330.5, rms=4.531 (0.000%) 004: dt: 0.5000, sse=8451311.0, rms=3.997 (0.000%) 005: dt: 0.5000, sse=8597256.0, rms=3.773 (0.000%) 006: dt: 0.5000, sse=8690250.0, rms=3.601 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8717640.0, rms=3.552 (0.000%) 008: dt: 0.2500, sse=5379594.5, rms=2.585 (0.000%) 009: dt: 0.2500, sse=4912662.0, rms=2.317 (0.000%) 010: dt: 0.2500, sse=4717352.5, rms=2.214 (0.000%) 011: dt: 0.2500, sse=4640247.0, rms=2.136 (0.000%) 012: dt: 0.2500, sse=4595322.0, rms=2.071 (0.000%) 013: dt: 0.2500, sse=4564673.5, rms=2.016 (0.000%) 014: dt: 0.2500, sse=4543605.0, rms=1.960 (0.000%) 015: dt: 0.2500, sse=4531133.5, rms=1.909 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4508915.0, rms=1.861 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4454550.5, rms=1.820 (0.000%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.4, 338 (248) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.3 (%27.5))] %82 local maxima, %14 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 (0.05-->5.54) (max @ vno 106389 --> 106390) face area 0.35 +- 0.16 (0.00-->3.51) mean absolute distance = 0.26 +- 0.39 4779 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5175222.5, rms=4.57 018: dt: 0.5000, sse=5585276.0, rms=2.983 (0.000%) rms = 3.03, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5204607.0, rms=2.412 (0.000%) 020: dt: 0.2500, sse=5044381.5, rms=1.949 (0.000%) 021: dt: 0.2500, sse=4951668.5, rms=1.734 (0.000%) 022: dt: 0.2500, sse=4901714.0, rms=1.639 (0.000%) 023: dt: 0.2500, sse=4870915.0, rms=1.575 (0.000%) rms = 1.54, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4845074.0, rms=1.536 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4805285.0, rms=1.504 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.8, 299 (177) missing vertices, mean dist -0.1 [0.3 (%73.3)->0.2 (%26.7))] %89 local maxima, % 6 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 (0.03-->5.76) (max @ vno 106389 --> 106390) face area 0.34 +- 0.16 (0.00-->3.82) mean absolute distance = 0.21 +- 0.31 4518 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5062480.5, rms=3.32 026: dt: 0.5000, sse=5360238.5, rms=2.551 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5034442.0, rms=1.836 (0.000%) 028: dt: 0.2500, sse=4945647.0, rms=1.471 (0.000%) 029: dt: 0.2500, sse=4938475.5, rms=1.365 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4913894.5, rms=1.353 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4865666.0, rms=1.323 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.6, 272 (144) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))] %91 local maxima, % 4 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4877999.0, rms=1.63 rms = 1.70, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4949433.0, rms=1.239 (0.000%) 033: dt: 0.2500, sse=5126906.0, rms=1.051 (0.000%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.05, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5119353.0, rms=1.049 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 12 non-cortical segments detected only using segment with 2728 vertices erasing segment 1 (vno[0] = 90007) erasing segment 2 (vno[0] = 91433) erasing segment 3 (vno[0] = 119414) erasing segment 4 (vno[0] = 122463) erasing segment 5 (vno[0] = 124386) erasing segment 6 (vno[0] = 125361) erasing segment 7 (vno[0] = 125559) erasing segment 8 (vno[0] = 133520) erasing segment 9 (vno[0] = 133561) erasing segment 10 (vno[0] = 136412) erasing segment 11 (vno[0] = 169228) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.88) refinement took 7.3 minutes #-------------------------------------------- #@# Smooth2 rh Fri Apr 15 19:51:14 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 Apr 15 19:51:20 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.1 mm, total surface area = 101932 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 223 vertices thresholded to be in k1 ~ [-0.25 0.51], k2 ~ [-0.10 0.07] total integrated curvature = 0.517*4pi (6.495) --> 0 handles ICI = 1.9, FI = 14.7, variation=243.123 149 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 170 vertices thresholded to be in [-0.12 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.014, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Fri Apr 15 19:53:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm nmr01002 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 [ nmr01002/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 335 ] Gb_filter = 0 WARN: S lookup min: -0.306479 WARN: S explicit min: 0.000000 vertex = 156 #-------------------------------------------- #@# Sphere rh Fri Apr 15 19:54:01 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.264... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.61 pass 1: epoch 2 of 3 starting distance error %19.58 unfolding complete - removing small folds... starting distance error %19.49 removing remaining folds... final distance error %19.51 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.09 hours #-------------------------------------------- #@# Surf Reg rh Fri Apr 15 20:59:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.573 curvature mean = 0.016, std = 0.935 curvature mean = 0.026, std = 0.832 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 0.00) sse = 402946.6, tmin=2.9209 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 370425.8, tmin=4.3895 d=8.00 min @ (0.00, 0.00, -2.00) sse = 367567.8, tmin=5.9113 d=4.00 min @ (0.00, 0.00, 1.00) sse = 367468.7, tmin=7.4584 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 366553.4, tmin=9.0187 d=1.00 min @ (0.25, 0.00, 0.00) sse = 366430.9, tmin=10.5483 d=0.50 min @ (0.00, -0.12, 0.12) sse = 366393.1, tmin=12.0723 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 12.07 min curvature mean = -0.005, std = 0.933 curvature mean = 0.013, std = 0.922 curvature mean = -0.010, std = 0.938 curvature mean = 0.006, std = 0.960 curvature mean = -0.012, std = 0.935 curvature mean = 0.002, std = 0.979 2 Reading smoothwm curvature mean = -0.023, std = 0.290 curvature mean = 0.005, std = 0.069 curvature mean = 0.067, std = 0.322 curvature mean = 0.005, std = 0.082 curvature mean = 0.035, std = 0.509 curvature mean = 0.006, std = 0.088 curvature mean = 0.019, std = 0.656 curvature mean = 0.006, std = 0.089 curvature mean = 0.006, std = 0.772 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... #-------------------------------------------- #@# Jacobian white rh Fri Apr 15 21:43:32 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri Apr 15 21:43:35 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Apr 15 21:43:37 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 1298 labels changed using aseg relabeling using gibbs priors... 000: 3533 changed, 169459 examined... 001: 836 changed, 14953 examined... 002: 206 changed, 4659 examined... 003: 76 changed, 1240 examined... 004: 39 changed, 444 examined... 005: 8 changed, 208 examined... 006: 5 changed, 58 examined... 007: 5 changed, 26 examined... 008: 4 changed, 30 examined... 009: 4 changed, 15 examined... 010: 0 changed, 18 examined... 203 labels changed using aseg 000: 104 total segments, 66 labels (511 vertices) changed 001: 40 total segments, 2 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1775 vertices marked for relabeling... 1775 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 5 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Apr 15 21:44:43 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs nmr01002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.69) (max @ vno 29126 --> 46123) face area 0.28 +- 0.12 (0.00-->2.46) mean absolute distance = 0.69 +- 0.90 4509 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 18 points - only 0.00% unknown deleting segment 5 with 151 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown mean border=82.5, 454 (454) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %74 local maxima, %22 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.06-->5.06) (max @ vno 106389 --> 106390) face area 0.28 +- 0.13 (0.00-->2.48) mean absolute distance = 0.35 +- 0.60 3932 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6342178.5, rms=10.06 001: dt: 0.5000, sse=7211722.0, rms=7.129 (0.000%) 002: dt: 0.5000, sse=7735038.5, rms=5.450 (0.000%) 003: dt: 0.5000, sse=8175000.5, rms=4.529 (0.000%) 004: dt: 0.5000, sse=8458191.0, rms=3.995 (0.000%) 005: dt: 0.5000, sse=8603148.0, rms=3.771 (0.000%) 006: dt: 0.5000, sse=8697310.0, rms=3.599 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8725557.0, rms=3.550 (0.000%) 008: dt: 0.2500, sse=5382871.0, rms=2.583 (0.000%) 009: dt: 0.2500, sse=4915726.0, rms=2.316 (0.000%) 010: dt: 0.2500, sse=4720100.5, rms=2.213 (0.000%) 011: dt: 0.2500, sse=4643398.0, rms=2.135 (0.000%) 012: dt: 0.2500, sse=4598748.0, rms=2.070 (0.000%) 013: dt: 0.2500, sse=4567927.5, rms=2.015 (0.000%) 014: dt: 0.2500, sse=4547129.0, rms=1.959 (0.000%) 015: dt: 0.2500, sse=4534806.0, rms=1.908 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4512745.0, rms=1.861 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4458328.0, rms=1.820 (0.000%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 129 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 10 with 10 points - only 50.00% unknown deleting segment 11 with 16 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=85.4, 341 (248) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.3 (%27.5))] %82 local maxima, %14 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 (0.05-->5.54) (max @ vno 106389 --> 106390) face area 0.35 +- 0.16 (0.00-->3.51) mean absolute distance = 0.26 +- 0.39 4776 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5183405.5, rms=4.57 018: dt: 0.5000, sse=5592500.0, rms=2.984 (0.000%) rms = 3.03, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5212002.0, rms=2.413 (0.000%) 020: dt: 0.2500, sse=5053064.5, rms=1.950 (0.000%) 021: dt: 0.2500, sse=4959508.5, rms=1.735 (0.000%) 022: dt: 0.2500, sse=4909543.0, rms=1.640 (0.000%) 023: dt: 0.2500, sse=4878718.5, rms=1.576 (0.000%) rms = 1.54, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4852166.5, rms=1.537 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4812598.0, rms=1.505 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 25 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 140 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 50.00% unknown deleting segment 10 with 16 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group mean border=87.8, 304 (177) missing vertices, mean dist -0.1 [0.3 (%73.3)->0.2 (%26.7))] %89 local maxima, % 6 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 (0.03-->5.76) (max @ vno 106389 --> 106390) face area 0.34 +- 0.16 (0.00-->3.82) mean absolute distance = 0.21 +- 0.31 4517 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5070258.5, rms=3.32 026: dt: 0.5000, sse=5369505.5, rms=2.551 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5043560.5, rms=1.837 (0.000%) 028: dt: 0.2500, sse=4953623.0, rms=1.472 (0.000%) 029: dt: 0.2500, sse=4945798.5, rms=1.366 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4920660.5, rms=1.354 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4872761.5, rms=1.324 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 28 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 139 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown deleting segment 8 with 8 points - only 37.50% unknown deleting segment 9 with 16 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=88.6, 273 (144) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))] %91 local maxima, % 4 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=4885342.0, rms=1.63 rms = 1.70, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4957141.0, rms=1.238 (0.000%) 033: dt: 0.2500, sse=5136260.0, rms=1.049 (0.000%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.05, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5129148.0, rms=1.047 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=61.2, 218 (218) missing vertices, mean dist 1.6 [1.2 (%0.0)->2.6 (%100.0))] %17 local maxima, %42 large gradients and %37 min vals, 2505 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=27881006.0, rms=27.55 001: dt: 0.5000, sse=21338146.0, rms=23.588 (0.000%) 002: dt: 0.5000, sse=16552063.0, rms=20.242 (0.000%) 003: dt: 0.5000, sse=13183127.0, rms=17.495 (0.000%) 004: dt: 0.5000, sse=10982614.0, rms=15.261 (0.000%) 005: dt: 0.5000, sse=9526904.0, rms=13.447 (0.000%) 006: dt: 0.5000, sse=8585024.0, rms=11.947 (0.000%) 007: dt: 0.5000, sse=7938805.5, rms=10.571 (0.000%) 008: dt: 0.5000, sse=7477140.5, rms=9.303 (0.000%) 009: dt: 0.5000, sse=7232781.0, rms=8.103 (0.000%) 010: dt: 0.5000, sse=7059033.5, rms=7.014 (0.000%) 011: dt: 0.5000, sse=7051007.5, rms=6.042 (0.000%) 012: dt: 0.5000, sse=7085286.5, rms=5.274 (0.000%) 013: dt: 0.5000, sse=7179857.5, rms=4.689 (0.000%) 014: dt: 0.5000, sse=7320414.5, rms=4.313 (0.000%) 015: dt: 0.5000, sse=7416581.0, rms=4.023 (0.000%) 016: dt: 0.5000, sse=7465767.0, rms=3.840 (0.000%) 017: dt: 0.5000, sse=7519638.5, rms=3.678 (0.000%) 018: dt: 0.5000, sse=7529441.0, rms=3.607 (0.000%) 019: dt: 0.5000, sse=7580778.5, rms=3.538 (0.000%) rms = 3.52, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7588352.0, rms=3.522 (0.000%) 021: dt: 0.2500, sse=5350677.5, rms=2.853 (0.000%) 022: dt: 0.2500, sse=5135933.0, rms=2.688 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5005851.5, rms=2.675 (0.000%) 024: dt: 0.1250, sse=4768676.0, rms=2.550 (0.000%) rms = 2.53, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4735750.5, rms=2.534 (0.000%) positioning took 3.2 minutes mean border=59.3, 1590 (33) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.6 (%51.9))] %33 local maxima, %33 large gradients and %29 min vals, 831 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=5374306.5, rms=4.29 026: dt: 0.5000, sse=5696649.0, rms=3.631 (0.000%) 027: dt: 0.5000, sse=7388696.5, rms=3.568 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=7074321.0, rms=3.563 (0.000%) 029: dt: 0.2500, sse=5812274.5, rms=2.813 (0.000%) 030: dt: 0.2500, sse=5657612.5, rms=2.602 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5552418.0, rms=2.539 (0.000%) 032: dt: 0.1250, sse=5364612.0, rms=2.450 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5319814.0, rms=2.431 (0.000%) positioning took 1.1 minutes mean border=58.0, 1966 (9) missing vertices, mean dist 0.1 [0.2 (%40.0)->0.4 (%60.0))] %47 local maxima, %19 large gradients and %29 min vals, 987 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=5488984.5, rms=3.24 rms = 3.29, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5293517.5, rms=2.844 (0.000%) 035: dt: 0.2500, sse=5304216.5, rms=2.579 (0.000%) 036: dt: 0.2500, sse=5499368.0, rms=2.503 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5578026.0, rms=2.495 (0.000%) 038: dt: 0.1250, sse=5417729.0, rms=2.383 (0.000%) rms = 2.36, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5427996.0, rms=2.362 (0.000%) positioning took 0.9 minutes mean border=57.3, 3658 (7) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.3 (%54.9))] %50 local maxima, %15 large gradients and %28 min vals, 816 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5460754.0, rms=2.58 rms = 2.96, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5361700.5, rms=2.417 (0.000%) 041: dt: 0.2500, sse=5576891.0, rms=2.354 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5649385.0, rms=2.346 (0.000%) 043: dt: 0.1250, sse=5551497.5, rms=2.266 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5575850.0, rms=2.252 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area.pial vertex spacing 0.99 +- 0.41 (0.06-->7.50) (max @ vno 117005 --> 115834) face area 0.39 +- 0.29 (0.00-->6.74) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed thickness calculation complete, 1224:1871 truncations. 35715 vertices at 0 distance 112003 vertices at 1 distance 103739 vertices at 2 distance 47669 vertices at 3 distance 16817 vertices at 4 distance 5431 vertices at 5 distance 1771 vertices at 6 distance 560 vertices at 7 distance 236 vertices at 8 distance 128 vertices at 9 distance 98 vertices at 10 distance 86 vertices at 11 distance 50 vertices at 12 distance 38 vertices at 13 distance 34 vertices at 14 distance 23 vertices at 15 distance 17 vertices at 16 distance 16 vertices at 17 distance 10 vertices at 18 distance 5 vertices at 19 distance 18 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness positioning took 14.2 minutes #-------------------------------------------- #@# Surf Volume rh Fri Apr 15 21:58:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Fri Apr 15 21:58:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts pctsurfcon --s nmr01002 --rh-only Log file is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts/pctsurfcon.log Fri Apr 15 21:58:54 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-75 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.wm.mgh --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 92619 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.wm.mgh Dim: 169459 1 1 mri_vol2surf --mov /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.gm.mgh --projfrac 0.3 --regheader nmr01002 --cortex srcvol = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/orig.mgz as target reference. Loading label /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Reading surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 110224 Masking with /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.cortex.label Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.gm.mgh Dim: 169459 1 1 mri_concat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.wm.mgh /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/tmp.pctsurfcon.14251/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh --annot nmr01002 rh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh --annot nmr01002 rh aparc --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-75 machine x86_64 user dwakeman UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.w-g.pct.mgh Vertex Area is 0.655322 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1711 1182.978 2 2002 caudalanteriorcingulate 1226 846.324 3 2003 caudalmiddlefrontal 4389 2822.058 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2871 1867.317 6 2006 entorhinal 733 486.950 7 2007 fusiform 5995 3975.253 8 2008 inferiorparietal 11169 7336.178 9 2009 inferiortemporal 5796 3868.840 10 2010 isthmuscingulate 1643 1060.726 11 2011 lateraloccipital 7463 4810.848 12 2012 lateralorbitofrontal 4166 2836.432 13 2013 lingual 5928 3880.728 14 2014 medialorbitofrontal 3107 2124.193 15 2015 middletemporal 6236 4148.621 16 2016 parahippocampal 1310 870.070 17 2017 paracentral 2374 1527.357 18 2018 parsopercularis 2833 1889.481 19 2019 parsorbitalis 1441 957.421 20 2020 parstriangularis 3056 2007.624 21 2021 pericalcarine 2582 1719.278 22 2022 postcentral 6912 4314.819 23 2023 posteriorcingulate 2102 1413.816 24 2024 precentral 9406 5660.451 25 2025 precuneus 9084 5972.379 26 2026 rostralanteriorcingulate 1139 759.083 27 2027 rostralmiddlefrontal 11473 7627.775 28 2028 superiorfrontal 12150 8197.867 29 2029 superiorparietal 10284 6578.268 30 2030 superiortemporal 7088 4670.059 31 2031 supramarginal 7234 4768.718 32 2032 frontalpole 517 347.786 33 2033 temporalpole 699 469.459 34 2034 transversetemporal 844 521.308 35 2035 insula 4236 2841.459 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Apr 15 21:59:04 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1711 1183 2930 2.507 0.451 0.105 0.022 14 1.6 bankssts 1226 846 1959 2.235 0.802 0.148 0.041 20 1.9 caudalanteriorcingulate 4389 2822 8725 2.573 0.673 0.147 0.088 196 12.9 caudalmiddlefrontal 2871 1867 3526 1.768 0.427 0.151 0.058 58 6.8 cuneus 733 487 2651 3.801 0.830 0.151 0.069 13 2.1 entorhinal 5995 3975 12201 2.722 0.558 0.133 0.044 88 9.8 fusiform 11169 7336 19429 2.480 0.514 0.139 0.045 167 20.3 inferiorparietal 5796 3869 13112 2.961 0.729 0.144 0.080 353 22.8 inferiortemporal 1643 1061 2589 2.348 0.746 0.157 0.079 42 3.8 isthmuscingulate 7463 4811 11978 2.296 0.602 0.148 0.048 115 14.8 lateraloccipital 4166 2836 7361 2.325 0.688 0.160 0.063 93 10.2 lateralorbitofrontal 5928 3881 7970 2.031 0.651 0.156 0.075 113 15.7 lingual 3107 2124 5925 2.322 0.717 0.155 0.063 68 7.7 medialorbitofrontal 6236 4149 14940 3.033 0.722 0.142 0.045 107 11.3 middletemporal 1310 870 2450 2.550 0.543 0.123 0.076 23 2.6 parahippocampal 2374 1527 3900 2.477 0.554 0.120 0.037 23 3.9 paracentral 2833 1889 5807 2.775 0.577 0.146 0.082 213 13.0 parsopercularis 1441 957 3860 3.118 0.826 0.174 0.068 32 3.9 parsorbitalis 3056 2008 5988 2.573 0.675 0.140 0.052 50 6.7 parstriangularis 2582 1719 2464 1.520 0.414 0.145 0.050 41 4.8 pericalcarine 6912 4315 10036 2.099 0.667 0.129 0.065 142 20.7 postcentral 2102 1414 3364 2.288 0.679 0.154 0.172 122 4.8 posteriorcingulate 9406 5660 15995 2.594 0.602 0.113 0.047 142 15.4 precentral 9084 5972 14390 2.356 0.545 0.146 0.059 343 25.2 precuneus 1139 759 2028 2.571 0.611 0.147 0.046 20 2.1 rostralanteriorcingulate 11473 7628 20157 2.319 0.634 0.153 0.061 232 26.8 rostralmiddlefrontal 12150 8198 28132 2.812 0.831 0.145 0.083 407 30.3 superiorfrontal 10284 6578 15945 2.223 0.588 0.134 0.092 171 19.5 superiorparietal 7088 4670 14628 2.842 0.563 0.135 0.042 102 12.3 superiortemporal 7234 4769 13464 2.643 0.562 0.139 0.040 105 11.8 supramarginal 517 348 971 2.318 0.728 0.163 0.052 10 1.1 frontalpole 699 469 2525 4.217 0.667 0.158 0.061 11 1.8 temporalpole 844 521 1452 2.433 0.372 0.116 0.031 11 1.0 transversetemporal 4236 2841 8092 2.927 0.724 0.144 0.069 97 11.1 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Apr 15 21:59:24 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/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... 27 labels changed using aseg relabeling using gibbs priors... 000: 11925 changed, 169459 examined... 001: 2872 changed, 45266 examined... 002: 956 changed, 14702 examined... 003: 455 changed, 5219 examined... 004: 225 changed, 2507 examined... 005: 106 changed, 1307 examined... 006: 67 changed, 629 examined... 007: 33 changed, 360 examined... 008: 19 changed, 164 examined... 009: 8 changed, 121 examined... 010: 5 changed, 54 examined... 011: 4 changed, 30 examined... 012: 1 changed, 22 examined... 013: 0 changed, 8 examined... 25 labels changed using aseg 000: 365 total segments, 278 labels (3800 vertices) changed 001: 109 total segments, 23 labels (168 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 183 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1054 vertices marked for relabeling... 1054 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Apr 15 22:00:38 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1466 997 2448 2.121 0.671 0.155 0.063 35 3.8 G_and_S_frontomargin 1680 1159 3554 2.791 0.617 0.151 0.049 27 3.3 G_and_S_occipital_inf 1703 986 2803 2.414 0.611 0.114 0.042 17 3.3 G_and_S_paracentral 1645 1072 3130 2.653 0.481 0.143 0.043 27 2.8 G_and_S_subcentral 1977 1309 3442 2.286 0.581 0.160 0.061 43 5.2 G_and_S_transv_frontopol 3110 2117 5723 2.439 0.754 0.141 0.045 47 5.8 G_and_S_cingul-Ant 1504 1069 3505 2.964 0.913 0.137 0.042 19 2.6 G_and_S_cingul-Mid-Ant 1596 1095 2804 2.541 0.441 0.138 0.041 23 2.4 G_and_S_cingul-Mid-Post 728 458 1457 2.838 0.550 0.186 0.083 18 2.3 G_cingul-Post-dorsal 274 168 550 2.584 0.564 0.157 0.063 6 0.6 G_cingul-Post-ventral 2523 1680 3084 1.697 0.414 0.154 0.058 51 5.7 G_cuneus 1722 1149 4458 2.937 0.616 0.168 0.118 211 12.0 G_front_inf-Opercular 416 281 1157 3.141 0.710 0.162 0.056 8 0.9 G_front_inf-Orbital 1641 1055 3796 2.758 0.600 0.155 0.065 38 4.4 G_front_inf-Triangul 5500 3597 12590 2.642 0.671 0.157 0.062 130 13.5 G_front_middle 7766 5217 19684 2.915 0.740 0.152 0.057 139 18.5 G_front_sup 656 459 1584 3.376 0.595 0.160 0.073 15 1.9 G_Ins_lg_and_S_cent_ins 870 556 2186 3.128 0.734 0.165 0.077 28 2.4 G_insular_short 3131 1965 5940 2.572 0.509 0.149 0.057 58 7.4 G_occipital_middle 2215 1384 3308 2.096 0.536 0.143 0.049 37 4.5 G_occipital_sup 2005 1272 4649 2.896 0.532 0.148 0.068 46 4.3 G_oc-temp_lat-fusifor 3656 2306 5025 1.937 0.674 0.165 0.099 91 10.7 G_oc-temp_med-Lingual 1779 1165 4454 3.144 0.817 0.155 0.100 54 6.3 G_oc-temp_med-Parahip 3116 2099 7910 2.881 0.815 0.180 0.078 90 10.0 G_orbital 3494 2243 7139 2.556 0.511 0.152 0.054 76 7.7 G_pariet_inf-Angular 4016 2609 9088 2.823 0.530 0.155 0.047 78 7.9 G_pariet_inf-Supramar 3183 2015 5793 2.370 0.578 0.142 0.051 60 6.7 G_parietal_sup 2475 1404 3873 2.173 0.594 0.137 0.075 77 8.5 G_postcentral 3665 1897 7620 2.977 0.562 0.107 0.055 84 7.5 G_precentral 4310 2745 7829 2.430 0.552 0.152 0.077 284 17.0 G_precuneus 825 570 2050 2.532 0.694 0.181 0.091 22 3.1 G_rectus 432 299 865 2.744 0.641 0.127 0.061 10 0.8 G_subcallosal 671 412 1316 2.530 0.371 0.129 0.036 11 1.0 G_temp_sup-G_T_transv 2446 1543 6465 3.029 0.504 0.142 0.046 43 4.8 G_temp_sup-Lateral 683 465 1926 3.965 0.889 0.136 0.047 9 1.2 G_temp_sup-Plan_polar 1345 895 2520 2.735 0.514 0.125 0.048 18 2.5 G_temp_sup-Plan_tempo 3336 2171 8662 3.132 0.803 0.155 0.102 314 18.9 G_temporal_inf 3853 2514 10387 3.196 0.676 0.153 0.052 79 8.1 G_temporal_middle 607 394 778 2.138 0.413 0.097 0.020 3 0.5 Lat_Fis-ant-Horizont 419 283 553 2.472 0.339 0.137 0.046 4 0.7 Lat_Fis-ant-Vertical 1910 1273 2612 2.598 0.521 0.135 0.041 22 3.1 Lat_Fis-post 3961 2405 5054 1.956 0.519 0.152 0.055 65 8.9 Pole_occipital 2403 1598 7849 3.590 0.698 0.161 0.076 58 6.6 Pole_temporal 3298 2224 3749 1.902 0.687 0.149 0.051 52 7.3 S_calcarine 3346 2212 3532 1.801 0.585 0.117 0.078 42 10.1 S_central 1286 876 1798 2.162 0.384 0.104 0.023 9 1.2 S_cingul-Marginalis 811 527 1280 2.588 0.498 0.131 0.042 10 1.3 S_circular_insula_ant 1277 870 2015 2.702 0.482 0.094 0.020 6 1.1 S_circular_insula_inf 1804 1221 2618 2.468 0.403 0.107 0.026 10 2.0 S_circular_insula_sup 1308 899 2378 2.626 0.501 0.103 0.021 8 1.2 S_collat_transv_ant 786 521 1195 2.393 0.595 0.156 0.049 12 1.6 S_collat_transv_post 2119 1439 3213 2.356 0.407 0.131 0.039 23 3.3 S_front_inf 3268 2142 4838 2.089 0.564 0.138 0.053 52 5.9 S_front_middle 4022 2593 6746 2.434 0.821 0.157 0.195 403 17.5 S_front_sup 801 519 1131 2.360 0.499 0.136 0.053 10 1.3 S_interm_prim-Jensen 4055 2666 5325 2.143 0.609 0.131 0.162 65 7.6 S_intrapariet_and_P_trans 1004 700 1328 2.145 0.484 0.127 0.031 9 1.2 S_oc_middle_and_Lunatus 1961 1324 2682 2.194 0.407 0.122 0.031 18 2.3 S_oc_sup_and_transversal 497 348 977 2.381 0.553 0.123 0.031 6 0.7 S_occipital_ant 1372 946 2059 2.421 0.360 0.136 0.038 17 2.1 S_oc-temp_lat 2437 1701 3672 2.413 0.332 0.110 0.025 16 2.6 S_oc-temp_med_and_Lingual 458 323 819 2.541 0.695 0.178 0.072 8 1.5 S_orbital_lateral 915 654 1286 2.002 0.790 0.117 0.048 13 1.3 S_orbital_med-olfact 1498 1037 2217 2.034 0.592 0.150 0.053 25 3.1 S_orbital-H_Shaped 3070 2062 3900 2.135 0.526 0.135 0.046 38 5.4 S_parieto_occipital 1851 1193 1615 1.750 0.648 0.149 0.199 123 3.9 S_pericallosal 2717 1850 3494 2.156 0.414 0.119 0.031 24 3.4 S_postcentral 2036 1360 3010 2.471 0.442 0.115 0.027 17 2.4 S_precentral-inf-part 1853 1248 2706 2.436 0.423 0.119 0.031 16 2.2 S_precentral-sup-part 358 247 530 2.253 0.739 0.122 0.030 3 0.4 S_suborbital 2101 1400 3490 2.553 0.483 0.152 0.051 35 4.3 S_subparietal 1346 917 2118 2.639 0.651 0.114 0.027 11 1.6 S_temporal_inf 8431 5721 13025 2.478 0.465 0.122 0.030 85 10.4 S_temporal_sup 398 274 575 2.414 0.404 0.129 0.024 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Apr 15 22:01:01 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 nmr01002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1565 labels changed using aseg relabeling using gibbs priors... 000: 3192 changed, 169459 examined... 001: 804 changed, 13894 examined... 002: 225 changed, 4447 examined... 003: 79 changed, 1345 examined... 004: 34 changed, 465 examined... 005: 20 changed, 212 examined... 006: 15 changed, 123 examined... 007: 12 changed, 76 examined... 008: 9 changed, 69 examined... 009: 5 changed, 47 examined... 010: 1 changed, 27 examined... 011: 1 changed, 7 examined... 012: 4 changed, 7 examined... 013: 1 changed, 12 examined... 014: 0 changed, 7 examined... 313 labels changed using aseg 000: 79 total segments, 46 labels (217 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 69 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 831 vertices marked for relabeling... 831 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 5 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Apr 15 22:02:06 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab nmr01002 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1283 881 2120 2.319 0.852 0.150 0.041 21 2.1 caudalanteriorcingulate 4644 2957 8999 2.539 0.694 0.155 0.165 408 17.6 caudalmiddlefrontal 3611 2380 4349 1.764 0.416 0.148 0.053 66 8.0 cuneus 732 503 2547 3.646 0.863 0.154 0.066 13 2.0 entorhinal 5191 3447 10331 2.686 0.523 0.132 0.045 77 8.4 fusiform 10526 6907 18323 2.490 0.517 0.140 0.045 161 19.4 inferiorparietal 6535 4358 15027 2.975 0.727 0.144 0.076 364 24.3 inferiortemporal 1708 1108 2674 2.339 0.733 0.157 0.082 44 4.1 isthmuscingulate 7908 5098 12587 2.273 0.602 0.146 0.047 119 15.2 lateraloccipital 4938 3374 9366 2.368 0.770 0.164 0.070 123 13.1 lateralorbitofrontal 5944 3894 7984 2.030 0.651 0.156 0.075 114 15.8 lingual 2443 1676 4840 2.387 0.714 0.154 0.065 56 6.3 medialorbitofrontal 7398 4956 16868 2.932 0.714 0.138 0.042 117 12.7 middletemporal 1273 836 2368 2.547 0.550 0.120 0.077 22 2.4 parahippocampal 2492 1606 4182 2.492 0.553 0.121 0.038 26 4.2 paracentral 2951 1969 5947 2.765 0.575 0.146 0.079 215 13.2 parsopercularis 1522 1009 3271 2.661 0.649 0.157 0.055 29 3.4 parsorbitalis 3138 2049 6120 2.582 0.661 0.141 0.053 53 6.8 parstriangularis 2531 1684 2420 1.524 0.414 0.144 0.050 40 4.6 pericalcarine 7552 4745 10968 2.116 0.655 0.128 0.062 148 21.7 postcentral 2171 1465 3508 2.310 0.693 0.153 0.164 121 4.8 posteriorcingulate 9106 5453 15641 2.608 0.602 0.113 0.047 140 15.0 precentral 9179 5987 14651 2.352 0.538 0.144 0.058 344 25.2 precuneus 1281 850 2254 2.515 0.630 0.147 0.045 22 2.2 rostralanteriorcingulate 6797 4561 12782 2.433 0.700 0.155 0.062 136 16.2 rostralmiddlefrontal 16924 11374 35763 2.630 0.820 0.144 0.055 290 36.4 superiorfrontal 8690 5559 13662 2.263 0.591 0.136 0.103 152 17.3 superiorparietal 9341 6170 20034 2.939 0.706 0.136 0.048 152 18.8 superiortemporal 6900 4520 12821 2.654 0.571 0.140 0.042 101 11.3 supramarginal 831 513 1413 2.428 0.367 0.115 0.030 10 1.0 transversetemporal 3657 2476 7119 2.951 0.646 0.136 0.050 59 7.1 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Fri Apr 15 22:02:26 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR nmr01002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.0 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.4 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.1 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.03-->3.60) (max @ vno 74575 --> 75800) face area 0.33 +- 0.15 (0.00-->2.60) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 308 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown deleting segment 7 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 23 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 77 points - only 0.00% unknown 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.60) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5266744.0, rms=0.00 rms = 0.90, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5266744.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 23 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 77 points - only 0.00% unknown 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 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.60) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5266744.0, rms=0.00 rms = 0.90, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5266744.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 23 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 77 points - only 0.00% unknown 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 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.60) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5266744.0, rms=0.00 rms = 0.90, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5266744.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 308 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 23 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 77 points - only 0.00% unknown 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=5266744.0, rms=0.00 rms = 0.90, time step reduction 1 of 3 to 0.250... rms = 0.22, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5266744.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [100.70 185.30], gm=143.00+-14.10, and vertices in regions > 135.9 17262 surface locations found to contain inconsistent values (17226 in, 36 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=542594.9, rms=0.20 001: dt: 0.5000, sse=507817.9, rms=0.196 (0.000%) 002: dt: 0.5000, sse=480700.8, rms=0.184 (0.000%) 003: dt: 0.5000, sse=463871.7, rms=0.175 (0.000%) 004: dt: 0.5000, sse=451129.3, rms=0.166 (0.000%) 005: dt: 0.5000, sse=440823.0, rms=0.157 (0.000%) 006: dt: 0.5000, sse=432768.5, rms=0.149 (0.000%) 007: dt: 0.5000, sse=426514.2, rms=0.142 (0.000%) 008: dt: 0.5000, sse=420982.3, rms=0.136 (0.000%) 009: dt: 0.5000, sse=416145.8, rms=0.130 (0.000%) 010: dt: 0.5000, sse=411800.8, rms=0.125 (0.000%) 011: dt: 0.5000, sse=407980.1, rms=0.120 (0.000%) 012: dt: 0.5000, sse=404682.0, rms=0.116 (0.000%) 013: dt: 0.5000, sse=401887.1, rms=0.112 (0.000%) 014: dt: 0.5000, sse=398986.9, rms=0.109 (0.000%) 015: dt: 0.5000, sse=396505.5, rms=0.106 (0.000%) 016: dt: 0.5000, sse=393998.6, rms=0.103 (0.000%) 017: dt: 0.5000, sse=392007.4, rms=0.101 (0.000%) 018: dt: 0.5000, sse=390158.1, rms=0.099 (0.000%) 019: dt: 0.5000, sse=388154.7, rms=0.097 (0.000%) 020: dt: 0.5000, sse=386105.8, rms=0.095 (0.000%) 021: dt: 0.5000, sse=384324.8, rms=0.094 (0.000%) 022: dt: 0.5000, sse=382820.6, rms=0.093 (0.000%) 023: dt: 0.5000, sse=381297.3, rms=0.092 (0.000%) 024: dt: 0.5000, sse=380090.8, rms=0.091 (0.000%) 025: dt: 0.5000, sse=378666.9, rms=0.090 (0.000%) 026: dt: 0.5000, sse=377339.4, rms=0.090 (0.000%) 027: dt: 0.5000, sse=376457.5, rms=0.090 (0.000%) 028: dt: 0.5000, sse=375290.9, rms=0.089 (0.000%) 029: dt: 0.5000, sse=374137.7, rms=0.089 (0.000%) 030: dt: 0.5000, sse=373023.6, rms=0.089 (0.000%) positioning took 4.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [95.00 185.00], gm=140.00+-15.00, and vertices in regions > 132.5 1182 surface locations found to contain inconsistent values (1140 in, 42 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=37029.4, rms=0.04 031: dt: 0.5000, sse=36895.3, rms=0.039 (0.000%) 032: dt: 0.5000, sse=36811.2, rms=0.036 (0.000%) 033: dt: 0.5000, sse=36753.0, rms=0.034 (0.000%) 034: dt: 0.5000, sse=36708.1, rms=0.032 (0.000%) 035: dt: 0.5000, sse=36690.5, rms=0.030 (0.000%) 036: dt: 0.5000, sse=36679.2, rms=0.029 (0.000%) 037: dt: 0.5000, sse=36670.9, rms=0.028 (0.000%) 038: dt: 0.5000, sse=36689.5, rms=0.027 (0.000%) 039: dt: 0.5000, sse=36680.2, rms=0.025 (0.000%) 040: dt: 0.5000, sse=36686.4, rms=0.024 (0.000%) 041: dt: 0.5000, sse=36704.7, rms=0.023 (0.000%) 042: dt: 0.5000, sse=36712.9, rms=0.022 (0.000%) 043: dt: 0.5000, sse=36721.2, rms=0.022 (0.000%) 044: dt: 0.5000, sse=36719.3, rms=0.021 (0.000%) 045: dt: 0.5000, sse=36727.0, rms=0.020 (0.000%) 046: dt: 0.5000, sse=36720.9, rms=0.019 (0.000%) 047: dt: 0.5000, sse=36740.6, rms=0.019 (0.000%) 048: dt: 0.5000, sse=36748.3, rms=0.018 (0.000%) 049: dt: 0.5000, sse=36761.0, rms=0.018 (0.000%) 050: dt: 0.5000, sse=36767.6, rms=0.017 (0.000%) 051: dt: 0.5000, sse=36786.8, rms=0.017 (0.000%) 052: dt: 0.5000, sse=36812.4, rms=0.017 (0.000%) 053: dt: 0.5000, sse=36830.6, rms=0.016 (0.000%) 054: dt: 0.5000, sse=36832.1, rms=0.016 (0.000%) 055: dt: 0.5000, sse=36824.2, rms=0.016 (0.000%) 056: dt: 0.5000, sse=36830.3, rms=0.016 (0.000%) 057: dt: 0.5000, sse=36833.9, rms=0.016 (0.000%) 058: dt: 0.5000, sse=36828.9, rms=0.016 (0.000%) 059: dt: 0.5000, sse=36835.7, rms=0.016 (0.000%) 060: dt: 0.5000, sse=36838.0, rms=0.016 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [95.30 184.70], gm=140.00+-14.90, and vertices in regions > 132.5 341 surface locations found to contain inconsistent values (300 in, 41 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3706.4, rms=0.01 061: dt: 0.5000, sse=3707.6, rms=0.013 (0.000%) 062: dt: 0.5000, sse=3706.9, rms=0.012 (0.000%) 063: dt: 0.5000, sse=3705.1, rms=0.012 (0.000%) 064: dt: 0.5000, sse=3704.8, rms=0.011 (0.000%) 065: dt: 0.5000, sse=3704.9, rms=0.011 (0.000%) 066: dt: 0.5000, sse=3706.0, rms=0.011 (0.000%) 067: dt: 0.5000, sse=3706.6, rms=0.010 (0.000%) 068: dt: 0.5000, sse=3706.1, rms=0.010 (0.000%) 069: dt: 0.5000, sse=3708.0, rms=0.010 (0.000%) 070: dt: 0.5000, sse=3707.4, rms=0.010 (0.000%) 071: dt: 0.5000, sse=3707.5, rms=0.010 (0.000%) 072: dt: 0.5000, sse=3707.4, rms=0.010 (0.000%) 073: dt: 0.5000, sse=3708.7, rms=0.009 (0.000%) 074: dt: 0.5000, sse=3708.9, rms=0.010 (0.000%) 075: dt: 0.5000, sse=3711.4, rms=0.010 (0.000%) 076: dt: 0.5000, sse=3709.7, rms=0.010 (0.000%) 077: dt: 0.5000, sse=3710.6, rms=0.009 (0.000%) 078: dt: 0.5000, sse=3710.0, rms=0.009 (0.000%) 079: dt: 0.5000, sse=3712.1, rms=0.010 (0.000%) 080: dt: 0.5000, sse=3711.8, rms=0.010 (0.000%) 081: dt: 0.5000, sse=3711.2, rms=0.009 (0.000%) 082: dt: 0.5000, sse=3711.8, rms=0.009 (0.000%) 083: dt: 0.5000, sse=3712.8, rms=0.010 (0.000%) 084: dt: 0.5000, sse=3714.1, rms=0.010 (0.000%) 085: dt: 0.5000, sse=3714.4, rms=0.010 (0.000%) 086: dt: 0.5000, sse=3715.1, rms=0.010 (0.000%) 087: dt: 0.5000, sse=3715.4, rms=0.010 (0.000%) 088: dt: 0.5000, sse=3717.6, rms=0.010 (0.000%) 089: dt: 0.5000, sse=3716.3, rms=0.010 (0.000%) 090: dt: 0.5000, sse=3716.2, rms=0.010 (0.000%) positioning took 3.7 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [95.30 184.70], gm=140.00+-14.90, and vertices in regions > 132.5 79 surface locations found to contain inconsistent values (38 in, 41 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=378.2, rms=0.01 091: dt: 0.5000, sse=378.5, rms=0.007 (0.000%) 092: dt: 0.5000, sse=377.7, rms=0.007 (0.000%) 093: dt: 0.5000, sse=378.6, rms=0.007 (0.000%) 094: dt: 0.5000, sse=378.7, rms=0.007 (0.000%) 095: dt: 0.5000, sse=378.8, rms=0.007 (0.000%) 096: dt: 0.5000, sse=378.2, rms=0.007 (0.000%) 097: dt: 0.5000, sse=378.2, rms=0.007 (0.000%) 098: dt: 0.5000, sse=378.3, rms=0.007 (0.000%) 099: dt: 0.5000, sse=377.8, rms=0.007 (0.000%) 100: dt: 0.5000, sse=378.0, rms=0.007 (0.000%) 101: dt: 0.5000, sse=377.7, rms=0.007 (0.000%) 102: dt: 0.5000, sse=377.8, rms=0.007 (0.000%) 103: dt: 0.5000, sse=378.1, rms=0.007 (0.000%) 104: dt: 0.5000, sse=377.6, rms=0.007 (0.000%) 105: dt: 0.5000, sse=378.1, rms=0.007 (0.000%) 106: dt: 0.5000, sse=377.9, rms=0.007 (0.000%) 107: dt: 0.5000, sse=377.5, rms=0.007 (0.000%) 108: dt: 0.5000, sse=377.5, rms=0.007 (0.000%) 109: dt: 0.5000, sse=377.8, rms=0.007 (0.000%) 110: dt: 0.5000, sse=377.7, rms=0.007 (0.000%) 111: dt: 0.5000, sse=377.6, rms=0.007 (0.000%) 112: dt: 0.5000, sse=377.6, rms=0.007 (0.000%) 113: dt: 0.5000, sse=377.4, rms=0.007 (0.000%) 114: dt: 0.5000, sse=377.7, rms=0.007 (0.000%) 115: dt: 0.5000, sse=377.8, rms=0.007 (0.000%) 116: dt: 0.5000, sse=378.7, rms=0.007 (0.000%) 117: dt: 0.5000, sse=378.4, rms=0.007 (0.000%) 118: dt: 0.5000, sse=379.0, rms=0.007 (0.000%) 119: dt: 0.5000, sse=378.5, rms=0.007 (0.000%) 120: dt: 0.5000, sse=378.6, rms=0.007 (0.000%) positioning took 3.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.area.pial vertex spacing 0.96 +- 0.40 (0.05-->6.32) (max @ vno 117187 --> 117166) face area 0.37 +- 0.28 (0.00-->6.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1069:1176 truncations. 37264 vertices at 0 distance 113594 vertices at 1 distance 106758 vertices at 2 distance 47360 vertices at 3 distance 16336 vertices at 4 distance 5272 vertices at 5 distance 1708 vertices at 6 distance 581 vertices at 7 distance 214 vertices at 8 distance 105 vertices at 9 distance 73 vertices at 10 distance 39 vertices at 11 distance 33 vertices at 12 distance 29 vertices at 13 distance 28 vertices at 14 distance 16 vertices at 15 distance 11 vertices at 16 distance 14 vertices at 17 distance 14 vertices at 18 distance 9 vertices at 19 distance 6 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.thickness positioning took 18.7 minutes /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/scripts cp -v /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.woFLAIR.pial `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial' -> `/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR nmr01002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 77.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 19 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 151 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5089223.0, rms=0.00 rms = 1.16, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=5089223.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 151 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown 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 0.89 +- 0.25 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5089223.0, rms=0.00 rms = 1.16, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=5089223.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 151 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown 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 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=5089223.0, rms=0.00 rms = 1.16, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=5089223.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 151 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown 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=5089223.0, rms=0.00 rms = 1.16, time step reduction 1 of 3 to 0.250... rms = 0.29, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=5089223.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [99.10 184.90], gm=142.00+-14.30, and vertices in regions > 134.8 16909 surface locations found to contain inconsistent values (16816 in, 93 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=547641.8, rms=0.18 001: dt: 0.5000, sse=512711.8, rms=0.177 (0.000%) 002: dt: 0.5000, sse=485381.8, rms=0.165 (0.000%) 003: dt: 0.5000, sse=468449.6, rms=0.156 (0.000%) 004: dt: 0.5000, sse=455595.7, rms=0.147 (0.000%) 005: dt: 0.5000, sse=445658.2, rms=0.139 (0.000%) 006: dt: 0.5000, sse=437359.6, rms=0.132 (0.000%) 007: dt: 0.5000, sse=430918.5, rms=0.126 (0.000%) 008: dt: 0.5000, sse=425396.0, rms=0.120 (0.000%) 009: dt: 0.5000, sse=420836.2, rms=0.115 (0.000%) 010: dt: 0.5000, sse=416488.1, rms=0.110 (0.000%) 011: dt: 0.5000, sse=412748.3, rms=0.106 (0.000%) 012: dt: 0.5000, sse=409130.2, rms=0.103 (0.000%) 013: dt: 0.5000, sse=406294.8, rms=0.100 (0.000%) 014: dt: 0.5000, sse=403491.6, rms=0.097 (0.000%) 015: dt: 0.5000, sse=400755.2, rms=0.095 (0.000%) 016: dt: 0.5000, sse=398385.7, rms=0.093 (0.000%) 017: dt: 0.5000, sse=396164.2, rms=0.092 (0.000%) 018: dt: 0.5000, sse=394068.4, rms=0.090 (0.000%) 019: dt: 0.5000, sse=392213.1, rms=0.089 (0.000%) 020: dt: 0.5000, sse=390548.4, rms=0.088 (0.000%) 021: dt: 0.5000, sse=388986.3, rms=0.088 (0.000%) 022: dt: 0.5000, sse=387179.1, rms=0.087 (0.000%) 023: dt: 0.5000, sse=385567.3, rms=0.087 (0.000%) 024: dt: 0.5000, sse=384189.9, rms=0.087 (0.000%) 025: dt: 0.5000, sse=382906.2, rms=0.087 (0.000%) 026: dt: 0.5000, sse=381388.2, rms=0.087 (0.000%) 027: dt: 0.5000, sse=380030.0, rms=0.087 (0.000%) 028: dt: 0.5000, sse=378791.5, rms=0.087 (0.000%) 029: dt: 0.5000, sse=377725.1, rms=0.087 (0.000%) 030: dt: 0.5000, sse=376805.8, rms=0.087 (0.000%) positioning took 3.9 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.00 175.00], gm=142.00+-11.00, and vertices in regions > 136.5 24572 surface locations found to contain inconsistent values (24265 in, 307 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=40685.2, rms=0.15 031: dt: 0.5000, sse=40199.3, rms=0.139 (0.000%) 032: dt: 0.5000, sse=39801.0, rms=0.128 (0.000%) 033: dt: 0.5000, sse=39718.9, rms=0.120 (0.000%) 034: dt: 0.5000, sse=39823.7, rms=0.112 (0.000%) 035: dt: 0.5000, sse=40007.7, rms=0.107 (0.000%) 036: dt: 0.5000, sse=40181.9, rms=0.102 (0.000%) 037: dt: 0.5000, sse=40345.2, rms=0.097 (0.000%) 038: dt: 0.5000, sse=40488.2, rms=0.093 (0.000%) 039: dt: 0.5000, sse=40615.5, rms=0.090 (0.000%) 040: dt: 0.5000, sse=40775.8, rms=0.087 (0.000%) 041: dt: 0.5000, sse=40895.2, rms=0.084 (0.000%) 042: dt: 0.5000, sse=40998.4, rms=0.081 (0.000%) 043: dt: 0.5000, sse=41077.2, rms=0.078 (0.000%) 044: dt: 0.5000, sse=41147.8, rms=0.075 (0.000%) 045: dt: 0.5000, sse=41217.0, rms=0.073 (0.000%) 046: dt: 0.5000, sse=41292.0, rms=0.070 (0.000%) 047: dt: 0.5000, sse=41371.2, rms=0.068 (0.000%) 048: dt: 0.5000, sse=41408.9, rms=0.066 (0.000%) 049: dt: 0.5000, sse=41476.9, rms=0.064 (0.000%) 050: dt: 0.5000, sse=41531.4, rms=0.062 (0.000%) 051: dt: 0.5000, sse=41585.8, rms=0.060 (0.000%) 052: dt: 0.5000, sse=41642.3, rms=0.058 (0.000%) 053: dt: 0.5000, sse=41703.6, rms=0.056 (0.000%) 054: dt: 0.5000, sse=41750.6, rms=0.054 (0.000%) 055: dt: 0.5000, sse=41790.7, rms=0.053 (0.000%) 056: dt: 0.5000, sse=41830.9, rms=0.051 (0.000%) 057: dt: 0.5000, sse=41883.4, rms=0.050 (0.000%) 058: dt: 0.5000, sse=41930.3, rms=0.048 (0.000%) 059: dt: 0.5000, sse=41986.9, rms=0.047 (0.000%) 060: dt: 0.5000, sse=42039.3, rms=0.046 (0.000%) positioning took 3.8 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.30 174.70], gm=142.00+-10.90, and vertices in regions > 136.5 5330 surface locations found to contain inconsistent values (5049 in, 281 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4812.5, rms=0.06 061: dt: 0.5000, sse=4789.5, rms=0.062 (0.000%) 062: dt: 0.5000, sse=4750.9, rms=0.059 (0.000%) 063: dt: 0.5000, sse=4728.0, rms=0.057 (0.000%) 064: dt: 0.5000, sse=4707.8, rms=0.055 (0.000%) 065: dt: 0.5000, sse=4684.7, rms=0.053 (0.000%) 066: dt: 0.5000, sse=4666.1, rms=0.052 (0.000%) 067: dt: 0.5000, sse=4646.1, rms=0.050 (0.000%) 068: dt: 0.5000, sse=4631.0, rms=0.049 (0.000%) 069: dt: 0.5000, sse=4615.6, rms=0.047 (0.000%) 070: dt: 0.5000, sse=4606.7, rms=0.046 (0.000%) 071: dt: 0.5000, sse=4594.8, rms=0.045 (0.000%) 072: dt: 0.5000, sse=4584.0, rms=0.044 (0.000%) 073: dt: 0.5000, sse=4573.7, rms=0.043 (0.000%) 074: dt: 0.5000, sse=4564.2, rms=0.042 (0.000%) 075: dt: 0.5000, sse=4551.9, rms=0.040 (0.000%) 076: dt: 0.5000, sse=4548.2, rms=0.039 (0.000%) 077: dt: 0.5000, sse=4539.6, rms=0.038 (0.000%) 078: dt: 0.5000, sse=4539.2, rms=0.038 (0.000%) 079: dt: 0.5000, sse=4534.0, rms=0.037 (0.000%) 080: dt: 0.5000, sse=4530.1, rms=0.036 (0.000%) 081: dt: 0.5000, sse=4526.3, rms=0.035 (0.000%) 082: dt: 0.5000, sse=4524.0, rms=0.035 (0.000%) 083: dt: 0.5000, sse=4523.4, rms=0.034 (0.000%) 084: dt: 0.5000, sse=4524.4, rms=0.033 (0.000%) 085: dt: 0.5000, sse=4522.2, rms=0.033 (0.000%) 086: dt: 0.5000, sse=4519.6, rms=0.032 (0.000%) 087: dt: 0.5000, sse=4516.4, rms=0.031 (0.000%) 088: dt: 0.5000, sse=4518.1, rms=0.031 (0.000%) 089: dt: 0.5000, sse=4516.0, rms=0.031 (0.000%) 090: dt: 0.5000, sse=4512.5, rms=0.030 (0.000%) positioning took 3.7 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [109.30 174.70], gm=142.00+-10.90, and vertices in regions > 136.5 670 surface locations found to contain inconsistent values (391 in, 279 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=657.0, rms=0.04 091: dt: 0.5000, sse=654.8, rms=0.037 (0.000%) 092: dt: 0.5000, sse=645.3, rms=0.036 (0.000%) 093: dt: 0.5000, sse=635.8, rms=0.035 (0.000%) 094: dt: 0.5000, sse=627.4, rms=0.034 (0.000%) 095: dt: 0.5000, sse=620.6, rms=0.033 (0.000%) 096: dt: 0.5000, sse=616.0, rms=0.033 (0.000%) 097: dt: 0.5000, sse=611.6, rms=0.033 (0.000%) 098: dt: 0.5000, sse=605.6, rms=0.032 (0.000%) 099: dt: 0.5000, sse=600.2, rms=0.031 (0.000%) 100: dt: 0.5000, sse=599.4, rms=0.031 (0.000%) 101: dt: 0.5000, sse=593.5, rms=0.031 (0.000%) 102: dt: 0.5000, sse=590.2, rms=0.030 (0.000%) 103: dt: 0.5000, sse=583.9, rms=0.030 (0.000%) 104: dt: 0.5000, sse=581.3, rms=0.029 (0.000%) 105: dt: 0.5000, sse=579.1, rms=0.029 (0.000%) 106: dt: 0.5000, sse=575.1, rms=0.029 (0.000%) 107: dt: 0.5000, sse=571.5, rms=0.028 (0.000%) 108: dt: 0.5000, sse=569.2, rms=0.028 (0.000%) 109: dt: 0.5000, sse=568.9, rms=0.028 (0.000%) 110: dt: 0.5000, sse=565.4, rms=0.027 (0.000%) 111: dt: 0.5000, sse=562.5, rms=0.027 (0.000%) 112: dt: 0.5000, sse=558.7, rms=0.027 (0.000%) 113: dt: 0.5000, sse=556.6, rms=0.026 (0.000%) 114: dt: 0.5000, sse=556.8, rms=0.026 (0.000%) 115: dt: 0.5000, sse=555.2, rms=0.026 (0.000%) 116: dt: 0.5000, sse=554.7, rms=0.026 (0.000%) 117: dt: 0.5000, sse=554.5, rms=0.026 (0.000%) 118: dt: 0.5000, sse=552.9, rms=0.026 (0.000%) 119: dt: 0.5000, sse=553.1, rms=0.026 (0.000%) 120: dt: 0.5000, sse=551.1, rms=0.026 (0.000%) positioning took 3.6 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.area.pial vertex spacing 0.97 +- 0.40 (0.04-->7.45) (max @ vno 117005 --> 115834) face area 0.37 +- 0.28 (0.00-->6.60) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed thickness calculation complete, 913:1326 truncations. 38883 vertices at 0 distance 115607 vertices at 1 distance 101736 vertices at 2 distance 45081 vertices at 3 distance 15471 vertices at 4 distance 5052 vertices at 5 distance 1613 vertices at 6 distance 499 vertices at 7 distance 188 vertices at 8 distance 125 vertices at 9 distance 82 vertices at 10 distance 63 vertices at 11 distance 39 vertices at 12 distance 22 vertices at 13 distance 22 vertices at 14 distance 8 vertices at 15 distance 12 vertices at 16 distance 8 vertices at 17 distance 5 vertices at 18 distance 10 vertices at 19 distance 12 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.thickness positioning took 18.4 minutes #-------------------------------------------- #@# Surf Volume lh Fri Apr 15 22:39:48 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 ] #-------------------------------------------- #@# Surf Volume rh Fri Apr 15 22:39:48 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 ] #-------------------------------------------- #@# Cortical ribbon mask Fri Apr 15 22:39:48 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon nmr01002 SUBJECTS_DIR is /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 47 writing volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Apr 15 23:01:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002 sysname Linux hostname compute-0-75 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Computing euler number orig.nofix lheno = -38, rheno = -44 orig.nofix lhholes = 20, rhholes = 23 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 284391.231 284111.000 diff= 280.2 pctdiff= 0.099 rhCtxGM: 275257.704 275164.000 diff= 93.7 pctdiff= 0.034 lhCtxWM: 291224.196 291924.000 diff= -699.8 pctdiff=-0.240 rhCtxWM: 290551.730 290463.000 diff= 88.7 pctdiff= 0.031 SubCortGMVol 65073.000 SupraTentVol 1245936.861 (1244988.000) diff=948.861 pctdiff=0.076 SupraTentVolNotVent 1208163.861 (1207215.000) diff=948.861 pctdiff=0.079 BrainSegVol 1391668.000 (1389201.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1350634.000 (1350074.861) diff=559.139 pctdiff=0.041 BrainSegVolNotVent 1350634.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 19118 19118.055 4 5 Left-Inf-Lat-Vent 520 520.060 5 7 Left-Cerebellum-White-Matter 19700 19699.701 6 8 Left-Cerebellum-Cortex 53472 53472.230 7 10 Left-Thalamus-Proper 8963 8962.595 8 11 Left-Caudate 3573 3573.187 9 12 Left-Putamen 6421 6421.121 10 13 Left-Pallidum 1439 1438.815 11 14 3rd-Ventricle 722 721.945 12 15 4th-Ventricle 1958 1957.972 13 16 Brain-Stem 27112 27112.328 14 17 Left-Hippocampus 4400 4400.408 15 18 Left-Amygdala 1787 1786.623 16 24 CSF 902 902.354 17 26 Left-Accumbens-area 573 573.266 18 28 Left-VentralDC 4634 4634.012 19 30 Left-vessel 220 219.571 20 31 Left-choroid-plexus 1494 1493.786 23 43 Right-Lateral-Ventricle 14433 14432.729 24 44 Right-Inf-Lat-Vent 502 502.259 25 46 Right-Cerebellum-White-Matter 18732 18731.957 26 47 Right-Cerebellum-Cortex 53362 53361.777 27 49 Right-Thalamus-Proper 7901 7900.568 28 50 Right-Caudate 3964 3964.413 29 51 Right-Putamen 5970 5970.317 30 52 Right-Pallidum 1727 1727.467 31 53 Right-Hippocampus 5094 5093.581 32 54 Right-Amygdala 1979 1978.811 33 58 Right-Accumbens-area 715 714.996 34 60 Right-VentralDC 4636 4636.441 35 62 Right-vessel 265 264.728 36 63 Right-choroid-plexus 1793 1792.552 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1813 1813.132 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 39 39.252 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 275 274.977 45 251 CC_Posterior 1374 1374.238 46 252 CC_Mid_Posterior 547 546.627 47 253 CC_Central 503 502.871 48 254 CC_Mid_Anterior 605 604.529 49 255 CC_Anterior 1351 1351.204 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Apr 15 23:02:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --volmask SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 557575 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 557575 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Apr 15 23:05:56 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_aparc2aseg --s nmr01002 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects subject nmr01002 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading lh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial Loading lh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading rh pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial Loading rh annotations from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/ribbon.mgz Loading filled from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9213 vertices from left hemi Ripped 10262 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 = 1137180 Used brute-force search on 540 voxels Fixing Parahip LH WM Found 29 clusters 0 k 1.000000 1 k 1.000000 2 k 2302.000000 3 k 4.000000 4 k 4.000000 5 k 2.000000 6 k 9.000000 7 k 2.000000 8 k 1.000000 9 k 2.000000 10 k 4.000000 11 k 4.000000 12 k 1.000000 13 k 1.000000 14 k 2.000000 15 k 2.000000 16 k 5.000000 17 k 4.000000 18 k 2.000000 19 k 1.000000 20 k 1.000000 21 k 1.000000 22 k 1.000000 23 k 8.000000 24 k 6.000000 25 k 59.000000 26 k 2.000000 27 k 1.000000 28 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 2206.000000 4 k 30.000000 5 k 1.000000 6 k 3.000000 7 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject nmr01002 --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject nmr01002 --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-75 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 284391.231 284111.000 diff= 280.2 pctdiff= 0.099 rhCtxGM: 275257.704 275164.000 diff= 93.7 pctdiff= 0.034 lhCtxWM: 291224.196 291924.000 diff= -699.8 pctdiff=-0.240 rhCtxWM: 290551.730 290463.000 diff= 88.7 pctdiff= 0.031 SubCortGMVol 65073.000 SupraTentVol 1245936.861 (1244988.000) diff=948.861 pctdiff=0.076 SupraTentVolNotVent 1208163.861 (1207215.000) diff=948.861 pctdiff=0.079 BrainSegVol 1391668.000 (1389201.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1350634.000 (1350074.861) diff=559.139 pctdiff=0.041 BrainSegVolNotVent 1350634.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2684 2684.245 2 3002 wm-lh-caudalanteriorcingulate 3238 3237.823 3 3003 wm-lh-caudalmiddlefrontal 8888 8888.001 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2638 2638.340 6 3006 wm-lh-entorhinal 1249 1249.379 7 3007 wm-lh-fusiform 8684 8683.943 8 3008 wm-lh-inferiorparietal 12352 12352.467 9 3009 wm-lh-inferiortemporal 8531 8531.092 10 3010 wm-lh-isthmuscingulate 5388 5387.755 11 3011 wm-lh-lateraloccipital 12182 12182.030 12 3012 wm-lh-lateralorbitofrontal 7918 7917.752 13 3013 wm-lh-lingual 6863 6863.447 14 3014 wm-lh-medialorbitofrontal 4781 4780.878 15 3015 wm-lh-middletemporal 7753 7753.443 16 3016 wm-lh-parahippocampal 2283 2283.130 17 3017 wm-lh-paracentral 3529 3529.417 18 3018 wm-lh-parsopercularis 4117 4116.991 19 3019 wm-lh-parsorbitalis 1161 1161.232 20 3020 wm-lh-parstriangularis 3967 3966.732 21 3021 wm-lh-pericalcarine 3093 3092.974 22 3022 wm-lh-postcentral 9604 9603.519 23 3023 wm-lh-posteriorcingulate 5082 5081.928 24 3024 wm-lh-precentral 14860 14860.157 25 3025 wm-lh-precuneus 13407 13407.077 26 3026 wm-lh-rostralanteriorcingulate 3704 3704.267 27 3027 wm-lh-rostralmiddlefrontal 17603 17602.977 28 3028 wm-lh-superiorfrontal 22785 22785.176 29 3029 wm-lh-superiorparietal 14973 14973.005 30 3030 wm-lh-superiortemporal 10732 10732.082 31 3031 wm-lh-supramarginal 12799 12799.281 32 3032 wm-lh-frontalpole 296 295.537 33 3033 wm-lh-temporalpole 1024 1023.531 34 3034 wm-lh-transversetemporal 1045 1044.774 35 3035 wm-lh-insula 10405 10404.585 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 2958 2957.606 120 4002 wm-rh-caudalanteriorcingulate 3463 3463.125 121 4003 wm-rh-caudalmiddlefrontal 6367 6367.453 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2782 2782.231 124 4006 wm-rh-entorhinal 1001 1001.175 125 4007 wm-rh-fusiform 7922 7921.902 126 4008 wm-rh-inferiorparietal 17376 17375.695 127 4009 wm-rh-inferiortemporal 8374 8373.602 128 4010 wm-rh-isthmuscingulate 3898 3897.867 129 4011 wm-rh-lateraloccipital 8929 8929.303 130 4012 wm-rh-lateralorbitofrontal 7635 7634.811 131 4013 wm-rh-lingual 7385 7384.667 132 4014 wm-rh-medialorbitofrontal 3734 3734.282 133 4015 wm-rh-middletemporal 7168 7167.550 134 4016 wm-rh-parahippocampal 2262 2262.382 135 4017 wm-rh-paracentral 4869 4868.886 136 4018 wm-rh-parsopercularis 4903 4903.288 137 4019 wm-rh-parsorbitalis 1985 1984.911 138 4020 wm-rh-parstriangularis 4783 4783.045 139 4021 wm-rh-pericalcarine 3559 3558.781 140 4022 wm-rh-postcentral 8066 8065.835 141 4023 wm-rh-posteriorcingulate 5258 5257.889 142 4024 wm-rh-precentral 15920 15920.214 143 4025 wm-rh-precuneus 14660 14659.681 144 4026 wm-rh-rostralanteriorcingulate 2989 2989.454 145 4027 wm-rh-rostralmiddlefrontal 17585 17584.504 146 4028 wm-rh-superiorfrontal 20218 20218.291 147 4029 wm-rh-superiorparietal 14077 14076.578 148 4030 wm-rh-superiortemporal 9855 9855.320 149 4031 wm-rh-supramarginal 11564 11563.930 150 4032 wm-rh-frontalpole 512 512.463 151 4033 wm-rh-temporalpole 809 809.428 152 4034 wm-rh-transversetemporal 744 744.482 153 4035 wm-rh-insula 11329 11329.292 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 41716 41716.078 237 5002 Right-UnsegmentedWhiteMatter 42957 42956.703 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label #-------------------------------------------- #@# BA Labels lh Fri Apr 15 23:13:40 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.label --trgsubject nmr01002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 644 Checking for and removing duplicates Writing label file ./lh.BA1.label 4773 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.label --trgsubject nmr01002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 822 Checking for and removing duplicates Writing label file ./lh.BA2.label 8731 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.label --trgsubject nmr01002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 478 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.label --trgsubject nmr01002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 880 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6863 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.label --trgsubject nmr01002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 888 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6672 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.label --trgsubject nmr01002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 645 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4715 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.label --trgsubject nmr01002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 3039 Checking for and removing duplicates Writing label file ./lh.BA6.label 16628 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.label --trgsubject nmr01002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 708 Checking for and removing duplicates Writing label file ./lh.BA44.label 4889 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.label --trgsubject nmr01002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 1709 Checking for and removing duplicates Writing label file ./lh.BA45.label 5131 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.label --trgsubject nmr01002 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 2285 Checking for and removing duplicates Writing label file ./lh.V1.label 6926 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.label --trgsubject nmr01002 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 4395 Checking for and removing duplicates Writing label file ./lh.V2.label 12509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.label --trgsubject nmr01002 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 171356 Number of reverse mapping hits = 645 Checking for and removing duplicates Writing label file ./lh.MT.label 2663 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.perirhinal.label --trgsubject nmr01002 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 327 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1526 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 361 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2357 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 305 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2624 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 178 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1727 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1594 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 313 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2225 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.thresh.label --trgsubject nmr01002 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 559 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.thresh.label --trgsubject nmr01002 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1640 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 5045 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.thresh.label --trgsubject nmr01002 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 1879 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5213 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.thresh.label --trgsubject nmr01002 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 171356 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 643 mri_label2label: Done mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-75 machine x86_64 user dwakeman subject nmr01002 hemi lh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 120769 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.BA.annot mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-75 machine x86_64 user dwakeman subject nmr01002 hemi lh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 142545 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab nmr01002 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/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 1481 771 2271 2.211 0.428 0.140 0.061 42 4.1 BA1 4239 2790 6294 2.308 0.461 0.125 0.037 45 6.2 BA2 1232 819 1296 1.927 0.564 0.135 0.047 16 2.1 BA3a 2996 1926 3741 1.878 0.666 0.119 0.037 40 4.4 BA3b 1700 920 2867 2.642 0.620 0.136 0.106 56 8.4 BA4a 1383 900 2142 2.322 0.628 0.161 0.175 184 8.5 BA4p 12306 7942 24910 2.706 0.587 0.139 0.073 288 26.3 BA6 2780 1843 5163 2.613 0.378 0.130 0.039 36 4.2 BA44 4258 2818 8060 2.557 0.455 0.145 0.047 69 7.9 BA45 4428 2836 4722 1.664 0.488 0.155 0.072 81 13.7 V1 10059 6436 12715 1.964 0.516 0.165 0.067 192 27.1 V2 2333 1552 4209 2.727 0.690 0.153 0.100 130 11.3 MT 1392 922 3005 2.736 0.837 0.136 0.051 33 3.3 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab nmr01002 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1034 489 1463 2.183 0.416 0.138 0.067 24 3.3 BA1 1673 1106 2721 2.293 0.471 0.121 0.034 28 2.4 BA2 942 628 884 1.823 0.511 0.149 0.052 14 1.8 BA3a 1842 1213 1827 1.531 0.414 0.109 0.031 15 2.3 BA3b 1662 910 2799 2.636 0.626 0.135 0.098 50 6.1 BA4a 1120 749 1733 2.320 0.610 0.179 0.206 183 8.5 BA4p 6951 4352 13019 2.600 0.587 0.134 0.091 203 17.7 BA6 1806 1202 3484 2.619 0.358 0.138 0.042 28 3.1 BA44 1600 1045 3380 2.608 0.416 0.142 0.045 25 2.9 BA45 4715 3022 5050 1.656 0.493 0.156 0.070 87 14.7 V1 4883 3110 5701 1.842 0.489 0.171 0.075 98 14.2 V2 583 396 1125 2.825 0.664 0.133 0.129 88 5.0 MT #-------------------------------------------- #@# BA Labels rh Fri Apr 15 23:18:13 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.label --trgsubject nmr01002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 505 Checking for and removing duplicates Writing label file ./rh.BA1.label 4467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.label --trgsubject nmr01002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 653 Checking for and removing duplicates Writing label file ./rh.BA2.label 7340 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.label --trgsubject nmr01002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4212 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.label --trgsubject nmr01002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 552 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5074 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.label --trgsubject nmr01002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 901 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6648 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.label --trgsubject nmr01002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 557 Checking for and removing duplicates Writing label file ./rh.BA4p.label 5030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.label --trgsubject nmr01002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 2124 Checking for and removing duplicates Writing label file ./rh.BA6.label 14380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.label --trgsubject nmr01002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 1627 Checking for and removing duplicates Writing label file ./rh.BA44.label 8539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.label --trgsubject nmr01002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 1960 Checking for and removing duplicates Writing label file ./rh.BA45.label 7315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.label --trgsubject nmr01002 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 2464 Checking for and removing duplicates Writing label file ./rh.V1.label 7191 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.label --trgsubject nmr01002 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 4345 Checking for and removing duplicates Writing label file ./rh.V2.label 12361 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.label --trgsubject nmr01002 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = nmr01002 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/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 169459 Number of reverse mapping hits = 472 Checking for and removing duplicates Writing label file ./rh.MT.label 2404 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.perirhinal.label --trgsubject nmr01002 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 948 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1017 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2856 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 359 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2542 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 291 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1579 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 1187 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8146 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 390 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.thresh.label --trgsubject nmr01002 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 547 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1725 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.thresh.label --trgsubject nmr01002 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 1638 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4870 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.thresh.label --trgsubject nmr01002 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 2153 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5590 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.thresh.label --trgsubject nmr01002 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = nmr01002 trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white Reading target registration /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 169459 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 322 mri_label2label: Done mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-75 machine x86_64 user dwakeman subject nmr01002 hemi rh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 121151 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.BA.annot mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label cmdline mris_label2annot --s nmr01002 --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-75 machine x86_64 user dwakeman subject nmr01002 hemi rh SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 142306 unhit vertices Writing annot to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab nmr01002 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/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 1066 558 1606 2.156 0.389 0.141 0.048 18 2.5 BA1 3429 2301 4838 2.147 0.410 0.118 0.032 32 4.6 BA2 1012 675 847 1.695 0.473 0.152 0.043 13 1.8 BA3a 2404 1462 2675 1.696 0.650 0.130 0.114 83 13.4 BA3b 2092 1139 3548 2.693 0.510 0.110 0.067 57 5.3 BA4a 1376 878 1895 2.204 0.420 0.103 0.069 13 2.0 BA4p 9211 5836 19058 2.813 0.647 0.128 0.043 121 16.3 BA6 4653 3101 8574 2.642 0.488 0.136 0.065 238 15.7 BA44 5423 3550 9934 2.512 0.528 0.147 0.052 94 11.6 BA45 4900 3082 4762 1.557 0.458 0.145 0.069 87 11.6 V1 9884 6445 12389 1.974 0.573 0.158 0.059 183 23.5 V2 2005 1349 3430 2.529 0.605 0.137 0.040 26 3.2 MT 853 569 2087 3.133 0.834 0.145 0.059 13 1.9 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab nmr01002 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 746 361 972 1.981 0.386 0.138 0.048 12 1.6 BA1 1946 1314 2807 2.086 0.390 0.110 0.029 16 2.2 BA2 900 600 691 1.671 0.420 0.154 0.044 10 1.7 BA3a 1995 1227 1974 1.594 0.628 0.129 0.127 77 12.4 BA3b 1297 686 2130 2.705 0.530 0.121 0.091 38 4.4 BA4a 1100 730 1532 2.202 0.414 0.100 0.074 11 1.3 BA4p 6032 3705 11677 2.764 0.549 0.125 0.041 78 10.2 BA6 1262 854 2740 2.886 0.542 0.157 0.132 192 10.4 BA44 1659 1064 3322 2.657 0.495 0.152 0.062 33 4.0 BA45 4604 2938 4469 1.549 0.450 0.144 0.068 80 10.6 V1 5337 3378 6146 1.817 0.539 0.165 0.063 118 14.1 V2 275 166 506 2.458 0.396 0.145 0.043 4 0.5 MT /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Apr 15 23:22:42 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o nmr01002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject nmr01002. processing subject lh.EC_average... reading output surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1249 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label nmr01002 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/lh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 458 284 1078 2.657 0.764 0.117 0.039 4 0.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Apr 15 23:23:01 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o nmr01002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject nmr01002. processing subject rh.EC_average... reading output surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 1008 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label nmr01002 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/mri/wm.mgz... reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.white... reading input pial surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/surf/rh.pial... reading input white surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002/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 362 242 917 3.252 0.890 0.138 0.054 5 0.7 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Fri Apr 15 16:20:59 EDT 2016 Ended at Fri Apr 15 23:23:19 EDT 2016 #@#%# recon-all-run-time-hours 7.039 recon-all -s nmr01002 finished without error at Fri Apr 15 23:23:19 EDT 2016 New invocation of recon-all Mon Apr 18 16:43:22 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2 /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002_only_wm2 -autorecon2-wm -openmp 8 subjid nmr01002_only_wm2 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux compute-0-54 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 58720256 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 9651432 23225820 4 27540 8574544 -/+ buffers/cache: 1049348 31827904 Swap: 67108860 74364 67034496 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 8 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/18-20:43:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: dwakeman Machine: compute-0-54 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Mon Apr 18 16:43:31 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2917 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 40 seconds. #-------------------------------------------- #@# Mask BFS Mon Apr 18 16:47:13 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1879483 voxels in mask (pct= 11.20) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Apr 18 16:47:15 EDT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-54 machine x86_64 user dwakeman 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 927 values in range Counting number of voxels Found 927 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-54 machine x86_64 user dwakeman input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 0 deletes, 927 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 (105.0): 104.7 +- 6.5 [80.0 --> 125.0] GM (73.0) : 71.8 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.4 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5521 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6051 filled 337 bright non-wm voxels segmented. 3333 diagonally connected voxels added... white matter segmentation took 1.8 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 0.61 minutes reading wm segmentation from wm.seg.mgz... 219 voxels added to wm to prevent paths from MTL structures to cortex 2739 additional wm voxels added 0 additional wm voxels added SEG EDIT: 76008 voxels turned on, 58347 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+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 32 found - 32 modified | TOTAL: 58 pass 2 (xy-): 0 found - 32 modified | TOTAL: 58 pass 1 (yz+): 33 found - 33 modified | TOTAL: 91 pass 2 (yz+): 0 found - 33 modified | TOTAL: 91 pass 1 (yz-): 16 found - 16 modified | TOTAL: 107 pass 2 (yz-): 0 found - 16 modified | TOTAL: 107 pass 1 (xz+): 22 found - 22 modified | TOTAL: 129 pass 2 (xz+): 0 found - 22 modified | TOTAL: 129 pass 1 (xz-): 18 found - 18 modified | TOTAL: 147 pass 2 (xz-): 0 found - 18 modified | TOTAL: 147 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 18 found - 18 modified | TOTAL: 31 pass 2 (+++): 0 found - 18 modified | TOTAL: 31 pass 1 (+++): 12 found - 12 modified | TOTAL: 43 pass 2 (+++): 0 found - 12 modified | TOTAL: 43 pass 1 (+++): 15 found - 15 modified | TOTAL: 58 pass 2 (+++): 0 found - 15 modified | TOTAL: 58 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 84 found - 84 modified | TOTAL: 208 pass 2 (+-): 0 found - 84 modified | TOTAL: 208 pass 1 (--): 91 found - 91 modified | TOTAL: 299 pass 2 (--): 0 found - 91 modified | TOTAL: 299 pass 1 (-+): 104 found - 104 modified | TOTAL: 403 pass 2 (-+): 0 found - 104 modified | TOTAL: 403 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 626 (out of 717426: 0.087256) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 927 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Mon Apr 18 16:49:55 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3639 (min = 350, max = 1400), aspect = 1.41 (min = 0.10, max = 0.75) need search nearby using seed (127, 121, 155), TAL = (1.0, 27.0, 7.0) talairach voxel to voxel transform 0.961 0.080 -0.079 3.033; -0.109 0.873 -0.240 41.374; 0.072 0.194 1.050 -41.403; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 121, 155) --> (1.0, 27.0, 7.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (1.00, 27.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 7.00) SRC: (105.25, 97.89, 152.56) search lh wm seed point around talairach space (-17.00, 27.00, 7.00), SRC: (139.85, 93.96, 155.14) 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 Mon Apr 18 16:50:44 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 19 (out of 347268: 0.005471) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 2944 vertices, 3132 faces slice 40: 10921 vertices, 11278 faces slice 50: 22273 vertices, 22668 faces slice 60: 34740 vertices, 35181 faces slice 70: 47149 vertices, 47532 faces slice 80: 59678 vertices, 60114 faces slice 90: 72395 vertices, 72851 faces slice 100: 85976 vertices, 86438 faces slice 110: 98341 vertices, 98802 faces slice 120: 111100 vertices, 111556 faces slice 130: 123616 vertices, 124049 faces slice 140: 134919 vertices, 135312 faces slice 150: 144969 vertices, 145304 faces slice 160: 153120 vertices, 153436 faces slice 170: 160115 vertices, 160371 faces slice 180: 166375 vertices, 166591 faces slice 190: 171266 vertices, 171444 faces slice 200: 172828 vertices, 172866 faces slice 210: 172828 vertices, 172866 faces slice 220: 172828 vertices, 172866 faces slice 230: 172828 vertices, 172866 faces slice 240: 172828 vertices, 172866 faces slice 250: 172828 vertices, 172866 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... 172828 voxel in cpt #1: X=-38 [v=172828,e=518598,f=345732] located at (-23.818184, -26.572702, 31.230940) For the whole surface: X=-38 [v=172828,e=518598,f=345732] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Apr 18 16:50:52 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Mon Apr 18 16:50:58 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts avg radius = 51.0 mm, total surface area = 90513 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Apr 18 16:51:52 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.54 (0.00-->6.55) (max @ vno 129289 --> 130308) face area 0.02 +- 0.03 (-0.09-->0.52) scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.808, avgs=0 005/300: dt: 0.9000, rms radial error=176.547, avgs=0 010/300: dt: 0.9000, rms radial error=175.989, avgs=0 015/300: dt: 0.9000, rms radial error=175.257, avgs=0 020/300: dt: 0.9000, rms radial error=174.425, avgs=0 025/300: dt: 0.9000, rms radial error=173.535, avgs=0 030/300: dt: 0.9000, rms radial error=172.613, avgs=0 035/300: dt: 0.9000, rms radial error=171.674, avgs=0 040/300: dt: 0.9000, rms radial error=170.728, avgs=0 045/300: dt: 0.9000, rms radial error=169.779, avgs=0 050/300: dt: 0.9000, rms radial error=168.830, avgs=0 055/300: dt: 0.9000, rms radial error=167.885, avgs=0 060/300: dt: 0.9000, rms radial error=166.943, avgs=0 065/300: dt: 0.9000, rms radial error=166.005, avgs=0 070/300: dt: 0.9000, rms radial error=165.073, avgs=0 075/300: dt: 0.9000, rms radial error=164.145, avgs=0 080/300: dt: 0.9000, rms radial error=163.222, avgs=0 085/300: dt: 0.9000, rms radial error=162.304, avgs=0 090/300: dt: 0.9000, rms radial error=161.392, avgs=0 095/300: dt: 0.9000, rms radial error=160.484, avgs=0 100/300: dt: 0.9000, rms radial error=159.581, avgs=0 105/300: dt: 0.9000, rms radial error=158.683, avgs=0 110/300: dt: 0.9000, rms radial error=157.790, avgs=0 115/300: dt: 0.9000, rms radial error=156.902, avgs=0 120/300: dt: 0.9000, rms radial error=156.019, avgs=0 125/300: dt: 0.9000, rms radial error=155.140, avgs=0 130/300: dt: 0.9000, rms radial error=154.267, avgs=0 135/300: dt: 0.9000, rms radial error=153.398, avgs=0 140/300: dt: 0.9000, rms radial error=152.534, avgs=0 145/300: dt: 0.9000, rms radial error=151.675, avgs=0 150/300: dt: 0.9000, rms radial error=150.820, avgs=0 155/300: dt: 0.9000, rms radial error=149.971, avgs=0 160/300: dt: 0.9000, rms radial error=149.125, avgs=0 165/300: dt: 0.9000, rms radial error=148.285, avgs=0 170/300: dt: 0.9000, rms radial error=147.449, avgs=0 175/300: dt: 0.9000, rms radial error=146.618, avgs=0 180/300: dt: 0.9000, rms radial error=145.791, avgs=0 185/300: dt: 0.9000, rms radial error=144.969, avgs=0 190/300: dt: 0.9000, rms radial error=144.152, avgs=0 195/300: dt: 0.9000, rms radial error=143.339, avgs=0 200/300: dt: 0.9000, rms radial error=142.530, avgs=0 205/300: dt: 0.9000, rms radial error=141.726, avgs=0 210/300: dt: 0.9000, rms radial error=140.927, avgs=0 215/300: dt: 0.9000, rms radial error=140.132, avgs=0 220/300: dt: 0.9000, rms radial error=139.341, avgs=0 225/300: dt: 0.9000, rms radial error=138.555, avgs=0 230/300: dt: 0.9000, rms radial error=137.773, avgs=0 235/300: dt: 0.9000, rms radial error=136.996, avgs=0 240/300: dt: 0.9000, rms radial error=136.223, avgs=0 245/300: dt: 0.9000, rms radial error=135.454, avgs=0 250/300: dt: 0.9000, rms radial error=134.690, avgs=0 255/300: dt: 0.9000, rms radial error=133.930, avgs=0 260/300: dt: 0.9000, rms radial error=133.174, avgs=0 265/300: dt: 0.9000, rms radial error=132.422, avgs=0 270/300: dt: 0.9000, rms radial error=131.675, avgs=0 275/300: dt: 0.9000, rms radial error=130.932, avgs=0 280/300: dt: 0.9000, rms radial error=130.193, avgs=0 285/300: dt: 0.9000, rms radial error=129.458, avgs=0 290/300: dt: 0.9000, rms radial error=128.727, avgs=0 295/300: dt: 0.9000, rms radial error=128.001, avgs=0 300/300: dt: 0.9000, rms radial error=127.278, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20908.40 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 = 3769.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 431.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00517 epoch 4 (K=640.0), pass 1, starting sse = 25.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/17 = 0.01369 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Apr 18 16:59:00 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002_only_wm2 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=172828, nf=345732, ne=518598, g=20) 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... 3174 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3257 (-4.6629) -vertex loglikelihood: -6.1497 (-3.0749) -normal dot loglikelihood: -3.6182 (-3.6182) -quad curv loglikelihood: -6.3064 (-3.1532) Total Loglikelihood : -25.4000 CORRECTING DEFECT 0 (vertices=18, convex hull=22) After retessellation of defect 0, euler #=-22 (170915,512130,341193) : difference with theory (-23) = -1 CORRECTING DEFECT 1 (vertices=27, convex hull=75) After retessellation of defect 1, euler #=-21 (170927,512198,341250) : difference with theory (-22) = -1 CORRECTING DEFECT 2 (vertices=69, convex hull=64) After retessellation of defect 2, euler #=-20 (170936,512254,341298) : difference with theory (-21) = -1 CORRECTING DEFECT 3 (vertices=26, convex hull=32) After retessellation of defect 3, euler #=-19 (170940,512276,341317) : difference with theory (-20) = -1 CORRECTING DEFECT 4 (vertices=22, convex hull=61) After retessellation of defect 4, euler #=-18 (170952,512336,341366) : difference with theory (-19) = -1 CORRECTING DEFECT 5 (vertices=80, convex hull=86) After retessellation of defect 5, euler #=-17 (170964,512403,341422) : difference with theory (-18) = -1 CORRECTING DEFECT 6 (vertices=26, convex hull=69) After retessellation of defect 6, euler #=-16 (170979,512475,341480) : difference with theory (-17) = -1 CORRECTING DEFECT 7 (vertices=819, convex hull=349) After retessellation of defect 7, euler #=-16 (171193,513301,342092) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=25, convex hull=31) After retessellation of defect 8, euler #=-15 (171197,513322,342110) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=34) After retessellation of defect 9, euler #=-14 (171202,513350,342134) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=50, convex hull=26) After retessellation of defect 10, euler #=-13 (171207,513374,342154) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-12 (171214,513405,342179) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=363, convex hull=95) After retessellation of defect 12, euler #=-11 (171237,513513,342265) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=10, convex hull=23) After retessellation of defect 13, euler #=-10 (171239,513523,342274) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=9, convex hull=25) After retessellation of defect 14, euler #=-9 (171242,513540,342289) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=79, convex hull=67) After retessellation of defect 15, euler #=-8 (171258,513622,342356) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=32) After retessellation of defect 16, euler #=-7 (171264,513648,342377) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=19) After retessellation of defect 17, euler #=-6 (171265,513657,342386) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=51) After retessellation of defect 18, euler #=-5 (171280,513717,342432) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=76) After retessellation of defect 19, euler #=-4 (171303,513814,342507) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=42, convex hull=50) After retessellation of defect 20, euler #=-3 (171318,513876,342555) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=69) After retessellation of defect 21, euler #=-2 (171329,513934,342603) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=41, convex hull=76) After retessellation of defect 22, euler #=-1 (171350,514030,342679) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=16, convex hull=27) After retessellation of defect 23, euler #=0 (171354,514050,342696) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=8, convex hull=18) After retessellation of defect 24, euler #=1 (171355,514057,342703) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=15, convex hull=15) After retessellation of defect 25, euler #=2 (171356,514062,342708) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (33.6%), 160 crossovers (66.4%), 94 vertices were eliminated building final representation... 1472 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=171356, nf=342708, ne=514062, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.8 minutes 0 defective edges removing intersecting faces 000: 141 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 171356 - 514062 + 342708 = 2 --> 0 holes F =2V-4: 342708 = 342712-4 (0) 2E=3F: 1028124 = 1028124 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Apr 18 17:16:56 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs nmr01002_only_wm2 lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.0 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.4 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4846 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=81.7, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.8)->0.8 (%65.2))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.10-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.56 4106 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6549240.5, rms=10.18 001: dt: 0.5000, sse=7446538.0, rms=7.192 (0.000%) 002: dt: 0.5000, sse=7916716.0, rms=5.428 (0.000%) 003: dt: 0.5000, sse=8368161.5, rms=4.396 (0.000%) 004: dt: 0.5000, sse=8619471.0, rms=3.764 (0.000%) 005: dt: 0.5000, sse=8796283.0, rms=3.473 (0.000%) 006: dt: 0.5000, sse=8840013.0, rms=3.279 (0.000%) 007: dt: 0.5000, sse=8901644.0, rms=3.226 (0.000%) 008: dt: 0.5000, sse=8858166.0, rms=3.144 (0.000%) rms = 3.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6120095.0, rms=2.322 (0.000%) 010: dt: 0.2500, sse=5105572.0, rms=1.911 (0.000%) 011: dt: 0.2500, sse=4843470.0, rms=1.816 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4746325.0, rms=1.782 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4664403.5, rms=1.740 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=84.9, 94 (24) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.49) mean absolute distance = 0.26 +- 0.38 4758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5489852.5, rms=4.84 014: dt: 0.5000, sse=5833355.0, rms=3.049 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6453838.0, rms=3.020 (0.000%) 016: dt: 0.2500, sse=5449253.5, rms=1.841 (0.000%) 017: dt: 0.2500, sse=5276166.0, rms=1.594 (0.000%) 018: dt: 0.2500, sse=5121221.5, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5089623.0, rms=1.483 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5007341.5, rms=1.449 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.5, 123 (17) missing vertices, mean dist -0.1 [0.3 (%75.0)->0.2 (%25.0))] %90 local maxima, % 5 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 +- 0.24 (0.10-->3.61) (max @ vno 75800 --> 74575) face area 0.33 +- 0.16 (0.00-->2.66) mean absolute distance = 0.20 +- 0.31 4377 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5289322.5, rms=3.43 021: dt: 0.5000, sse=5521510.5, rms=2.554 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5187069.5, rms=1.786 (0.000%) 023: dt: 0.2500, sse=5094396.0, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5085621.0, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=5034150.0, rms=1.313 (0.000%) rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4994697.5, rms=1.278 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.3, 112 (14) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))] %92 local maxima, % 3 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5009834.5, rms=1.61 rms = 1.70, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5100041.0, rms=1.186 (0.000%) 028: dt: 0.2500, sse=5288887.0, rms=0.981 (0.000%) rms = 1.00, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5287264.5, rms=0.979 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 2139 vertices erasing segment 1 (vno[0] = 84151) erasing segment 2 (vno[0] = 95362) erasing segment 3 (vno[0] = 101746) erasing segment 4 (vno[0] = 105209) erasing segment 5 (vno[0] = 110214) erasing segment 6 (vno[0] = 111310) erasing segment 7 (vno[0] = 118503) erasing segment 8 (vno[0] = 123094) erasing segment 9 (vno[0] = 123467) erasing segment 10 (vno[0] = 124283) erasing segment 11 (vno[0] = 124325) erasing segment 12 (vno[0] = 124399) erasing segment 13 (vno[0] = 126884) erasing segment 14 (vno[0] = 127923) erasing segment 15 (vno[0] = 129142) erasing segment 16 (vno[0] = 129145) erasing segment 17 (vno[0] = 171209) erasing segment 18 (vno[0] = 171260) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/label/lh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.area vertex spacing 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.61) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.5, 177 (177) missing vertices, mean dist 1.6 [0.2 (%0.0)->2.7 (%100.0))] %17 local maxima, %43 large gradients and %37 min vals, 2146 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=28960796.0, rms=27.91 001: dt: 0.5000, sse=22056324.0, rms=23.832 (0.000%) 002: dt: 0.5000, sse=16991750.0, rms=20.377 (0.000%) 003: dt: 0.5000, sse=13370633.0, rms=17.516 (0.000%) 004: dt: 0.5000, sse=10928576.0, rms=15.167 (0.000%) 005: dt: 0.5000, sse=9359566.0, rms=13.261 (0.000%) 006: dt: 0.5000, sse=8426187.0, rms=11.713 (0.000%) 007: dt: 0.5000, sse=7886961.0, rms=10.356 (0.000%) 008: dt: 0.5000, sse=7601448.5, rms=9.138 (0.000%) 009: dt: 0.5000, sse=7372783.5, rms=8.002 (0.000%) 010: dt: 0.5000, sse=7298640.0, rms=6.976 (0.000%) 011: dt: 0.5000, sse=7269682.5, rms=6.090 (0.000%) 012: dt: 0.5000, sse=7435847.5, rms=5.403 (0.000%) 013: dt: 0.5000, sse=7505698.0, rms=4.886 (0.000%) 014: dt: 0.5000, sse=7674428.5, rms=4.514 (0.000%) 015: dt: 0.5000, sse=7718474.5, rms=4.243 (0.000%) 016: dt: 0.5000, sse=7798157.0, rms=4.052 (0.000%) 017: dt: 0.5000, sse=7788584.0, rms=3.919 (0.000%) 018: dt: 0.5000, sse=7889739.0, rms=3.815 (0.000%) 019: dt: 0.5000, sse=7819922.5, rms=3.725 (0.000%) 020: dt: 0.5000, sse=7864769.0, rms=3.657 (0.000%) rms = 3.62, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=7838339.0, rms=3.620 (0.000%) 022: dt: 0.2500, sse=5401900.0, rms=2.920 (0.000%) 023: dt: 0.2500, sse=5183218.0, rms=2.725 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5045811.5, rms=2.696 (0.000%) 025: dt: 0.1250, sse=4804418.5, rms=2.578 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4768077.0, rms=2.562 (0.000%) positioning took 3.4 minutes mean border=58.4, 1541 (26) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))] %35 local maxima, %31 large gradients and %29 min vals, 966 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=5443943.0, rms=4.43 027: dt: 0.5000, sse=5755357.5, rms=3.610 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5338672.5, rms=3.063 (0.000%) 029: dt: 0.2500, sse=5448425.0, rms=2.807 (0.000%) 030: dt: 0.2500, sse=5358573.5, rms=2.693 (0.000%) 031: dt: 0.2500, sse=5414915.0, rms=2.633 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5392877.0, rms=2.595 (0.000%) 033: dt: 0.1250, sse=5213600.5, rms=2.469 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5208941.5, rms=2.443 (0.000%) positioning took 1.1 minutes mean border=56.9, 1950 (5) missing vertices, mean dist 0.1 [0.2 (%39.4)->0.3 (%60.6))] %50 local maxima, %17 large gradients and %29 min vals, 992 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=5383167.5, rms=3.27 rms = 3.41, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5187246.5, rms=2.833 (0.000%) 036: dt: 0.2500, sse=5233564.0, rms=2.582 (0.000%) 037: dt: 0.2500, sse=5443654.0, rms=2.507 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5521985.5, rms=2.495 (0.000%) 039: dt: 0.1250, sse=5355142.5, rms=2.388 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5374715.0, rms=2.368 (0.000%) positioning took 0.9 minutes mean border=56.2, 3775 (4) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.3 (%54.9))] %52 local maxima, %13 large gradients and %28 min vals, 812 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5410821.0, rms=2.59 rms = 3.02, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5309167.5, rms=2.425 (0.000%) 042: dt: 0.2500, sse=5531031.0, rms=2.371 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=5609158.5, rms=2.360 (0.000%) 044: dt: 0.1250, sse=5503065.5, rms=2.280 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=5536211.0, rms=2.264 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.07-->6.43) (max @ vno 117187 --> 117166) face area 0.38 +- 0.29 (0.00-->7.21) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1435:1848 truncations. 35458 vertices at 0 distance 111434 vertices at 1 distance 107653 vertices at 2 distance 48747 vertices at 3 distance 17326 vertices at 4 distance 5520 vertices at 5 distance 1821 vertices at 6 distance 590 vertices at 7 distance 267 vertices at 8 distance 143 vertices at 9 distance 106 vertices at 10 distance 70 vertices at 11 distance 39 vertices at 12 distance 50 vertices at 13 distance 32 vertices at 14 distance 31 vertices at 15 distance 12 vertices at 16 distance 16 vertices at 17 distance 13 vertices at 18 distance 11 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.thickness positioning took 14.7 minutes #-------------------------------------------- #@# Smooth2 lh Mon Apr 18 17:31:39 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Mon Apr 18 17:31:45 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.2 mm, total surface area = 102557 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.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=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 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 257 vertices thresholded to be in k1 ~ [-0.30 0.46], k2 ~ [-0.09 0.08] total integrated curvature = 0.468*4pi (5.886) --> 1 handles ICI = 1.7, FI = 12.0, variation=201.451 159 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 160 vertices thresholded to be in [-0.13 0.20] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Mon Apr 18 17:34:25 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm nmr01002_only_wm2 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 [ nmr01002_only_wm2/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 [ 277 ] Gb_filter = 0 WARN: S lookup min: -0.445948 WARN: S explicit min: 0.000000 vertex = 560 #-------------------------------------------- #@# Tessellate rh Mon Apr 18 17:34:31 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 12 (out of 343297: 0.003496) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 13 vertices, 18 faces slice 30: 3524 vertices, 3726 faces slice 40: 12191 vertices, 12543 faces slice 50: 24263 vertices, 24721 faces slice 60: 37970 vertices, 38423 faces slice 70: 50740 vertices, 51184 faces slice 80: 63449 vertices, 63848 faces slice 90: 76677 vertices, 77126 faces slice 100: 89742 vertices, 90186 faces slice 110: 102644 vertices, 103108 faces slice 120: 115080 vertices, 115532 faces slice 130: 126417 vertices, 126823 faces slice 140: 136806 vertices, 137193 faces slice 150: 145819 vertices, 146191 faces slice 160: 153286 vertices, 153555 faces slice 170: 159585 vertices, 159818 faces slice 180: 165524 vertices, 165760 faces slice 190: 169604 vertices, 169783 faces slice 200: 171064 vertices, 171108 faces slice 210: 171064 vertices, 171108 faces slice 220: 171064 vertices, 171108 faces slice 230: 171064 vertices, 171108 faces slice 240: 171064 vertices, 171108 faces slice 250: 171064 vertices, 171108 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... 171064 voxel in cpt #1: X=-44 [v=171064,e=513324,f=342216] located at (31.930441, -29.514544, 25.405790) For the whole surface: X=-44 [v=171064,e=513324,f=342216] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Apr 18 17:34:40 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Mon Apr 18 17:34:45 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts avg radius = 50.9 mm, total surface area = 89972 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Apr 18 17:35:39 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.53 (0.00-->5.85) (max @ vno 73619 --> 74940) face area 0.02 +- 0.03 (-0.22-->0.64) scaling brain by 0.281... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.683, avgs=0 005/300: dt: 0.9000, rms radial error=176.428, avgs=0 010/300: dt: 0.9000, rms radial error=175.871, avgs=0 015/300: dt: 0.9000, rms radial error=175.139, avgs=0 020/300: dt: 0.9000, rms radial error=174.306, avgs=0 025/300: dt: 0.9000, rms radial error=173.414, avgs=0 030/300: dt: 0.9000, rms radial error=172.492, avgs=0 035/300: dt: 0.9000, rms radial error=171.553, avgs=0 040/300: dt: 0.9000, rms radial error=170.607, avgs=0 045/300: dt: 0.9000, rms radial error=169.658, avgs=0 050/300: dt: 0.9000, rms radial error=168.711, avgs=0 055/300: dt: 0.9000, rms radial error=167.766, avgs=0 060/300: dt: 0.9000, rms radial error=166.826, avgs=0 065/300: dt: 0.9000, rms radial error=165.889, avgs=0 070/300: dt: 0.9000, rms radial error=164.957, avgs=0 075/300: dt: 0.9000, rms radial error=164.031, avgs=0 080/300: dt: 0.9000, rms radial error=163.109, avgs=0 085/300: dt: 0.9000, rms radial error=162.193, avgs=0 090/300: dt: 0.9000, rms radial error=161.281, avgs=0 095/300: dt: 0.9000, rms radial error=160.375, avgs=0 100/300: dt: 0.9000, rms radial error=159.474, avgs=0 105/300: dt: 0.9000, rms radial error=158.578, avgs=0 110/300: dt: 0.9000, rms radial error=157.688, avgs=0 115/300: dt: 0.9000, rms radial error=156.803, avgs=0 120/300: dt: 0.9000, rms radial error=155.923, avgs=0 125/300: dt: 0.9000, rms radial error=155.047, avgs=0 130/300: dt: 0.9000, rms radial error=154.177, avgs=0 135/300: dt: 0.9000, rms radial error=153.311, avgs=0 140/300: dt: 0.9000, rms radial error=152.450, avgs=0 145/300: dt: 0.9000, rms radial error=151.594, avgs=0 150/300: dt: 0.9000, rms radial error=150.743, avgs=0 155/300: dt: 0.9000, rms radial error=149.896, avgs=0 160/300: dt: 0.9000, rms radial error=149.054, avgs=0 165/300: dt: 0.9000, rms radial error=148.216, avgs=0 170/300: dt: 0.9000, rms radial error=147.384, avgs=0 175/300: dt: 0.9000, rms radial error=146.555, avgs=0 180/300: dt: 0.9000, rms radial error=145.732, avgs=0 185/300: dt: 0.9000, rms radial error=144.913, avgs=0 190/300: dt: 0.9000, rms radial error=144.098, avgs=0 195/300: dt: 0.9000, rms radial error=143.288, avgs=0 200/300: dt: 0.9000, rms radial error=142.482, avgs=0 205/300: dt: 0.9000, rms radial error=141.681, avgs=0 210/300: dt: 0.9000, rms radial error=140.884, avgs=0 215/300: dt: 0.9000, rms radial error=140.091, avgs=0 220/300: dt: 0.9000, rms radial error=139.303, avgs=0 225/300: dt: 0.9000, rms radial error=138.519, avgs=0 230/300: dt: 0.9000, rms radial error=137.740, avgs=0 235/300: dt: 0.9000, rms radial error=136.964, avgs=0 240/300: dt: 0.9000, rms radial error=136.194, avgs=0 245/300: dt: 0.9000, rms radial error=135.427, avgs=0 250/300: dt: 0.9000, rms radial error=134.665, avgs=0 255/300: dt: 0.9000, rms radial error=133.907, avgs=0 260/300: dt: 0.9000, rms radial error=133.154, avgs=0 265/300: dt: 0.9000, rms radial error=132.404, avgs=0 270/300: dt: 0.9000, rms radial error=131.659, avgs=0 275/300: dt: 0.9000, rms radial error=130.918, avgs=0 280/300: dt: 0.9000, rms radial error=130.181, avgs=0 285/300: dt: 0.9000, rms radial error=129.448, avgs=0 290/300: dt: 0.9000, rms radial error=128.719, avgs=0 295/300: dt: 0.9000, rms radial error=127.994, avgs=0 300/300: dt: 0.9000, rms radial error=127.273, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20657.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3698.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 421.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00589 epoch 4 (K=640.0), pass 1, starting sse = 29.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/18 = 0.00983 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Apr 18 17:42:48 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002_only_wm2 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=171064, nf=342216, ne=513324, 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... 3535 ambiguous faces found in tessellation segmenting defects... 36 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 36 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4088 (-4.7044) -vertex loglikelihood: -6.1950 (-3.0975) -normal dot loglikelihood: -3.6422 (-3.6422) -quad curv loglikelihood: -6.4380 (-3.2190) Total Loglikelihood : -25.6840 CORRECTING DEFECT 0 (vertices=10, convex hull=34) After retessellation of defect 0, euler #=-32 (168843,505537,336662) : difference with theory (-33) = -1 CORRECTING DEFECT 1 (vertices=38, convex hull=51) After retessellation of defect 1, euler #=-31 (168848,505574,336695) : difference with theory (-32) = -1 CORRECTING DEFECT 2 (vertices=29, convex hull=50) After retessellation of defect 2, euler #=-30 (168856,505617,336731) : difference with theory (-31) = -1 CORRECTING DEFECT 3 (vertices=107, convex hull=88) After retessellation of defect 3, euler #=-29 (168880,505725,336816) : difference with theory (-30) = -1 CORRECTING DEFECT 4 (vertices=247, convex hull=134) After retessellation of defect 4, euler #=-28 (168940,505972,337004) : difference with theory (-29) = -1 CORRECTING DEFECT 5 (vertices=91, convex hull=87) After retessellation of defect 5, euler #=-27 (168966,506090,337097) : difference with theory (-28) = -1 CORRECTING DEFECT 6 (vertices=90, convex hull=126) After retessellation of defect 6, euler #=-26 (168996,506235,337213) : difference with theory (-27) = -1 CORRECTING DEFECT 7 (vertices=11, convex hull=26) After retessellation of defect 7, euler #=-25 (168999,506250,337226) : difference with theory (-26) = -1 CORRECTING DEFECT 8 (vertices=6, convex hull=28) After retessellation of defect 8, euler #=-24 (169002,506267,337241) : difference with theory (-25) = -1 CORRECTING DEFECT 9 (vertices=14, convex hull=25) After retessellation of defect 9, euler #=-23 (169007,506293,337263) : difference with theory (-24) = -1 CORRECTING DEFECT 10 (vertices=26, convex hull=40) After retessellation of defect 10, euler #=-22 (169023,506353,337308) : difference with theory (-23) = -1 CORRECTING DEFECT 11 (vertices=24, convex hull=64) After retessellation of defect 11, euler #=-21 (169034,506411,337356) : difference with theory (-22) = -1 CORRECTING DEFECT 12 (vertices=20, convex hull=43) After retessellation of defect 12, euler #=-20 (169044,506456,337392) : difference with theory (-21) = -1 CORRECTING DEFECT 13 (vertices=6, convex hull=21) After retessellation of defect 13, euler #=-19 (169047,506472,337406) : difference with theory (-20) = -1 CORRECTING DEFECT 14 (vertices=54, convex hull=67) After retessellation of defect 14, euler #=-18 (169070,506568,337480) : difference with theory (-19) = -1 CORRECTING DEFECT 15 (vertices=609, convex hull=387) After retessellation of defect 15, euler #=-17 (169158,507041,337866) : difference with theory (-18) = -1 CORRECTING DEFECT 16 (vertices=60, convex hull=87) normal vector of length zero at vertex 170256 with 3 faces normal vector of length zero at vertex 170256 with 3 faces After retessellation of defect 16, euler #=-16 (169191,507177,337970) : difference with theory (-17) = -1 CORRECTING DEFECT 17 (vertices=6, convex hull=14) After retessellation of defect 17, euler #=-15 (169192,507182,337975) : difference with theory (-16) = -1 CORRECTING DEFECT 18 (vertices=28, convex hull=67) After retessellation of defect 18, euler #=-14 (169202,507239,338023) : difference with theory (-15) = -1 CORRECTING DEFECT 19 (vertices=29, convex hull=26) After retessellation of defect 19, euler #=-13 (169210,507270,338047) : difference with theory (-14) = -1 CORRECTING DEFECT 20 (vertices=11, convex hull=28) After retessellation of defect 20, euler #=-12 (169211,507281,338058) : difference with theory (-13) = -1 CORRECTING DEFECT 21 (vertices=88, convex hull=107) After retessellation of defect 21, euler #=-12 (169255,507468,338201) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=11, convex hull=24) After retessellation of defect 22, euler #=-11 (169260,507493,338222) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=15, convex hull=14) After retessellation of defect 23, euler #=-10 (169262,507501,338229) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=59, convex hull=50) After retessellation of defect 24, euler #=-9 (169273,507548,338266) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=27, convex hull=36) After retessellation of defect 25, euler #=-8 (169281,507585,338296) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=47, convex hull=66) After retessellation of defect 26, euler #=-7 (169308,507697,338382) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=71, convex hull=91) After retessellation of defect 27, euler #=-6 (169348,507860,338506) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=52, convex hull=43) After retessellation of defect 28, euler #=-5 (169352,507890,338533) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=54) After retessellation of defect 29, euler #=-4 (169361,507939,338574) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=82, convex hull=118) After retessellation of defect 30, euler #=-3 (169421,508169,338745) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=56, convex hull=76) After retessellation of defect 31, euler #=-2 (169443,508268,338823) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=26, convex hull=28) After retessellation of defect 32, euler #=-1 (169447,508290,338842) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=45, convex hull=33) After retessellation of defect 33, euler #=0 (169449,508311,338862) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=60, convex hull=48) After retessellation of defect 34, euler #=1 (169456,508353,338898) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=43, convex hull=31) After retessellation of defect 35, euler #=2 (169459,508371,338914) : 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-->12.85) (max @ vno 29126 --> 46123) 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-->12.85) (max @ vno 29126 --> 46123) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 146 mutations (35.9%), 261 crossovers (64.1%), 149 vertices were eliminated building final representation... 1605 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=169459, nf=338914, ne=508371, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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: 229 intersecting 001: 12 intersecting 002: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 169459 - 508371 + 338914 = 2 --> 0 holes F =2V-4: 338914 = 338918-4 (0) 2E=3F: 1016742 = 1016742 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 54 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Mon Apr 18 18:08:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs nmr01002_only_wm2 rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.orig... computing class statistics... border white: 316445 voxels (1.89%) border gray 350766 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.69) (max @ vno 29126 --> 46123) face area 0.28 +- 0.12 (0.00-->2.46) mean absolute distance = 0.69 +- 0.90 4495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.5, 454 (454) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %74 local maxima, %22 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.06-->5.06) (max @ vno 106389 --> 106390) face area 0.28 +- 0.13 (0.00-->2.48) mean absolute distance = 0.35 +- 0.60 3929 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6338009.0, rms=10.07 001: dt: 0.5000, sse=7206390.0, rms=7.130 (0.000%) 002: dt: 0.5000, sse=7729556.0, rms=5.451 (0.000%) 003: dt: 0.5000, sse=8169330.5, rms=4.531 (0.000%) 004: dt: 0.5000, sse=8451311.0, rms=3.997 (0.000%) 005: dt: 0.5000, sse=8597256.0, rms=3.773 (0.000%) 006: dt: 0.5000, sse=8690250.0, rms=3.601 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8717640.0, rms=3.552 (0.000%) 008: dt: 0.2500, sse=5379594.5, rms=2.585 (0.000%) 009: dt: 0.2500, sse=4912662.0, rms=2.317 (0.000%) 010: dt: 0.2500, sse=4717352.5, rms=2.214 (0.000%) 011: dt: 0.2500, sse=4640247.0, rms=2.136 (0.000%) 012: dt: 0.2500, sse=4595322.0, rms=2.071 (0.000%) 013: dt: 0.2500, sse=4564673.5, rms=2.016 (0.000%) 014: dt: 0.2500, sse=4543605.0, rms=1.960 (0.000%) 015: dt: 0.2500, sse=4531133.5, rms=1.909 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4508915.0, rms=1.861 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4454550.5, rms=1.820 (0.000%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.4, 338 (248) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.3 (%27.5))] %82 local maxima, %14 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 (0.05-->5.54) (max @ vno 106389 --> 106390) face area 0.35 +- 0.16 (0.00-->3.51) mean absolute distance = 0.26 +- 0.39 4779 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5175222.5, rms=4.57 018: dt: 0.5000, sse=5585276.0, rms=2.983 (0.000%) rms = 3.03, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5204607.0, rms=2.412 (0.000%) 020: dt: 0.2500, sse=5044381.5, rms=1.949 (0.000%) 021: dt: 0.2500, sse=4951668.5, rms=1.734 (0.000%) 022: dt: 0.2500, sse=4901714.0, rms=1.639 (0.000%) 023: dt: 0.2500, sse=4870915.0, rms=1.575 (0.000%) rms = 1.54, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4845074.0, rms=1.536 (0.000%) rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4805285.0, rms=1.504 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.8, 299 (177) missing vertices, mean dist -0.1 [0.3 (%73.3)->0.2 (%26.7))] %89 local maxima, % 6 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 (0.03-->5.76) (max @ vno 106389 --> 106390) face area 0.34 +- 0.16 (0.00-->3.82) mean absolute distance = 0.21 +- 0.31 4518 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5062480.5, rms=3.32 026: dt: 0.5000, sse=5360238.5, rms=2.551 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5034442.0, rms=1.836 (0.000%) 028: dt: 0.2500, sse=4945647.0, rms=1.471 (0.000%) 029: dt: 0.2500, sse=4938475.5, rms=1.365 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4913894.5, rms=1.353 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4865666.0, rms=1.323 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.6, 272 (144) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))] %91 local maxima, % 4 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4877999.0, rms=1.63 rms = 1.70, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4949433.0, rms=1.239 (0.000%) 033: dt: 0.2500, sse=5126906.0, rms=1.051 (0.000%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.05, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5119353.0, rms=1.049 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 12 non-cortical segments detected only using segment with 2728 vertices erasing segment 1 (vno[0] = 90007) erasing segment 2 (vno[0] = 91433) erasing segment 3 (vno[0] = 119414) erasing segment 4 (vno[0] = 122463) erasing segment 5 (vno[0] = 124386) erasing segment 6 (vno[0] = 125361) erasing segment 7 (vno[0] = 125559) erasing segment 8 (vno[0] = 133520) erasing segment 9 (vno[0] = 133561) erasing segment 10 (vno[0] = 136412) erasing segment 11 (vno[0] = 169228) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/label/rh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->5.81) (max @ vno 106389 --> 106390) face area 0.33 +- 0.16 (0.00-->3.88) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=61.2, 218 (218) missing vertices, mean dist 1.6 [1.1 (%0.1)->2.6 (%99.9))] %17 local maxima, %42 large gradients and %37 min vals, 2506 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=27875750.0, rms=27.55 001: dt: 0.5000, sse=21335076.0, rms=23.587 (0.000%) 002: dt: 0.5000, sse=16550031.0, rms=20.242 (0.000%) 003: dt: 0.5000, sse=13183216.0, rms=17.495 (0.000%) 004: dt: 0.5000, sse=10985158.0, rms=15.263 (0.000%) 005: dt: 0.5000, sse=9527617.0, rms=13.449 (0.000%) 006: dt: 0.5000, sse=8591832.0, rms=11.948 (0.000%) 007: dt: 0.5000, sse=7942194.5, rms=10.572 (0.000%) 008: dt: 0.5000, sse=7481265.5, rms=9.305 (0.000%) 009: dt: 0.5000, sse=7232935.0, rms=8.103 (0.000%) 010: dt: 0.5000, sse=7059806.0, rms=7.015 (0.000%) 011: dt: 0.5000, sse=7051092.5, rms=6.041 (0.000%) 012: dt: 0.5000, sse=7086292.5, rms=5.275 (0.000%) 013: dt: 0.5000, sse=7178785.5, rms=4.689 (0.000%) 014: dt: 0.5000, sse=7326007.5, rms=4.315 (0.000%) 015: dt: 0.5000, sse=7423010.0, rms=4.025 (0.000%) 016: dt: 0.5000, sse=7466050.5, rms=3.843 (0.000%) 017: dt: 0.5000, sse=7521898.5, rms=3.679 (0.000%) 018: dt: 0.5000, sse=7529894.5, rms=3.610 (0.000%) 019: dt: 0.5000, sse=7581533.0, rms=3.538 (0.000%) rms = 3.52, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7575812.5, rms=3.523 (0.000%) 021: dt: 0.2500, sse=5345466.5, rms=2.854 (0.000%) 022: dt: 0.2500, sse=5133809.5, rms=2.688 (0.000%) rms = 2.68, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5004031.5, rms=2.675 (0.000%) 024: dt: 0.1250, sse=4764704.0, rms=2.549 (0.000%) rms = 2.53, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4732838.5, rms=2.534 (0.000%) positioning took 3.3 minutes mean border=59.3, 1570 (33) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.6 (%51.9))] %33 local maxima, %33 large gradients and %29 min vals, 835 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=5371835.0, rms=4.29 026: dt: 0.5000, sse=5700765.5, rms=3.635 (0.000%) 027: dt: 0.5000, sse=7379703.0, rms=3.568 (0.000%) rms = 3.57, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=7077776.5, rms=3.566 (0.000%) 029: dt: 0.2500, sse=5810239.0, rms=2.815 (0.000%) 030: dt: 0.2500, sse=5656559.5, rms=2.605 (0.000%) rms = 2.61, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5551816.0, rms=2.542 (0.000%) 032: dt: 0.1250, sse=5363362.0, rms=2.453 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5317445.0, rms=2.433 (0.000%) positioning took 1.1 minutes mean border=58.0, 1973 (8) missing vertices, mean dist 0.1 [0.2 (%40.0)->0.4 (%60.0))] %47 local maxima, %19 large gradients and %29 min vals, 982 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=5486836.0, rms=3.24 rms = 3.29, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5291770.5, rms=2.846 (0.000%) 035: dt: 0.2500, sse=5302576.5, rms=2.580 (0.000%) 036: dt: 0.2500, sse=5497685.0, rms=2.502 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5578770.5, rms=2.491 (0.000%) 038: dt: 0.1250, sse=5415021.0, rms=2.379 (0.000%) rms = 2.36, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5425818.5, rms=2.358 (0.000%) positioning took 0.9 minutes mean border=57.3, 3693 (6) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.3 (%54.9))] %50 local maxima, %15 large gradients and %28 min vals, 812 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5458966.5, rms=2.57 rms = 2.95, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5360164.0, rms=2.415 (0.000%) 041: dt: 0.2500, sse=5572585.5, rms=2.351 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5644237.5, rms=2.343 (0.000%) 043: dt: 0.1250, sse=5546472.5, rms=2.262 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5572287.5, rms=2.248 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.area.pial vertex spacing 0.99 +- 0.41 (0.06-->7.70) (max @ vno 117005 --> 115834) face area 0.39 +- 0.29 (0.00-->6.68) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed 0 of 169459 vertices processed 25000 of 169459 vertices processed 50000 of 169459 vertices processed 75000 of 169459 vertices processed 100000 of 169459 vertices processed 125000 of 169459 vertices processed 150000 of 169459 vertices processed thickness calculation complete, 1245:1897 truncations. 35677 vertices at 0 distance 111998 vertices at 1 distance 103668 vertices at 2 distance 47632 vertices at 3 distance 16859 vertices at 4 distance 5488 vertices at 5 distance 1802 vertices at 6 distance 593 vertices at 7 distance 250 vertices at 8 distance 123 vertices at 9 distance 90 vertices at 10 distance 74 vertices at 11 distance 48 vertices at 12 distance 29 vertices at 13 distance 35 vertices at 14 distance 22 vertices at 15 distance 17 vertices at 16 distance 17 vertices at 17 distance 9 vertices at 18 distance 5 vertices at 19 distance 18 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.thickness positioning took 14.9 minutes #-------------------------------------------- #@# Smooth2 rh Mon Apr 18 18:23:24 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Mon Apr 18 18:23:29 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.1 mm, total surface area = 101932 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 222 vertices thresholded to be in k1 ~ [-0.25 0.50], k2 ~ [-0.10 0.07] total integrated curvature = 0.514*4pi (6.463) --> 0 handles ICI = 1.9, FI = 14.7, variation=243.178 154 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 169 vertices thresholded to be in [-0.12 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.014, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Mon Apr 18 18:26:04 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm nmr01002_only_wm2 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 [ nmr01002_only_wm2/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 335 ] Gb_filter = 0 WARN: S lookup min: -0.306479 WARN: S explicit min: 0.000000 vertex = 156 #-------------------------------------------- #@# ASeg Stats Mon Apr 18 18:26:14 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002_only_wm2 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002_only_wm2 sysname Linux hostname compute-0-54 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Computing euler number orig.nofix lheno = -38, rheno = -44 orig.nofix lhholes = 20, rhholes = 23 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 293167.105 284111.000 diff= 9056.1 pctdiff= 3.089 rhCtxGM: 288494.608 275164.000 diff=13330.6 pctdiff= 4.621 lhCtxWM: 291224.196 291924.000 diff= -699.8 pctdiff=-0.240 rhCtxWM: 290551.730 290463.000 diff= 88.7 pctdiff= 0.031 SubCortGMVol 65073.000 SupraTentVol 1267949.640 (1244988.000) diff=22961.640 pctdiff=1.811 SupraTentVolNotVent 1230176.640 (1207215.000) diff=22961.640 pctdiff=1.867 BrainSegVol 1391668.000 (1389201.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1350634.000 (1372087.640) diff=-21453.640 pctdiff=-1.588 BrainSegVolNotVent 1350634.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 19118 19118.055 4 5 Left-Inf-Lat-Vent 520 520.060 5 7 Left-Cerebellum-White-Matter 19700 19699.701 6 8 Left-Cerebellum-Cortex 53472 53472.230 7 10 Left-Thalamus-Proper 8963 8962.595 8 11 Left-Caudate 3573 3573.187 9 12 Left-Putamen 6421 6421.121 10 13 Left-Pallidum 1439 1438.815 11 14 3rd-Ventricle 722 721.945 12 15 4th-Ventricle 1958 1957.972 13 16 Brain-Stem 27112 27112.328 14 17 Left-Hippocampus 4400 4400.408 15 18 Left-Amygdala 1787 1786.623 16 24 CSF 902 902.354 17 26 Left-Accumbens-area 573 573.266 18 28 Left-VentralDC 4634 4634.012 19 30 Left-vessel 220 219.571 20 31 Left-choroid-plexus 1494 1493.786 23 43 Right-Lateral-Ventricle 14433 14432.729 24 44 Right-Inf-Lat-Vent 502 502.259 25 46 Right-Cerebellum-White-Matter 18732 18731.957 26 47 Right-Cerebellum-Cortex 53362 53361.777 27 49 Right-Thalamus-Proper 7901 7900.568 28 50 Right-Caudate 3964 3964.413 29 51 Right-Putamen 5970 5970.317 30 52 Right-Pallidum 1727 1727.467 31 53 Right-Hippocampus 5094 5093.581 32 54 Right-Amygdala 1979 1978.811 33 58 Right-Accumbens-area 715 714.996 34 60 Right-VentralDC 4636 4636.441 35 62 Right-vessel 265 264.728 36 63 Right-choroid-plexus 1793 1792.552 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1813 1813.132 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 39 39.252 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 275 274.977 45 251 CC_Posterior 1374 1374.238 46 252 CC_Mid_Posterior 547 546.627 47 253 CC_Central 503 502.871 48 254 CC_Mid_Anterior 605 604.529 49 255 CC_Anterior 1351 1351.204 Reporting on 45 segmentations mri_segstats done #------------------------------------------ Started at Mon Apr 18 16:43:21 EDT 2016 Ended at Mon Apr 18 18:27:59 EDT 2016 #@#%# recon-all-run-time-hours 1.744 recon-all -s nmr01002_only_wm2 finished without error at Mon Apr 18 18:27:59 EDT 2016 New invocation of recon-all Tue Apr 19 11:32:21 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2 /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002_only_wm2 -autorecon2-wm subjid nmr01002_only_wm2 setenv SUBJECTS_DIR /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux compute-0-39 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 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 95989 total used free shared buffers cached Mem: 24604396 23171428 1432968 4 2692 23664 -/+ buffers/cache: 23145072 1459324 Swap: 67108860 13747528 53361332 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:32-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:35-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:35-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:35-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:35-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:35-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:36-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:36-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:36-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:37-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:37-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:37-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:37-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:38-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:38-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:38-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:38-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:39-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:39-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:39-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:39-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:40-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/04/19-15:32:40-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: dwakeman Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Tue Apr 19 11:32:41 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2917 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 16, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 39 seconds. #-------------------------------------------- #@# Mask BFS Tue Apr 19 11:36:23 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1879483 voxels in mask (pct= 11.20) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Apr 19 11:36:27 EDT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-39 machine x86_64 user dwakeman 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 929 values in range Counting number of voxels Found 929 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-39 machine x86_64 user dwakeman input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 0 deletes, 929 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 (105.0): 104.7 +- 6.5 [80.0 --> 125.0] GM (73.0) : 71.8 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.4 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5521 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6051 filled 337 bright non-wm voxels segmented. 3333 diagonally connected voxels added... white matter segmentation took 2.5 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 0.67 minutes reading wm segmentation from wm.seg.mgz... 219 voxels added to wm to prevent paths from MTL structures to cortex 2739 additional wm voxels added 0 additional wm voxels added SEG EDIT: 76008 voxels turned on, 58347 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+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 32 found - 32 modified | TOTAL: 58 pass 2 (xy-): 0 found - 32 modified | TOTAL: 58 pass 1 (yz+): 33 found - 33 modified | TOTAL: 91 pass 2 (yz+): 0 found - 33 modified | TOTAL: 91 pass 1 (yz-): 16 found - 16 modified | TOTAL: 107 pass 2 (yz-): 0 found - 16 modified | TOTAL: 107 pass 1 (xz+): 22 found - 22 modified | TOTAL: 129 pass 2 (xz+): 0 found - 22 modified | TOTAL: 129 pass 1 (xz-): 18 found - 18 modified | TOTAL: 147 pass 2 (xz-): 0 found - 18 modified | TOTAL: 147 Iteration Number : 1 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 18 found - 18 modified | TOTAL: 31 pass 2 (+++): 0 found - 18 modified | TOTAL: 31 pass 1 (+++): 12 found - 12 modified | TOTAL: 43 pass 2 (+++): 0 found - 12 modified | TOTAL: 43 pass 1 (+++): 15 found - 15 modified | TOTAL: 58 pass 2 (+++): 0 found - 15 modified | TOTAL: 58 Iteration Number : 1 pass 1 (++): 124 found - 124 modified | TOTAL: 124 pass 2 (++): 0 found - 124 modified | TOTAL: 124 pass 1 (+-): 84 found - 84 modified | TOTAL: 208 pass 2 (+-): 0 found - 84 modified | TOTAL: 208 pass 1 (--): 91 found - 91 modified | TOTAL: 299 pass 2 (--): 0 found - 91 modified | TOTAL: 299 pass 1 (-+): 104 found - 104 modified | TOTAL: 403 pass 2 (-+): 0 found - 104 modified | TOTAL: 403 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 4 found - 4 modified | TOTAL: 11 pass 2 (yz-): 0 found - 4 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 1 found - 1 modified | TOTAL: 13 pass 2 (xz-): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 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 = 626 (out of 717428: 0.087256) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 929 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue Apr 19 11:39:54 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.024 -0.106 0.053 3.473; 0.104 1.079 0.255 -34.419; -0.089 -0.192 0.902 45.547; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3639 (min = 350, max = 1400), aspect = 1.41 (min = 0.10, max = 0.75) need search nearby using seed (127, 121, 155), TAL = (1.0, 27.0, 7.0) talairach voxel to voxel transform 0.961 0.080 -0.079 3.033; -0.109 0.873 -0.240 41.374; 0.072 0.194 1.050 -41.403; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 121, 155) --> (1.0, 27.0, 7.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.00, 27.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 27.00, 7.00) SRC: (105.25, 97.89, 152.56) search lh wm seed point around talairach space (-17.00, 27.00, 7.00), SRC: (139.85, 93.96, 155.14) 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 Apr 19 11:40:47 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 19 (out of 347268: 0.005471) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 2944 vertices, 3132 faces slice 40: 10921 vertices, 11278 faces slice 50: 22273 vertices, 22668 faces slice 60: 34740 vertices, 35181 faces slice 70: 47149 vertices, 47532 faces slice 80: 59678 vertices, 60114 faces slice 90: 72395 vertices, 72851 faces slice 100: 85976 vertices, 86438 faces slice 110: 98341 vertices, 98802 faces slice 120: 111100 vertices, 111556 faces slice 130: 123616 vertices, 124049 faces slice 140: 134919 vertices, 135312 faces slice 150: 144969 vertices, 145304 faces slice 160: 153120 vertices, 153436 faces slice 170: 160115 vertices, 160371 faces slice 180: 166375 vertices, 166591 faces slice 190: 171266 vertices, 171444 faces slice 200: 172828 vertices, 172866 faces slice 210: 172828 vertices, 172866 faces slice 220: 172828 vertices, 172866 faces slice 230: 172828 vertices, 172866 faces slice 240: 172828 vertices, 172866 faces slice 250: 172828 vertices, 172866 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... 172828 voxel in cpt #1: X=-38 [v=172828,e=518598,f=345732] located at (-23.818184, -26.572702, 31.230940) For the whole surface: X=-38 [v=172828,e=518598,f=345732] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Apr 19 11:40:56 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Apr 19 11:41:02 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts avg radius = 51.0 mm, total surface area = 90513 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Apr 19 11:41:56 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.54 (0.00-->6.55) (max @ vno 129289 --> 130308) face area 0.02 +- 0.03 (-0.09-->0.52) scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.808, avgs=0 005/300: dt: 0.9000, rms radial error=176.547, avgs=0 010/300: dt: 0.9000, rms radial error=175.989, avgs=0 015/300: dt: 0.9000, rms radial error=175.257, avgs=0 020/300: dt: 0.9000, rms radial error=174.425, avgs=0 025/300: dt: 0.9000, rms radial error=173.535, avgs=0 030/300: dt: 0.9000, rms radial error=172.613, avgs=0 035/300: dt: 0.9000, rms radial error=171.674, avgs=0 040/300: dt: 0.9000, rms radial error=170.728, avgs=0 045/300: dt: 0.9000, rms radial error=169.779, avgs=0 050/300: dt: 0.9000, rms radial error=168.830, avgs=0 055/300: dt: 0.9000, rms radial error=167.885, avgs=0 060/300: dt: 0.9000, rms radial error=166.943, avgs=0 065/300: dt: 0.9000, rms radial error=166.005, avgs=0 070/300: dt: 0.9000, rms radial error=165.073, avgs=0 075/300: dt: 0.9000, rms radial error=164.145, avgs=0 080/300: dt: 0.9000, rms radial error=163.222, avgs=0 085/300: dt: 0.9000, rms radial error=162.304, avgs=0 090/300: dt: 0.9000, rms radial error=161.392, avgs=0 095/300: dt: 0.9000, rms radial error=160.484, avgs=0 100/300: dt: 0.9000, rms radial error=159.581, avgs=0 105/300: dt: 0.9000, rms radial error=158.683, avgs=0 110/300: dt: 0.9000, rms radial error=157.790, avgs=0 115/300: dt: 0.9000, rms radial error=156.902, avgs=0 120/300: dt: 0.9000, rms radial error=156.019, avgs=0 125/300: dt: 0.9000, rms radial error=155.140, avgs=0 130/300: dt: 0.9000, rms radial error=154.267, avgs=0 135/300: dt: 0.9000, rms radial error=153.398, avgs=0 140/300: dt: 0.9000, rms radial error=152.534, avgs=0 145/300: dt: 0.9000, rms radial error=151.675, avgs=0 150/300: dt: 0.9000, rms radial error=150.820, avgs=0 155/300: dt: 0.9000, rms radial error=149.971, avgs=0 160/300: dt: 0.9000, rms radial error=149.125, avgs=0 165/300: dt: 0.9000, rms radial error=148.285, avgs=0 170/300: dt: 0.9000, rms radial error=147.449, avgs=0 175/300: dt: 0.9000, rms radial error=146.618, avgs=0 180/300: dt: 0.9000, rms radial error=145.791, avgs=0 185/300: dt: 0.9000, rms radial error=144.969, avgs=0 190/300: dt: 0.9000, rms radial error=144.152, avgs=0 195/300: dt: 0.9000, rms radial error=143.339, avgs=0 200/300: dt: 0.9000, rms radial error=142.530, avgs=0 205/300: dt: 0.9000, rms radial error=141.726, avgs=0 210/300: dt: 0.9000, rms radial error=140.927, avgs=0 215/300: dt: 0.9000, rms radial error=140.132, avgs=0 220/300: dt: 0.9000, rms radial error=139.341, avgs=0 225/300: dt: 0.9000, rms radial error=138.555, avgs=0 230/300: dt: 0.9000, rms radial error=137.773, avgs=0 235/300: dt: 0.9000, rms radial error=136.996, avgs=0 240/300: dt: 0.9000, rms radial error=136.223, avgs=0 245/300: dt: 0.9000, rms radial error=135.454, avgs=0 250/300: dt: 0.9000, rms radial error=134.690, avgs=0 255/300: dt: 0.9000, rms radial error=133.930, avgs=0 260/300: dt: 0.9000, rms radial error=133.174, avgs=0 265/300: dt: 0.9000, rms radial error=132.422, avgs=0 270/300: dt: 0.9000, rms radial error=131.675, avgs=0 275/300: dt: 0.9000, rms radial error=130.932, avgs=0 280/300: dt: 0.9000, rms radial error=130.193, avgs=0 285/300: dt: 0.9000, rms radial error=129.458, avgs=0 290/300: dt: 0.9000, rms radial error=128.727, avgs=0 295/300: dt: 0.9000, rms radial error=128.001, avgs=0 300/300: dt: 0.9000, rms radial error=127.278, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20908.40 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 = 3769.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 431.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00517 epoch 4 (K=640.0), pass 1, starting sse = 25.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.23/17 = 0.01369 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.14 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Apr 19 11:50:29 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002_only_wm2 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=172828, nf=345732, ne=518598, g=20) 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... 3174 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3257 (-4.6629) -vertex loglikelihood: -6.1497 (-3.0749) -normal dot loglikelihood: -3.6182 (-3.6182) -quad curv loglikelihood: -6.3064 (-3.1532) Total Loglikelihood : -25.4000 CORRECTING DEFECT 0 (vertices=18, convex hull=22) After retessellation of defect 0, euler #=-22 (170915,512130,341193) : difference with theory (-23) = -1 CORRECTING DEFECT 1 (vertices=27, convex hull=75) After retessellation of defect 1, euler #=-21 (170927,512198,341250) : difference with theory (-22) = -1 CORRECTING DEFECT 2 (vertices=69, convex hull=64) After retessellation of defect 2, euler #=-20 (170936,512254,341298) : difference with theory (-21) = -1 CORRECTING DEFECT 3 (vertices=26, convex hull=32) After retessellation of defect 3, euler #=-19 (170940,512276,341317) : difference with theory (-20) = -1 CORRECTING DEFECT 4 (vertices=22, convex hull=61) After retessellation of defect 4, euler #=-18 (170952,512336,341366) : difference with theory (-19) = -1 CORRECTING DEFECT 5 (vertices=80, convex hull=86) After retessellation of defect 5, euler #=-17 (170964,512403,341422) : difference with theory (-18) = -1 CORRECTING DEFECT 6 (vertices=26, convex hull=69) After retessellation of defect 6, euler #=-16 (170979,512475,341480) : difference with theory (-17) = -1 CORRECTING DEFECT 7 (vertices=819, convex hull=349) After retessellation of defect 7, euler #=-16 (171193,513301,342092) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=25, convex hull=31) After retessellation of defect 8, euler #=-15 (171197,513322,342110) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=34) After retessellation of defect 9, euler #=-14 (171202,513350,342134) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=50, convex hull=26) After retessellation of defect 10, euler #=-13 (171207,513374,342154) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-12 (171214,513405,342179) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=363, convex hull=95) After retessellation of defect 12, euler #=-11 (171237,513513,342265) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=10, convex hull=23) After retessellation of defect 13, euler #=-10 (171239,513523,342274) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=9, convex hull=25) After retessellation of defect 14, euler #=-9 (171242,513540,342289) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=79, convex hull=67) After retessellation of defect 15, euler #=-8 (171258,513622,342356) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=32) After retessellation of defect 16, euler #=-7 (171264,513648,342377) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=24, convex hull=19) After retessellation of defect 17, euler #=-6 (171265,513657,342386) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=51) After retessellation of defect 18, euler #=-5 (171280,513717,342432) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=35, convex hull=76) After retessellation of defect 19, euler #=-4 (171303,513814,342507) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=42, convex hull=50) After retessellation of defect 20, euler #=-3 (171318,513876,342555) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=69) After retessellation of defect 21, euler #=-2 (171329,513934,342603) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=41, convex hull=76) After retessellation of defect 22, euler #=-1 (171350,514030,342679) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=16, convex hull=27) After retessellation of defect 23, euler #=0 (171354,514050,342696) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=8, convex hull=18) After retessellation of defect 24, euler #=1 (171355,514057,342703) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=15, convex hull=15) After retessellation of defect 25, euler #=2 (171356,514062,342708) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.08-->9.13) (max @ vno 119966 --> 122216) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (33.6%), 160 crossovers (66.4%), 94 vertices were eliminated building final representation... 1472 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=171356, nf=342708, ne=514062, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.2 minutes 0 defective edges removing intersecting faces 000: 141 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 171356 - 514062 + 342708 = 2 --> 0 holes F =2V-4: 342708 = 342712-4 (0) 2E=3F: 1028124 = 1028124 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Apr 19 12:09:26 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs nmr01002_only_wm2 lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/wm.mgz... 21185 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.orig... computing class statistics... border white: 316439 voxels (1.89%) border gray 350764 voxels (2.09%) WM (95.0): 96.5 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.0 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.7 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.4 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.03) (max @ vno 126988 --> 171233) face area 0.28 +- 0.12 (0.00-->1.47) mean absolute distance = 0.71 +- 0.91 4846 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.7, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=81.7, 116 (116) missing vertices, mean dist 0.3 [0.6 (%34.8)->0.8 (%65.2))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.10-->3.42) (max @ vno 75800 --> 74575) face area 0.28 +- 0.13 (0.00-->1.75) mean absolute distance = 0.36 +- 0.56 4106 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6549240.5, rms=10.18 001: dt: 0.5000, sse=7446538.0, rms=7.192 (0.000%) 002: dt: 0.5000, sse=7916716.0, rms=5.428 (0.000%) 003: dt: 0.5000, sse=8368161.5, rms=4.396 (0.000%) 004: dt: 0.5000, sse=8619471.0, rms=3.764 (0.000%) 005: dt: 0.5000, sse=8796283.0, rms=3.473 (0.000%) 006: dt: 0.5000, sse=8840013.0, rms=3.279 (0.000%) 007: dt: 0.5000, sse=8901644.0, rms=3.226 (0.000%) 008: dt: 0.5000, sse=8858166.0, rms=3.144 (0.000%) rms = 3.15, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=6120095.0, rms=2.322 (0.000%) 010: dt: 0.2500, sse=5105572.0, rms=1.911 (0.000%) 011: dt: 0.2500, sse=4843470.0, rms=1.816 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4746325.0, rms=1.782 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4664403.5, rms=1.740 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=84.9, 94 (24) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.3 (%25.3))] %83 local maxima, %12 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 0.89 +- 0.24 (0.08-->3.41) (max @ vno 75800 --> 74575) face area 0.35 +- 0.16 (0.00-->2.49) mean absolute distance = 0.26 +- 0.38 4758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5489852.5, rms=4.84 014: dt: 0.5000, sse=5833355.0, rms=3.049 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6453838.0, rms=3.020 (0.000%) 016: dt: 0.2500, sse=5449253.5, rms=1.841 (0.000%) 017: dt: 0.2500, sse=5276166.0, rms=1.594 (0.000%) 018: dt: 0.2500, sse=5121221.5, rms=1.523 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5089623.0, rms=1.483 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5007341.5, rms=1.449 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.5, 123 (17) missing vertices, mean dist -0.1 [0.3 (%75.0)->0.2 (%25.0))] %90 local maxima, % 5 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 +- 0.24 (0.10-->3.61) (max @ vno 75800 --> 74575) face area 0.33 +- 0.16 (0.00-->2.66) mean absolute distance = 0.20 +- 0.31 4377 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5289322.5, rms=3.43 021: dt: 0.5000, sse=5521510.5, rms=2.554 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5187069.5, rms=1.786 (0.000%) 023: dt: 0.2500, sse=5094396.0, rms=1.418 (0.000%) 024: dt: 0.2500, sse=5085621.0, rms=1.314 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=5034150.0, rms=1.313 (0.000%) rms = 1.28, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4994697.5, rms=1.278 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.3, 112 (14) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))] %92 local maxima, % 3 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5009834.5, rms=1.61 rms = 1.70, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5100041.0, rms=1.186 (0.000%) 028: dt: 0.2500, sse=5288887.0, rms=0.981 (0.000%) rms = 1.00, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5287264.5, rms=0.979 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 2139 vertices erasing segment 1 (vno[0] = 84151) erasing segment 2 (vno[0] = 95362) erasing segment 3 (vno[0] = 101746) erasing segment 4 (vno[0] = 105209) erasing segment 5 (vno[0] = 110214) erasing segment 6 (vno[0] = 111310) erasing segment 7 (vno[0] = 118503) erasing segment 8 (vno[0] = 123094) erasing segment 9 (vno[0] = 123467) erasing segment 10 (vno[0] = 124283) erasing segment 11 (vno[0] = 124325) erasing segment 12 (vno[0] = 124399) erasing segment 13 (vno[0] = 126884) erasing segment 14 (vno[0] = 127923) erasing segment 15 (vno[0] = 129142) erasing segment 16 (vno[0] = 129145) erasing segment 17 (vno[0] = 171209) erasing segment 18 (vno[0] = 171260) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/label/lh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.area vertex spacing 0.88 +- 0.25 (0.08-->3.60) (max @ vno 75800 --> 74575) face area 0.33 +- 0.15 (0.00-->2.61) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.5, 177 (177) missing vertices, mean dist 1.6 [0.2 (%0.0)->2.7 (%100.0))] %17 local maxima, %43 large gradients and %37 min vals, 2146 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=28961156.0, rms=27.91 001: dt: 0.5000, sse=22056656.0, rms=23.832 (0.000%) 002: dt: 0.5000, sse=16992050.0, rms=20.377 (0.000%) 003: dt: 0.5000, sse=13370900.0, rms=17.516 (0.000%) 004: dt: 0.5000, sse=10928813.0, rms=15.167 (0.000%) 005: dt: 0.5000, sse=9359776.0, rms=13.261 (0.000%) 006: dt: 0.5000, sse=8426376.0, rms=11.713 (0.000%) 007: dt: 0.5000, sse=7887128.5, rms=10.356 (0.000%) 008: dt: 0.5000, sse=7601594.5, rms=9.138 (0.000%) 009: dt: 0.5000, sse=7372903.0, rms=8.002 (0.000%) 010: dt: 0.5000, sse=7298747.0, rms=6.977 (0.000%) 011: dt: 0.5000, sse=7269762.0, rms=6.091 (0.000%) 012: dt: 0.5000, sse=7435903.5, rms=5.403 (0.000%) 013: dt: 0.5000, sse=7505617.0, rms=4.886 (0.000%) 014: dt: 0.5000, sse=7674757.0, rms=4.514 (0.000%) 015: dt: 0.5000, sse=7718272.5, rms=4.243 (0.000%) 016: dt: 0.5000, sse=7798560.0, rms=4.052 (0.000%) 017: dt: 0.5000, sse=7787927.5, rms=3.919 (0.000%) 018: dt: 0.5000, sse=7890890.0, rms=3.815 (0.000%) 019: dt: 0.5000, sse=7818425.0, rms=3.725 (0.000%) 020: dt: 0.5000, sse=7864638.0, rms=3.657 (0.000%) rms = 3.62, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=7839481.5, rms=3.620 (0.000%) 022: dt: 0.2500, sse=5402053.5, rms=2.920 (0.000%) 023: dt: 0.2500, sse=5183350.0, rms=2.725 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5046009.0, rms=2.696 (0.000%) 025: dt: 0.1250, sse=4804380.5, rms=2.578 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4768387.0, rms=2.563 (0.000%) positioning took 3.5 minutes mean border=58.4, 1544 (26) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))] %35 local maxima, %31 large gradients and %29 min vals, 966 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=5444185.5, rms=4.43 027: dt: 0.5000, sse=5755994.0, rms=3.610 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5338768.5, rms=3.064 (0.000%) 029: dt: 0.2500, sse=5448826.0, rms=2.807 (0.000%) 030: dt: 0.2500, sse=5358850.0, rms=2.693 (0.000%) 031: dt: 0.2500, sse=5416080.5, rms=2.633 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5393155.0, rms=2.595 (0.000%) 033: dt: 0.1250, sse=5213682.0, rms=2.468 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5209134.0, rms=2.443 (0.000%) positioning took 1.1 minutes mean border=56.9, 1951 (5) missing vertices, mean dist 0.1 [0.2 (%39.4)->0.3 (%60.6))] %50 local maxima, %17 large gradients and %29 min vals, 991 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=5383456.0, rms=3.27 rms = 3.41, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5187640.0, rms=2.833 (0.000%) 036: dt: 0.2500, sse=5233485.5, rms=2.582 (0.000%) 037: dt: 0.2500, sse=5445307.5, rms=2.507 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5522560.5, rms=2.495 (0.000%) 039: dt: 0.1250, sse=5355698.5, rms=2.388 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5375383.0, rms=2.368 (0.000%) positioning took 0.9 minutes mean border=56.2, 3778 (4) missing vertices, mean dist 0.0 [0.2 (%45.1)->0.3 (%54.9))] %52 local maxima, %13 large gradients and %28 min vals, 813 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5411462.0, rms=2.59 rms = 3.02, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5309744.0, rms=2.424 (0.000%) 042: dt: 0.2500, sse=5531456.0, rms=2.370 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=5607312.5, rms=2.359 (0.000%) 044: dt: 0.1250, sse=5503982.5, rms=2.279 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=5536754.0, rms=2.264 (0.000%) positioning took 0.8 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.07-->6.43) (max @ vno 117187 --> 117166) face area 0.38 +- 0.29 (0.00-->7.21) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed 0 of 171356 vertices processed 25000 of 171356 vertices processed 50000 of 171356 vertices processed 75000 of 171356 vertices processed 100000 of 171356 vertices processed 125000 of 171356 vertices processed 150000 of 171356 vertices processed thickness calculation complete, 1437:1843 truncations. 35445 vertices at 0 distance 111456 vertices at 1 distance 107635 vertices at 2 distance 48759 vertices at 3 distance 17326 vertices at 4 distance 5512 vertices at 5 distance 1826 vertices at 6 distance 591 vertices at 7 distance 268 vertices at 8 distance 142 vertices at 9 distance 106 vertices at 10 distance 68 vertices at 11 distance 37 vertices at 12 distance 49 vertices at 13 distance 32 vertices at 14 distance 32 vertices at 15 distance 12 vertices at 16 distance 17 vertices at 17 distance 15 vertices at 18 distance 11 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/lh.thickness positioning took 15.5 minutes #-------------------------------------------- #@# Smooth2 lh Tue Apr 19 12:24:56 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Apr 19 12:25:03 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.2 mm, total surface area = 102557 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.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=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.9 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 229 vertices thresholded to be in k1 ~ [-0.40 0.36], k2 ~ [-0.09 0.08] total integrated curvature = 0.467*4pi (5.865) --> 1 handles ICI = 1.7, FI = 12.0, variation=201.153 155 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 147 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Tue Apr 19 12:27:45 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm nmr01002_only_wm2 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 [ nmr01002_only_wm2/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 [ 277 ] Gb_filter = 0 WARN: S lookup min: -0.445948 WARN: S explicit min: 0.000000 vertex = 560 #-------------------------------------------- #@# Tessellate rh Tue Apr 19 12:27:52 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 12 (out of 343299: 0.003495) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 20: 13 vertices, 18 faces slice 30: 3524 vertices, 3726 faces slice 40: 12191 vertices, 12543 faces slice 50: 24263 vertices, 24721 faces slice 60: 37970 vertices, 38423 faces slice 70: 50740 vertices, 51184 faces slice 80: 63449 vertices, 63848 faces slice 90: 76677 vertices, 77126 faces slice 100: 89742 vertices, 90186 faces slice 110: 102644 vertices, 103108 faces slice 120: 115080 vertices, 115532 faces slice 130: 126411 vertices, 126817 faces slice 140: 136800 vertices, 137187 faces slice 150: 145813 vertices, 146185 faces slice 160: 153280 vertices, 153549 faces slice 170: 159579 vertices, 159812 faces slice 180: 165518 vertices, 165754 faces slice 190: 169598 vertices, 169777 faces slice 200: 171058 vertices, 171102 faces slice 210: 171058 vertices, 171102 faces slice 220: 171058 vertices, 171102 faces slice 230: 171058 vertices, 171102 faces slice 240: 171058 vertices, 171102 faces slice 250: 171058 vertices, 171102 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... 171058 voxel in cpt #1: X=-44 [v=171058,e=513306,f=342204] located at (31.930340, -29.515585, 25.404402) For the whole surface: X=-44 [v=171058,e=513306,f=342204] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Apr 19 12:28:02 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Apr 19 12:28:08 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts avg radius = 50.9 mm, total surface area = 89969 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Apr 19 12:29:03 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.53 (0.00-->6.12) (max @ vno 133548 --> 133549) face area 0.02 +- 0.03 (-0.22-->0.64) scaling brain by 0.281... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.683, avgs=0 005/300: dt: 0.9000, rms radial error=176.428, avgs=0 010/300: dt: 0.9000, rms radial error=175.871, avgs=0 015/300: dt: 0.9000, rms radial error=175.139, avgs=0 020/300: dt: 0.9000, rms radial error=174.306, avgs=0 025/300: dt: 0.9000, rms radial error=173.414, avgs=0 030/300: dt: 0.9000, rms radial error=172.492, avgs=0 035/300: dt: 0.9000, rms radial error=171.553, avgs=0 040/300: dt: 0.9000, rms radial error=170.607, avgs=0 045/300: dt: 0.9000, rms radial error=169.659, avgs=0 050/300: dt: 0.9000, rms radial error=168.711, avgs=0 055/300: dt: 0.9000, rms radial error=167.766, avgs=0 060/300: dt: 0.9000, rms radial error=166.826, avgs=0 065/300: dt: 0.9000, rms radial error=165.889, avgs=0 070/300: dt: 0.9000, rms radial error=164.957, avgs=0 075/300: dt: 0.9000, rms radial error=164.031, avgs=0 080/300: dt: 0.9000, rms radial error=163.109, avgs=0 085/300: dt: 0.9000, rms radial error=162.193, avgs=0 090/300: dt: 0.9000, rms radial error=161.281, avgs=0 095/300: dt: 0.9000, rms radial error=160.375, avgs=0 100/300: dt: 0.9000, rms radial error=159.474, avgs=0 105/300: dt: 0.9000, rms radial error=158.578, avgs=0 110/300: dt: 0.9000, rms radial error=157.688, avgs=0 115/300: dt: 0.9000, rms radial error=156.803, avgs=0 120/300: dt: 0.9000, rms radial error=155.923, avgs=0 125/300: dt: 0.9000, rms radial error=155.047, avgs=0 130/300: dt: 0.9000, rms radial error=154.177, avgs=0 135/300: dt: 0.9000, rms radial error=153.311, avgs=0 140/300: dt: 0.9000, rms radial error=152.450, avgs=0 145/300: dt: 0.9000, rms radial error=151.594, avgs=0 150/300: dt: 0.9000, rms radial error=150.743, avgs=0 155/300: dt: 0.9000, rms radial error=149.896, avgs=0 160/300: dt: 0.9000, rms radial error=149.054, avgs=0 165/300: dt: 0.9000, rms radial error=148.216, avgs=0 170/300: dt: 0.9000, rms radial error=147.383, avgs=0 175/300: dt: 0.9000, rms radial error=146.555, avgs=0 180/300: dt: 0.9000, rms radial error=145.731, avgs=0 185/300: dt: 0.9000, rms radial error=144.912, avgs=0 190/300: dt: 0.9000, rms radial error=144.097, avgs=0 195/300: dt: 0.9000, rms radial error=143.287, avgs=0 200/300: dt: 0.9000, rms radial error=142.481, avgs=0 205/300: dt: 0.9000, rms radial error=141.680, avgs=0 210/300: dt: 0.9000, rms radial error=140.883, avgs=0 215/300: dt: 0.9000, rms radial error=140.090, avgs=0 220/300: dt: 0.9000, rms radial error=139.302, avgs=0 225/300: dt: 0.9000, rms radial error=138.518, avgs=0 230/300: dt: 0.9000, rms radial error=137.739, avgs=0 235/300: dt: 0.9000, rms radial error=136.964, avgs=0 240/300: dt: 0.9000, rms radial error=136.193, avgs=0 245/300: dt: 0.9000, rms radial error=135.426, avgs=0 250/300: dt: 0.9000, rms radial error=134.664, avgs=0 255/300: dt: 0.9000, rms radial error=133.906, avgs=0 260/300: dt: 0.9000, rms radial error=133.153, avgs=0 265/300: dt: 0.9000, rms radial error=132.403, avgs=0 270/300: dt: 0.9000, rms radial error=131.658, avgs=0 275/300: dt: 0.9000, rms radial error=130.917, avgs=0 280/300: dt: 0.9000, rms radial error=130.180, avgs=0 285/300: dt: 0.9000, rms radial error=129.447, avgs=0 290/300: dt: 0.9000, rms radial error=128.718, avgs=0 295/300: dt: 0.9000, rms radial error=127.993, avgs=0 300/300: dt: 0.9000, rms radial error=127.272, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20656.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3697.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 421.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00591 epoch 4 (K=640.0), pass 1, starting sse = 29.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/18 = 0.01216 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.15 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Apr 19 12:38:06 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nmr01002_only_wm2 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=171058, nf=342204, ne=513306, 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 9 iterations marking ambiguous vertices... 3220 ambiguous faces found in tessellation segmenting defects... 35 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 35 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4073 (-4.7036) -vertex loglikelihood: -6.1944 (-3.0972) -normal dot loglikelihood: -3.6341 (-3.6341) -quad curv loglikelihood: -6.5246 (-3.2623) Total Loglikelihood : -25.7604 CORRECTING DEFECT 0 (vertices=5, convex hull=28) After retessellation of defect 0, euler #=-31 (169022,506137,337084) : difference with theory (-32) = -1 CORRECTING DEFECT 1 (vertices=13, convex hull=34) Warning - incorrect dp selected!!!!(-65.832095 >= -65.832103 ) After retessellation of defect 1, euler #=-30 (169024,506153,337099) : difference with theory (-31) = -1 CORRECTING DEFECT 2 (vertices=53, convex hull=62) After retessellation of defect 2, euler #=-29 (169035,506213,337149) : difference with theory (-30) = -1 CORRECTING DEFECT 3 (vertices=181, convex hull=122) After retessellation of defect 3, euler #=-28 (169072,506383,337283) : difference with theory (-29) = -1 CORRECTING DEFECT 4 (vertices=89, convex hull=85) After retessellation of defect 4, euler #=-27 (169083,506455,337345) : difference with theory (-28) = -1 CORRECTING DEFECT 5 (vertices=94, convex hull=128) After retessellation of defect 5, euler #=-26 (169118,506613,337469) : difference with theory (-27) = -1 CORRECTING DEFECT 6 (vertices=11, convex hull=26) After retessellation of defect 6, euler #=-25 (169121,506628,337482) : difference with theory (-26) = -1 CORRECTING DEFECT 7 (vertices=6, convex hull=28) After retessellation of defect 7, euler #=-24 (169124,506645,337497) : difference with theory (-25) = -1 CORRECTING DEFECT 8 (vertices=14, convex hull=25) After retessellation of defect 8, euler #=-23 (169129,506671,337519) : difference with theory (-24) = -1 CORRECTING DEFECT 9 (vertices=26, convex hull=40) After retessellation of defect 9, euler #=-22 (169137,506707,337548) : difference with theory (-23) = -1 CORRECTING DEFECT 10 (vertices=24, convex hull=64) After retessellation of defect 10, euler #=-21 (169153,506780,337606) : difference with theory (-22) = -1 CORRECTING DEFECT 11 (vertices=20, convex hull=43) After retessellation of defect 11, euler #=-20 (169163,506825,337642) : difference with theory (-21) = -1 CORRECTING DEFECT 12 (vertices=6, convex hull=21) After retessellation of defect 12, euler #=-19 (169166,506841,337656) : difference with theory (-20) = -1 CORRECTING DEFECT 13 (vertices=55, convex hull=66) After retessellation of defect 13, euler #=-18 (169189,506936,337729) : difference with theory (-19) = -1 CORRECTING DEFECT 14 (vertices=615, convex hull=386) After retessellation of defect 14, euler #=-17 (169216,507219,337986) : difference with theory (-18) = -1 CORRECTING DEFECT 15 (vertices=59, convex hull=87) After retessellation of defect 15, euler #=-16 (169248,507352,338088) : difference with theory (-17) = -1 CORRECTING DEFECT 16 (vertices=6, convex hull=14) After retessellation of defect 16, euler #=-15 (169249,507357,338093) : difference with theory (-16) = -1 CORRECTING DEFECT 17 (vertices=28, convex hull=67) After retessellation of defect 17, euler #=-14 (169264,507429,338151) : difference with theory (-15) = -1 CORRECTING DEFECT 18 (vertices=29, convex hull=26) After retessellation of defect 18, euler #=-13 (169272,507460,338175) : difference with theory (-14) = -1 CORRECTING DEFECT 19 (vertices=11, convex hull=28) After retessellation of defect 19, euler #=-12 (169273,507471,338186) : difference with theory (-13) = -1 CORRECTING DEFECT 20 (vertices=88, convex hull=107) After retessellation of defect 20, euler #=-12 (169320,507667,338335) : difference with theory (-12) = 0 CORRECTING DEFECT 21 (vertices=11, convex hull=24) After retessellation of defect 21, euler #=-11 (169325,507692,338356) : difference with theory (-11) = 0 CORRECTING DEFECT 22 (vertices=15, convex hull=14) After retessellation of defect 22, euler #=-10 (169327,507700,338363) : difference with theory (-10) = 0 CORRECTING DEFECT 23 (vertices=59, convex hull=52) After retessellation of defect 23, euler #=-9 (169336,507742,338397) : difference with theory (-9) = 0 CORRECTING DEFECT 24 (vertices=27, convex hull=36) After retessellation of defect 24, euler #=-8 (169344,507779,338427) : difference with theory (-8) = 0 CORRECTING DEFECT 25 (vertices=47, convex hull=66) After retessellation of defect 25, euler #=-7 (169358,507852,338487) : difference with theory (-7) = 0 CORRECTING DEFECT 26 (vertices=71, convex hull=90) After retessellation of defect 26, euler #=-6 (169402,508027,338619) : difference with theory (-6) = 0 CORRECTING DEFECT 27 (vertices=51, convex hull=41) After retessellation of defect 27, euler #=-5 (169405,508053,338643) : difference with theory (-5) = 0 CORRECTING DEFECT 28 (vertices=21, convex hull=54) After retessellation of defect 28, euler #=-4 (169418,508114,338692) : difference with theory (-4) = 0 CORRECTING DEFECT 29 (vertices=75, convex hull=114) After retessellation of defect 29, euler #=-3 (169475,508335,338857) : difference with theory (-3) = 0 CORRECTING DEFECT 30 (vertices=56, convex hull=75) After retessellation of defect 30, euler #=-2 (169493,508423,338928) : difference with theory (-2) = 0 CORRECTING DEFECT 31 (vertices=25, convex hull=29) After retessellation of defect 31, euler #=-1 (169496,508443,338946) : difference with theory (-1) = 0 CORRECTING DEFECT 32 (vertices=40, convex hull=35) After retessellation of defect 32, euler #=0 (169496,508454,338958) : difference with theory (0) = 0 CORRECTING DEFECT 33 (vertices=61, convex hull=51) After retessellation of defect 33, euler #=1 (169505,508504,339000) : difference with theory (1) = 0 CORRECTING DEFECT 34 (vertices=41, convex hull=21) After retessellation of defect 34, euler #=2 (169506,508512,339008) : 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-->9.05) (max @ vno 34835 --> 46339) 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-->9.05) (max @ vno 34835 --> 46339) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 138 mutations (39.5%), 211 crossovers (60.5%), 239 vertices were eliminated building final representation... 1552 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=169506, nf=339008, ne=508512, g=0) writing corrected surface to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 25.7 minutes 0 defective edges removing intersecting faces 000: 180 intersecting 001: 21 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 169506 - 508512 + 339008 = 2 --> 0 holes F =2V-4: 339008 = 339012-4 (0) 2E=3F: 1017024 = 1017024 (0) total defect index = 0 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 36 intersecting 001: 6 intersecting expanding nbhd size to 2 002: 12 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Apr 19 13:04:04 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs nmr01002_only_wm2 rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/filled.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/wm.mgz... 19499 bright wm thresholded. 465 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.orig... computing class statistics... border white: 316439 voxels (1.89%) border gray 350764 voxels (2.09%) WM (95.0): 96.4 +- 8.0 [70.0 --> 110.0] GM (83.0) : 81.1 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.49) (max @ vno 118545 --> 118563) face area 0.28 +- 0.12 (0.00-->2.40) mean absolute distance = 0.69 +- 0.91 4553 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.5, 421 (421) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %74 local maxima, %21 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.04-->3.95) (max @ vno 75618 --> 76970) face area 0.28 +- 0.13 (0.00-->2.55) mean absolute distance = 0.35 +- 0.60 4361 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6338101.0, rms=10.06 001: dt: 0.5000, sse=7206244.0, rms=7.132 (0.000%) 002: dt: 0.5000, sse=7732851.0, rms=5.453 (0.000%) 003: dt: 0.5000, sse=8168741.0, rms=4.533 (0.000%) 004: dt: 0.5000, sse=8450961.0, rms=3.997 (0.000%) 005: dt: 0.5000, sse=8603883.0, rms=3.773 (0.000%) 006: dt: 0.5000, sse=8681174.0, rms=3.602 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8714161.0, rms=3.553 (0.000%) 008: dt: 0.2500, sse=5360751.5, rms=2.588 (0.000%) 009: dt: 0.2500, sse=4904024.0, rms=2.317 (0.000%) 010: dt: 0.2500, sse=4700502.5, rms=2.212 (0.000%) 011: dt: 0.2500, sse=4631379.5, rms=2.129 (0.000%) 012: dt: 0.2500, sse=4592668.0, rms=2.070 (0.000%) 013: dt: 0.2500, sse=4562463.0, rms=2.013 (0.000%) 014: dt: 0.2500, sse=4539246.5, rms=1.959 (0.000%) 015: dt: 0.2500, sse=4517194.5, rms=1.903 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=4510084.5, rms=1.858 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=4450471.5, rms=1.818 (0.000%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.4, 324 (226) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.3 (%27.5))] %82 local maxima, %14 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 (0.05-->4.16) (max @ vno 129847 --> 129848) face area 0.35 +- 0.16 (0.00-->3.06) mean absolute distance = 0.26 +- 0.39 4792 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5168582.0, rms=4.56 018: dt: 0.5000, sse=5584849.5, rms=2.975 (0.000%) rms = 3.02, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5199023.0, rms=2.405 (0.000%) 020: dt: 0.2500, sse=5028092.0, rms=1.944 (0.000%) 021: dt: 0.2500, sse=4940134.0, rms=1.727 (0.000%) 022: dt: 0.2500, sse=4867988.0, rms=1.631 (0.000%) 023: dt: 0.2500, sse=4850118.0, rms=1.567 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4838362.0, rms=1.526 (0.000%) rms = 1.49, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4790093.5, rms=1.493 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 1 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 removing 2 vertex label from ripped group mean border=87.8, 270 (150) missing vertices, mean dist -0.1 [0.3 (%73.3)->0.2 (%26.7))] %89 local maxima, % 6 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 (0.03-->4.27) (max @ vno 129847 --> 129848) face area 0.34 +- 0.16 (0.00-->3.87) mean absolute distance = 0.21 +- 0.31 4500 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5047951.5, rms=3.31 026: dt: 0.5000, sse=5338972.5, rms=2.552 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5019330.0, rms=1.836 (0.000%) 028: dt: 0.2500, sse=4932011.0, rms=1.471 (0.000%) 029: dt: 0.2500, sse=4914633.0, rms=1.368 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4899313.0, rms=1.357 (0.000%) rms = 1.33, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4858704.5, rms=1.327 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 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=88.6, 233 (106) missing vertices, mean dist -0.0 [0.2 (%58.7)->0.2 (%41.3))] %91 local maxima, % 4 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4872650.0, rms=1.65 rms = 1.71, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4935300.5, rms=1.262 (0.000%) 033: dt: 0.2500, sse=5122621.5, rms=1.071 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5113312.5, rms=1.069 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 9 non-cortical segments detected only using segment with 2682 vertices erasing segment 1 (vno[0] = 119567) erasing segment 2 (vno[0] = 125526) erasing segment 3 (vno[0] = 125614) erasing segment 4 (vno[0] = 125744) erasing segment 5 (vno[0] = 133686) erasing segment 6 (vno[0] = 133727) erasing segment 7 (vno[0] = 134721) erasing segment 8 (vno[0] = 135704) writing cortex label to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/label/rh.cortex.label... writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->4.21) (max @ vno 129847 --> 129848) face area 0.33 +- 0.16 (0.00-->3.91) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=61.2, 202 (202) missing vertices, mean dist 1.6 [1.1 (%0.1)->2.6 (%99.9))] %17 local maxima, %42 large gradients and %37 min vals, 2527 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=27893140.0, rms=27.55 001: dt: 0.5000, sse=21345618.0, rms=23.592 (0.000%) 002: dt: 0.5000, sse=16555676.0, rms=20.246 (0.000%) 003: dt: 0.5000, sse=13189619.0, rms=17.496 (0.000%) 004: dt: 0.5000, sse=10970685.0, rms=15.260 (0.000%) 005: dt: 0.5000, sse=9509805.0, rms=13.442 (0.000%) 006: dt: 0.5000, sse=8559388.0, rms=11.938 (0.000%) 007: dt: 0.5000, sse=7918998.5, rms=10.563 (0.000%) 008: dt: 0.5000, sse=7457037.5, rms=9.292 (0.000%) 009: dt: 0.5000, sse=7193226.0, rms=8.093 (0.000%) 010: dt: 0.5000, sse=7046874.0, rms=6.998 (0.000%) 011: dt: 0.5000, sse=7016630.5, rms=6.029 (0.000%) 012: dt: 0.5000, sse=7070260.0, rms=5.256 (0.000%) 013: dt: 0.5000, sse=7167258.0, rms=4.680 (0.000%) 014: dt: 0.5000, sse=7307432.0, rms=4.297 (0.000%) 015: dt: 0.5000, sse=7411144.5, rms=4.013 (0.000%) 016: dt: 0.5000, sse=7430954.5, rms=3.828 (0.000%) 017: dt: 0.5000, sse=7500287.0, rms=3.674 (0.000%) 018: dt: 0.5000, sse=7502280.0, rms=3.597 (0.000%) 019: dt: 0.5000, sse=7565671.5, rms=3.531 (0.000%) rms = 3.51, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7562792.0, rms=3.513 (0.000%) 021: dt: 0.2500, sse=5316821.5, rms=2.846 (0.000%) 022: dt: 0.2500, sse=5100942.5, rms=2.683 (0.000%) rms = 2.66, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4970864.0, rms=2.662 (0.000%) 024: dt: 0.1250, sse=4738970.5, rms=2.541 (0.000%) rms = 2.53, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4711734.0, rms=2.526 (0.000%) positioning took 3.9 minutes mean border=59.4, 1597 (27) missing vertices, mean dist 0.1 [0.2 (%48.2)->0.6 (%51.8))] %33 local maxima, %33 large gradients and %29 min vals, 821 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=5345970.0, rms=4.26 026: dt: 0.5000, sse=5691735.5, rms=3.625 (0.000%) 027: dt: 0.5000, sse=7355727.5, rms=3.562 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=7075903.5, rms=3.557 (0.000%) 029: dt: 0.2500, sse=5781162.5, rms=2.794 (0.000%) 030: dt: 0.2500, sse=5642859.5, rms=2.582 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=5538265.5, rms=2.518 (0.000%) 032: dt: 0.1250, sse=5353996.0, rms=2.428 (0.000%) rms = 2.41, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5303484.5, rms=2.408 (0.000%) positioning took 1.1 minutes mean border=58.0, 1908 (12) missing vertices, mean dist 0.1 [0.2 (%40.0)->0.4 (%60.0))] %47 local maxima, %19 large gradients and %29 min vals, 1024 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=5473989.0, rms=3.22 rms = 3.27, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5277544.5, rms=2.829 (0.000%) 035: dt: 0.2500, sse=5289852.0, rms=2.566 (0.000%) 036: dt: 0.2500, sse=5492033.5, rms=2.488 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5563110.5, rms=2.484 (0.000%) 038: dt: 0.1250, sse=5399306.0, rms=2.372 (0.000%) rms = 2.35, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5415900.0, rms=2.351 (0.000%) positioning took 0.9 minutes mean border=57.3, 3675 (11) missing vertices, mean dist 0.1 [0.2 (%44.9)->0.3 (%55.1))] %50 local maxima, %15 large gradients and %28 min vals, 865 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/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5450368.5, rms=2.58 rms = 2.96, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5353272.5, rms=2.417 (0.000%) 041: dt: 0.2500, sse=5565400.5, rms=2.353 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5644096.5, rms=2.340 (0.000%) 043: dt: 0.1250, sse=5538904.0, rms=2.261 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5563351.5, rms=2.245 (0.000%) positioning took 0.7 minutes writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.area.pial vertex spacing 0.99 +- 0.41 (0.04-->7.15) (max @ vno 123537 --> 123521) face area 0.39 +- 0.29 (0.00-->6.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169506 vertices processed 25000 of 169506 vertices processed 50000 of 169506 vertices processed 75000 of 169506 vertices processed 100000 of 169506 vertices processed 125000 of 169506 vertices processed 150000 of 169506 vertices processed 0 of 169506 vertices processed 25000 of 169506 vertices processed 50000 of 169506 vertices processed 75000 of 169506 vertices processed 100000 of 169506 vertices processed 125000 of 169506 vertices processed 150000 of 169506 vertices processed thickness calculation complete, 1174:1893 truncations. 35711 vertices at 0 distance 112087 vertices at 1 distance 103461 vertices at 2 distance 47701 vertices at 3 distance 16979 vertices at 4 distance 5593 vertices at 5 distance 1743 vertices at 6 distance 620 vertices at 7 distance 249 vertices at 8 distance 133 vertices at 9 distance 83 vertices at 10 distance 57 vertices at 11 distance 48 vertices at 12 distance 29 vertices at 13 distance 26 vertices at 14 distance 20 vertices at 15 distance 14 vertices at 16 distance 10 vertices at 17 distance 14 vertices at 18 distance 10 vertices at 19 distance 18 vertices at 20 distance writing curvature file /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf/rh.thickness positioning took 16.1 minutes #-------------------------------------------- #@# Smooth2 rh Tue Apr 19 13:20:11 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/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 Apr 19 13:20:17 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.1 mm, total surface area = 101948 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.8 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 219 vertices thresholded to be in k1 ~ [-0.24 0.53], k2 ~ [-0.12 0.07] total integrated curvature = 0.510*4pi (6.405) --> 0 handles ICI = 1.9, FI = 14.7, variation=243.925 148 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 165 vertices thresholded to be in [-0.12 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.014, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Tue Apr 19 13:23:19 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm nmr01002_only_wm2 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 [ nmr01002_only_wm2/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 [ 343 ] Gb_filter = 0 WARN: S lookup min: -0.306479 WARN: S explicit min: 0.000000 vertex = 156 #-------------------------------------------- #@# ASeg Stats Tue Apr 19 13:23:27 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr01002_only_wm2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002_only_wm2 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject nmr01002_only_wm2 sysname Linux hostname compute-0-39 machine x86_64 user dwakeman UseRobust 0 atlas_icv (eTIV) = 1843650 mm^3 (det: 1.056657 ) Computing euler number orig.nofix lheno = -38, rheno = -44 orig.nofix lhholes = 20, rhholes = 23 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 293159.593 284111.000 diff= 9048.6 pctdiff= 3.087 rhCtxGM: 288550.509 275164.000 diff=13386.5 pctdiff= 4.639 lhCtxWM: 291224.196 291924.000 diff= -699.8 pctdiff=-0.240 rhCtxWM: 290483.286 290463.000 diff= 20.3 pctdiff= 0.007 SubCortGMVol 65073.000 SupraTentVol 1267929.584 (1244988.000) diff=22941.584 pctdiff=1.809 SupraTentVolNotVent 1230156.584 (1207215.000) diff=22941.584 pctdiff=1.865 BrainSegVol 1391668.000 (1389201.000) diff=2467.000 pctdiff=0.177 BrainSegVolNotVent 1350634.000 (1372067.584) diff=-21433.584 pctdiff=-1.587 BrainSegVolNotVent 1350634.000 CerebellumVol 143097.000 VentChorVol 37773.000 3rd4th5thCSF 3261.000 CSFVol 841.000, OptChiasmVol 275.000 MaskVol 1919383.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 19118 19118.055 4 5 Left-Inf-Lat-Vent 520 520.060 5 7 Left-Cerebellum-White-Matter 19700 19699.701 6 8 Left-Cerebellum-Cortex 53472 53472.230 7 10 Left-Thalamus-Proper 8963 8962.595 8 11 Left-Caudate 3573 3573.187 9 12 Left-Putamen 6421 6421.121 10 13 Left-Pallidum 1439 1438.815 11 14 3rd-Ventricle 722 721.945 12 15 4th-Ventricle 1958 1957.972 13 16 Brain-Stem 27112 27112.328 14 17 Left-Hippocampus 4400 4400.408 15 18 Left-Amygdala 1787 1786.623 16 24 CSF 902 902.354 17 26 Left-Accumbens-area 573 573.266 18 28 Left-VentralDC 4634 4634.012 19 30 Left-vessel 220 219.571 20 31 Left-choroid-plexus 1494 1493.786 23 43 Right-Lateral-Ventricle 14433 14432.729 24 44 Right-Inf-Lat-Vent 502 502.259 25 46 Right-Cerebellum-White-Matter 18732 18731.957 26 47 Right-Cerebellum-Cortex 53362 53361.777 27 49 Right-Thalamus-Proper 7901 7900.568 28 50 Right-Caudate 3964 3964.413 29 51 Right-Putamen 5970 5970.317 30 52 Right-Pallidum 1727 1727.467 31 53 Right-Hippocampus 5094 5093.581 32 54 Right-Amygdala 1979 1978.811 33 58 Right-Accumbens-area 715 714.996 34 60 Right-VentralDC 4636 4636.441 35 62 Right-vessel 265 264.728 36 63 Right-choroid-plexus 1793 1792.552 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1813 1813.132 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 39 39.252 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 275 274.977 45 251 CC_Posterior 1374 1374.238 46 252 CC_Mid_Posterior 547 546.627 47 253 CC_Central 503 502.871 48 254 CC_Mid_Anterior 605 604.529 49 255 CC_Anterior 1351 1351.204 Reporting on 45 segmentations mri_segstats done #------------------------------------------ Started at Tue Apr 19 11:32:18 EDT 2016 Ended at Tue Apr 19 13:26:47 EDT 2016 #@#%# recon-all-run-time-hours 1.908 recon-all -s nmr01002_only_wm2 finished without error at Tue Apr 19 13:26:48 EDT 2016