Tue Jun 14 16:00:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 /usr/local/freesurfer/stable6//bin/recon-all -all -nuintensitycor-3T -subjid AD08 -i /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD08/AD08_MR.nii subjid AD08 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 Linux compute-0-49 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 29360128 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 26063020 6814232 8 226604 6424436 -/+ buffers/cache: 19411980 13465272 Swap: 67108860 68192 67040668 pbsjob 11789906.launchpad.nmr.mgh.harvard.edu ######################################## program versions used $Id: recon-all,v 1.580 2016/05/13 15:04:55 greve Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: tkregister2.c,v 1.132 2016/05/04 22:17:15 greve Exp $ User: fdu0 Machine: compute-0-49 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 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_label2label.c,v 1.48 2016/03/16 23:36:50 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_ca_register.c,v 1.96 2016/04/30 02:37:04 fischl Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_ca_label.c,v 1.113 2016/05/13 18:02:49 fischl Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:22-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: fdu0 Machine: compute-0-49 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: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/06/14-20:00:23-GMT BuildTimeStamp: Jun 11 2016 02:03:02 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: fdu0 Machine: compute-0-49 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable6//average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif curvature.buckner40.2016-03-20.tif GCSDIR /usr/local/freesurfer/stable6//average GCS DKatlas.2016-03-20.gcs ####################################### /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD08/AD08_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig/001.mgz mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD08/AD08_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD08/AD08_MR.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jun 14 16:00:29 EDT 2016 Found 1 runs /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig/001.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/talairach.xfm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jun 14 16:00:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri /usr/local/freesurfer/stable6//bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux compute-0-49 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 Tue Jun 14 16:00:43 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1535 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1535/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1535/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1535/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jun 14 16:00:46 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.1535/nu0.mnc ./tmp.mri_nu_correct.mni.1535/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1535/0/ -iterations 1000 -distance 50 [fdu0@compute-0-49:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/] [2016-06-14 16:00:46] running: /usr/local/freesurfer/stable6//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1535/0/ ./tmp.mri_nu_correct.mni.1535/nu0.mnc ./tmp.mri_nu_correct.mni.1535/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000976841 mri_convert ./tmp.mri_nu_correct.mni.1535/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.1535/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1535/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Jun 14 16:02:03 EDT 2016 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Jun 14 16:02:03 EDT 2016 Ended at Tue Jun 14 16:03:17 EDT 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jun 14 16:03:19 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7785, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6//bin/extract_talairach_avi_QA.awk /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/talairach_avi.log TalAviQA: 0.97582 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Jun 14 16:03:19 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri /usr/local/freesurfer/stable6//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux compute-0-49 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 Tue Jun 14 16:03:19 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.2270 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2270/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2270/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2270/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jun 14 16:03:22 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.2270/nu0.mnc ./tmp.mri_nu_correct.mni.2270/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2270/0/ -iterations 1000 -distance 50 [fdu0@compute-0-49:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/] [2016-06-14 16:03:22] running: /usr/local/freesurfer/stable6//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2270/0/ ./tmp.mri_nu_correct.mni.2270/nu0.mnc ./tmp.mri_nu_correct.mni.2270/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 Number of iterations: 27 CV of field change: 0.000976841 mri_binarize --i ./tmp.mri_nu_correct.mni.2270/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2270/ones.mgz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2270/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2270/ones.mgz sysname Linux hostname compute-0-49 machine x86_64 user fdu0 input ./tmp.mri_nu_correct.mni.2270/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2270/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2270/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2270/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2270/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2270/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2270/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2270/input.mean.dat sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2270/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2270/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2270/ones.mgz --i ./tmp.mri_nu_correct.mni.2270/nu1.mnc --sum ./tmp.mri_nu_correct.mni.2270/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2270/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2270/ones.mgz --i ./tmp.mri_nu_correct.mni.2270/nu1.mnc --sum ./tmp.mri_nu_correct.mni.2270/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2270/output.mean.dat sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2270/ones.mgz Loading ./tmp.mri_nu_correct.mni.2270/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2270/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2270/nu1.mnc ./tmp.mri_nu_correct.mni.2270/nu1.mnc mul 1.01734680848282913793 Saving result to './tmp.mri_nu_correct.mni.2270/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2270/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.2270/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.2270/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 12 seconds. mapping (10, 124) to ( 3, 110) Tue Jun 14 16:05:12 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Jun 14 16:05:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.04798 0.03005 0.03295 -1.24594; 0.02443 1.03440 0.18698 2.87847; -0.04359 -0.13410 1.10357 -3.82082; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 108 gm peak at 56 (56), valley at 43 (43) csf peak at 29, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 49 (49), valley at 38 (38) csf peak at 25, setting threshold to 41 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 52 seconds. #-------------------------------------------- #@# Skull Stripping Tue Jun 14 16:08:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/stable6//average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable6//average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (44, 47, 26) --> (207, 255, 229) using (98, 116, 128) as brain centroid... mean wm in atlas = 108, using box (78,90,103) --> (118, 141,153) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 7.0 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.485 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.410844 @ (-9.091, -9.091, -9.091) max log p = -4.275327 @ (4.545, 4.545, -4.545) max log p = -4.188837 @ (2.273, -2.273, -2.273) max log p = -4.163782 @ (1.136, 1.136, 1.136) max log p = -4.157019 @ (0.568, -1.705, -1.705) max log p = -4.151596 @ (0.284, 1.989, 0.284) Found translation: (-0.3, -5.4, -16.2): log p = -4.152 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.946, old_max_log_p =-4.152 (thresh=-4.1) 1.06375 0.00000 0.00000 -8.26299; 0.00000 1.14016 0.13053 -42.67365; 0.00000 -0.16136 1.06580 -0.74521; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.946, old_max_log_p =-3.946 (thresh=-3.9) 1.06375 0.00000 0.00000 -8.26299; 0.00000 1.14016 0.13053 -42.67365; 0.00000 -0.16136 1.06580 -0.74521; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.892, old_max_log_p =-3.946 (thresh=-3.9) 1.04334 0.00380 -0.03517 -1.79791; -0.00256 1.15537 0.16351 -48.79050; 0.03779 -0.19489 1.03973 4.66244; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.887, old_max_log_p =-3.892 (thresh=-3.9) 1.02138 0.04707 -0.06259 -2.01101; -0.03595 1.13277 0.16258 -41.15645; 0.07325 -0.19831 1.05749 -1.49433; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.887, old_max_log_p =-3.887 (thresh=-3.9) 1.02138 0.04707 -0.06259 -2.01101; -0.03595 1.13277 0.16258 -41.15645; 0.07325 -0.19831 1.05749 -1.49433; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.873, old_max_log_p =-3.887 (thresh=-3.9) 1.02498 0.04724 -0.06281 -2.45744; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.867, old_max_log_p =-3.873 (thresh=-3.9) 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.867, old_max_log_p =-3.867 (thresh=-3.9) 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.867 (old=-4.485) transform before final EM align: 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.02858 0.04740 -0.06303 -2.90544; -0.03586 1.13012 0.16220 -40.72676; 0.07308 -0.19785 1.05501 -1.23084; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1273.109457 mri_em_register stimesec 1.238811 mri_em_register ru_maxrss 609760 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157489 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 16 mri_em_register ru_nivcsw 1424 registration took 21 minutes and 15 seconds. mri_watershed -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/stable6//average/RB_all_withskull_2016-05-10.vc700.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=126 y=124 z=119 r=81 first estimation of the main basin volume: 2302300 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=154, y=122, z=82, Imax=255 CSF=18, 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=267011239 voxels, voxel volume =1.000 = 267011239 mmm3 = 267011.232 cm3 done. PostAnalyze...Basin Prior 369 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=127, z=116, r=10261 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 45585 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=25 , nb = -1033216626 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = -1044158684 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = 1067016277 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 1079583530 OTHER CSF_MIN=0, CSF_intensity=11, CSF_MAX=31 , nb = 1069275216 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 29, 24, 17, 68 after analyzing : 18, 24, 25, 35 RIGHT_CER before analyzing : 25, 25, 25, 65 after analyzing : 18, 25, 25, 35 LEFT_CER before analyzing : 20, 22, 27, 56 after analyzing : 20, 25, 27, 32 RIGHT_BRAIN before analyzing : 34, 28, 19, 70 after analyzing : 21, 28, 28, 38 LEFT_BRAIN before analyzing : 28, 24, 18, 68 after analyzing : 18, 24, 25, 35 OTHER before analyzing : 31, 43, 63, 95 after analyzing : 31, 56, 63, 65 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.698, std = 6.986 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.20, sigma = 4.58 after rotation: sse = 3.20, sigma = 4.58 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.25, its var is 3.78 before Erosion-Dilatation 0.27% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1616870 voxels, voxel volume = 1.000 mm3 = 1616870 mmm3 = 1616.870 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 29.029586 mri_watershed stimesec 0.550916 mri_watershed ru_maxrss 841744 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 216391 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 56 mri_watershed ru_nivcsw 42 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Jun 14 16:29:53 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (54, 61, 38) --> (195, 196, 207) using (101, 106, 123) as brain centroid... mean wm in atlas = 107, using box (84,89,102) --> (118, 122,143) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 6.1 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.125 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.026993 @ (-9.091, -9.091, -9.091) max log p = -3.878416 @ (4.545, 4.545, -4.545) max log p = -3.756564 @ (6.818, -2.273, -2.273) max log p = -3.700735 @ (-3.409, -1.136, 3.409) max log p = -3.700735 @ (0.000, 0.000, 0.000) max log p = -3.700735 @ (0.000, 0.000, 0.000) Found translation: (-1.1, -8.0, -12.5): log p = -3.701 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.554, old_max_log_p =-3.701 (thresh=-3.7) 1.07500 0.00000 0.00000 -10.72689; 0.00000 1.14016 0.13053 -41.18418; 0.00000 -0.15011 0.99144 7.60909; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.554, old_max_log_p =-3.554 (thresh=-3.6) 1.07500 0.00000 0.00000 -10.72689; 0.00000 1.14016 0.13053 -41.18418; 0.00000 -0.15011 0.99144 7.60909; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.440, old_max_log_p =-3.554 (thresh=-3.6) 1.05419 0.03838 0.00220 -13.20815; -0.03300 1.10472 0.19616 -40.19496; 0.00443 -0.22702 1.01822 15.54694; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.430, old_max_log_p =-3.440 (thresh=-3.4) 1.03442 0.03766 0.00215 -10.58418; -0.03300 1.10472 0.19616 -40.19496; 0.00443 -0.22702 1.01822 15.54694; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.430, old_max_log_p =-3.430 (thresh=-3.4) 1.03442 0.03766 0.00215 -10.58418; -0.03300 1.10472 0.19616 -40.19496; 0.00443 -0.22702 1.01822 15.54694; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.381, old_max_log_p =-3.430 (thresh=-3.4) 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.381, old_max_log_p =-3.381 (thresh=-3.4) 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.381 (old=-4.125) transform before final EM align: 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 943.822517 mri_em_register stimesec 0.961853 mri_em_register ru_maxrss 598992 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158866 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 16 mri_em_register ru_nivcsw 1206 registration took 15 minutes and 45 seconds. #-------------------------------------- #@# CA Normalize Tue Jun 14 16:45:38 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.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/stable6//average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (54, 63, 38) --> (195, 195, 207) using (101, 107, 123) as brain centroid... mean wm in atlas = 107, using box (84,91,102) --> (118, 123,143) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 6.2 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04845; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 67, 41) --> (192, 171, 201) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 27 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 69, 40) --> (130, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 68 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 148, 67) --> (174, 187, 120) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 148, 64) --> (126, 184, 120) Right_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 137, 102) --> (144, 200, 131) Brain_Stem: limiting intensities to 96.0 --> 132.0 0 of 11 (0.0%) samples deleted using 132 total control points for intensity normalization... bias field = 0.910 +- 0.096 0 of 132 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 67, 41) --> (192, 171, 201) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 120 (2.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 69, 40) --> (130, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 162 (1.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 148, 67) --> (174, 187, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 54 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 148, 64) --> (126, 184, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 60 (13.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 137, 102) --> (144, 200, 131) Brain_Stem: limiting intensities to 98.0 --> 132.0 49 of 62 (79.0%) samples deleted using 458 total control points for intensity normalization... bias field = 1.031 +- 0.098 0 of 379 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 67, 41) --> (192, 171, 201) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 132.0 86 of 278 (30.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 69, 40) --> (130, 170, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 305 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 148, 67) --> (174, 187, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 85 (37.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 148, 64) --> (126, 184, 120) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 55 (30.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 137, 102) --> (144, 200, 131) Brain_Stem: limiting intensities to 88.0 --> 132.0 44 of 120 (36.7%) samples deleted using 843 total control points for intensity normalization... bias field = 0.990 +- 0.071 2 of 655 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Tue Jun 14 16:47:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.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... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.20 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.938, neg=0, invalid=4512 0001: dt=211.814570, rms=0.846 (9.762%), neg=0, invalid=4512 0002: dt=209.003690, rms=0.824 (2.651%), neg=0, invalid=4512 0003: dt=243.120606, rms=0.811 (1.608%), neg=0, invalid=4512 0004: dt=129.472000, rms=0.805 (0.625%), neg=0, invalid=4512 0005: dt=1479.680000, rms=0.782 (2.972%), neg=0, invalid=4512 0006: dt=129.472000, rms=0.778 (0.434%), neg=0, invalid=4512 0007: dt=517.888000, rms=0.772 (0.797%), neg=0, invalid=4512 0008: dt=517.888000, rms=0.769 (0.377%), neg=0, invalid=4512 0009: dt=221.952000, rms=0.766 (0.404%), neg=0, invalid=4512 0010: dt=73.984000, rms=0.766 (0.026%), neg=0, invalid=4512 0011: dt=73.984000, rms=0.765 (0.035%), neg=0, invalid=4512 0012: dt=73.984000, rms=0.765 (0.063%), neg=0, invalid=4512 0013: dt=73.984000, rms=0.764 (0.116%), neg=0, invalid=4512 0014: dt=73.984000, rms=0.763 (0.190%), neg=0, invalid=4512 0015: dt=73.984000, rms=0.761 (0.232%), neg=0, invalid=4512 0016: dt=73.984000, rms=0.759 (0.228%), neg=0, invalid=4512 0017: dt=73.984000, rms=0.758 (0.205%), neg=0, invalid=4512 0018: dt=73.984000, rms=0.756 (0.188%), neg=0, invalid=4512 0019: dt=73.984000, rms=0.755 (0.180%), neg=0, invalid=4512 0020: dt=73.984000, rms=0.753 (0.183%), neg=0, invalid=4512 0021: dt=73.984000, rms=0.752 (0.201%), neg=0, invalid=4512 0022: dt=73.984000, rms=0.750 (0.215%), neg=0, invalid=4512 0023: dt=73.984000, rms=0.749 (0.212%), neg=0, invalid=4512 0024: dt=73.984000, rms=0.747 (0.191%), neg=0, invalid=4512 0025: dt=73.984000, rms=0.746 (0.165%), neg=0, invalid=4512 0026: dt=73.984000, rms=0.745 (0.142%), neg=0, invalid=4512 0027: dt=73.984000, rms=0.744 (0.143%), neg=0, invalid=4512 0028: dt=73.984000, rms=0.743 (0.160%), neg=0, invalid=4512 0029: dt=73.984000, rms=0.741 (0.171%), neg=0, invalid=4512 0030: dt=73.984000, rms=0.740 (0.171%), neg=0, invalid=4512 0031: dt=73.984000, rms=0.739 (0.149%), neg=0, invalid=4512 0032: dt=73.984000, rms=0.738 (0.130%), neg=0, invalid=4512 0033: dt=73.984000, rms=0.737 (0.115%), neg=0, invalid=4512 0034: dt=73.984000, rms=0.736 (0.109%), neg=0, invalid=4512 0035: dt=2071.552000, rms=0.734 (0.314%), neg=0, invalid=4512 0036: dt=32.368000, rms=0.734 (0.017%), neg=0, invalid=4512 0037: dt=32.368000, rms=0.734 (0.008%), neg=0, invalid=4512 0038: dt=32.368000, rms=0.734 (-0.011%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.734, neg=0, invalid=4512 0039: dt=92.480000, rms=0.734 (0.102%), neg=0, invalid=4512 0040: dt=129.472000, rms=0.733 (0.022%), neg=0, invalid=4512 0041: dt=129.472000, rms=0.733 (0.026%), neg=0, invalid=4512 0042: dt=129.472000, rms=0.733 (0.031%), neg=0, invalid=4512 0043: dt=129.472000, rms=0.733 (0.031%), neg=0, invalid=4512 0044: dt=129.472000, rms=0.733 (0.032%), neg=0, invalid=4512 0045: dt=129.472000, rms=0.732 (0.029%), neg=0, invalid=4512 0046: dt=129.472000, rms=0.732 (0.033%), neg=0, invalid=4512 0047: dt=129.472000, rms=0.732 (0.064%), neg=0, invalid=4512 0048: dt=129.472000, rms=0.731 (0.087%), neg=0, invalid=4512 0049: dt=129.472000, rms=0.730 (0.092%), neg=0, invalid=4512 0050: dt=129.472000, rms=0.730 (0.093%), neg=0, invalid=4512 0051: dt=129.472000, rms=0.729 (0.091%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=4512 0052: dt=189.494662, rms=0.724 (1.386%), neg=0, invalid=4512 0053: dt=145.152000, rms=0.713 (1.455%), neg=0, invalid=4512 0054: dt=82.944000, rms=0.709 (0.665%), neg=0, invalid=4512 0055: dt=171.912409, rms=0.705 (0.532%), neg=0, invalid=4512 0056: dt=77.650970, rms=0.700 (0.645%), neg=0, invalid=4512 0057: dt=103.680000, rms=0.699 (0.252%), neg=0, invalid=4512 0058: dt=124.416000, rms=0.695 (0.482%), neg=0, invalid=4512 0059: dt=36.288000, rms=0.694 (0.160%), neg=0, invalid=4512 0060: dt=36.288000, rms=0.693 (0.093%), neg=0, invalid=4512 0061: dt=36.288000, rms=0.692 (0.153%), neg=0, invalid=4512 0062: dt=36.288000, rms=0.691 (0.228%), neg=0, invalid=4512 0063: dt=36.288000, rms=0.689 (0.322%), neg=0, invalid=4512 0064: dt=36.288000, rms=0.686 (0.351%), neg=0, invalid=4512 0065: dt=36.288000, rms=0.684 (0.341%), neg=0, invalid=4512 0066: dt=36.288000, rms=0.681 (0.342%), neg=0, invalid=4512 0067: dt=36.288000, rms=0.679 (0.328%), neg=0, invalid=4512 0068: dt=36.288000, rms=0.677 (0.312%), neg=0, invalid=4512 0069: dt=36.288000, rms=0.675 (0.304%), neg=0, invalid=4512 0070: dt=36.288000, rms=0.673 (0.287%), neg=0, invalid=4512 0071: dt=36.288000, rms=0.671 (0.263%), neg=0, invalid=4512 0072: dt=36.288000, rms=0.670 (0.223%), neg=0, invalid=4512 0073: dt=36.288000, rms=0.669 (0.198%), neg=0, invalid=4512 0074: dt=36.288000, rms=0.667 (0.177%), neg=0, invalid=4512 0075: dt=36.288000, rms=0.666 (0.168%), neg=0, invalid=4512 0076: dt=36.288000, rms=0.665 (0.169%), neg=0, invalid=4512 0077: dt=36.288000, rms=0.664 (0.167%), neg=0, invalid=4512 0078: dt=36.288000, rms=0.663 (0.147%), neg=0, invalid=4512 0079: dt=36.288000, rms=0.662 (0.124%), neg=0, invalid=4512 0080: dt=36.288000, rms=0.661 (0.108%), neg=0, invalid=4512 0081: dt=145.152000, rms=0.661 (0.022%), neg=0, invalid=4512 0082: dt=145.152000, rms=0.661 (0.003%), neg=0, invalid=4512 0083: dt=145.152000, rms=0.661 (0.073%), neg=0, invalid=4512 0084: dt=145.152000, rms=0.661 (0.007%), neg=0, invalid=4512 0085: dt=145.152000, rms=0.660 (0.081%), neg=0, invalid=4512 0086: dt=145.152000, rms=0.660 (0.078%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.660, neg=0, invalid=4512 0087: dt=69.600000, rms=0.659 (0.214%), neg=0, invalid=4512 0088: dt=36.288000, rms=0.659 (0.015%), neg=0, invalid=4512 0089: dt=36.288000, rms=0.659 (0.001%), neg=0, invalid=4512 0090: dt=36.288000, rms=0.659 (-0.008%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.682, neg=0, invalid=4512 0091: dt=0.000000, rms=0.681 (0.092%), neg=0, invalid=4512 0092: dt=0.000000, rms=0.681 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.682, neg=0, invalid=4512 0093: dt=0.000000, rms=0.681 (0.092%), neg=0, invalid=4512 0094: dt=0.000000, rms=0.681 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.750, neg=0, invalid=4512 0095: dt=4.952941, rms=0.733 (2.213%), neg=0, invalid=4512 0096: dt=1.700000, rms=0.733 (0.048%), neg=0, invalid=4512 0097: dt=1.700000, rms=0.733 (-0.037%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.733, neg=0, invalid=4512 0098: dt=0.000000, rms=0.733 (0.061%), neg=0, invalid=4512 0099: dt=0.000000, rms=0.733 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.810, neg=0, invalid=4512 0100: dt=1.536000, rms=0.804 (0.717%), neg=0, invalid=4512 0101: dt=1.900621, rms=0.799 (0.669%), neg=0, invalid=4512 0102: dt=0.448000, rms=0.799 (0.052%), neg=0, invalid=4512 0103: dt=0.448000, rms=0.798 (0.038%), neg=0, invalid=4512 0104: dt=0.448000, rms=0.798 (0.032%), neg=0, invalid=4512 0105: dt=0.448000, rms=0.798 (-0.010%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.798, neg=0, invalid=4512 0106: dt=1.792000, rms=0.796 (0.295%), neg=0, invalid=4512 0107: dt=0.048000, rms=0.796 (0.001%), neg=0, invalid=4512 0108: dt=0.048000, rms=0.796 (-0.000%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.738, neg=0, invalid=4512 0109: dt=1.044974, rms=0.708 (4.017%), neg=0, invalid=4512 0110: dt=0.096000, rms=0.707 (0.180%), neg=0, invalid=4512 0111: dt=0.096000, rms=0.707 (-0.125%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=4512 0112: dt=0.028000, rms=0.707 (0.073%), neg=0, invalid=4512 0113: dt=0.004000, rms=0.707 (0.000%), neg=0, invalid=4512 0114: dt=0.004000, rms=0.707 (-0.001%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11252 (14) Left_Lateral_Ventricle (4): linear fit = 0.64 x + 0.0 (2279 voxels, overlap=0.515) Left_Lateral_Ventricle (4): linear fit = 0.64 x + 0.0 (2279 voxels, peak = 13), gca=12.9 gca peak = 0.15565 (16) mri peak = 0.10574 (16) Right_Lateral_Ventricle (43): linear fit = 0.86 x + 0.0 (1477 voxels, overlap=0.771) Right_Lateral_Ventricle (43): linear fit = 0.86 x + 0.0 (1477 voxels, peak = 14), gca=13.7 gca peak = 0.26829 (96) mri peak = 0.07748 (96) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (902 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (902 voxels, peak = 97), gca=97.4 gca peak = 0.20183 (93) mri peak = 0.09309 (95) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (745 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (745 voxels, peak = 94), gca=94.4 gca peak = 0.21683 (55) mri peak = 0.07129 (58) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (557 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (557 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.09127 (57) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (391 voxels, overlap=0.996) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (391 voxels, peak = 57), gca=57.1 gca peak = 0.11430 (101) mri peak = 0.07755 (101) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (54174 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (54174 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.07182 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (52672 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (52672 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.02553 (57) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (10271 voxels, overlap=0.091) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (10271 voxels, peak = 65), gca=64.6 gca peak = 0.15082 (58) mri peak = 0.02492 (59) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (11837 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (11837 voxels, peak = 64), gca=63.5 gca peak = 0.14161 (67) mri peak = 0.08719 (62) Right_Caudate (50): linear fit = 0.98 x + 0.0 (674 voxels, overlap=0.991) Right_Caudate (50): linear fit = 0.98 x + 0.0 (674 voxels, peak = 65), gca=65.3 gca peak = 0.15243 (71) mri peak = 0.09846 (68) Left_Caudate (11): linear fit = 0.94 x + 0.0 (483 voxels, overlap=0.653) Left_Caudate (11): linear fit = 0.94 x + 0.0 (483 voxels, peak = 67), gca=67.1 gca peak = 0.13336 (57) mri peak = 0.03159 ( 7) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (9047 voxels, overlap=0.039) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (9047 voxels, peak = 47), gca=47.0 gca peak = 0.13252 (56) mri peak = 0.02901 (55) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10442 voxels, overlap=0.190) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10442 voxels, peak = 53), gca=52.9 gca peak = 0.18181 (84) mri peak = 0.07244 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6119 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6119 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.06756 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4902 voxels, overlap=0.680) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4902 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.07359 (68) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (230 voxels, overlap=0.554) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (230 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.08216 (60) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (395 voxels, overlap=0.921) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (395 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.06518 (89) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (4146 voxels, overlap=0.924) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (4146 voxels, peak = 88), gca=88.0 gca peak = 0.11978 (83) mri peak = 0.06563 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3304 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3304 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.06208 (83) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1792 voxels, overlap=0.690) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1792 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.04748 (80) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1783 voxels, overlap=0.997) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1783 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.06956 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8072 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8072 voxels, peak = 89), gca=89.2 gca peak = 0.13281 (86) mri peak = 0.07522 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (808 voxels, overlap=0.572) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (808 voxels, peak = 94), gca=94.2 gca peak = 0.12801 (89) mri peak = 0.08225 (94) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (999 voxels, overlap=0.705) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (999 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 0.20112 (16) Third_Ventricle (14): linear fit = 0.64 x + 0.0 (81 voxels, overlap=0.111) Third_Ventricle (14): linear fit = 0.64 x + 0.0 (81 voxels, peak = 15), gca=14.8 gca peak = 0.15061 (21) mri peak = 0.15069 (13) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (340 voxels, overlap=0.694) Fourth_Ventricle (15): linear fit = 0.75 x + 0.0 (340 voxels, peak = 16), gca=15.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.06 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.75 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=4512 0115: dt=63.376623, rms=0.703 (0.507%), neg=0, invalid=4512 0116: dt=73.984000, rms=0.702 (0.076%), neg=0, invalid=4512 0117: dt=129.472000, rms=0.701 (0.106%), neg=0, invalid=4512 0118: dt=443.904000, rms=0.698 (0.429%), neg=0, invalid=4512 0119: dt=517.888000, rms=0.696 (0.316%), neg=0, invalid=4512 0120: dt=129.472000, rms=0.695 (0.186%), neg=0, invalid=4512 0121: dt=129.472000, rms=0.694 (0.077%), neg=0, invalid=4512 0122: dt=129.472000, rms=0.694 (0.052%), neg=0, invalid=4512 0123: dt=517.888000, rms=0.693 (0.140%), neg=0, invalid=4512 0124: dt=92.480000, rms=0.692 (0.102%), neg=0, invalid=4512 0125: dt=1183.744000, rms=0.690 (0.289%), neg=0, invalid=4512 0126: dt=73.984000, rms=0.689 (0.132%), neg=0, invalid=4512 0127: dt=129.472000, rms=0.689 (0.028%), neg=0, invalid=4512 0128: dt=129.472000, rms=0.689 (0.043%), neg=0, invalid=4512 0129: dt=129.472000, rms=0.688 (0.067%), neg=0, invalid=4512 0130: dt=129.472000, rms=0.688 (0.086%), neg=0, invalid=4512 0131: dt=129.472000, rms=0.687 (0.105%), neg=0, invalid=4512 0132: dt=129.472000, rms=0.686 (0.125%), neg=0, invalid=4512 0133: dt=129.472000, rms=0.685 (0.131%), neg=0, invalid=4512 0134: dt=129.472000, rms=0.684 (0.129%), neg=0, invalid=4512 0135: dt=129.472000, rms=0.684 (0.119%), neg=0, invalid=4512 0136: dt=129.472000, rms=0.683 (0.116%), neg=0, invalid=4512 0137: dt=129.472000, rms=0.682 (0.118%), neg=0, invalid=4512 0138: dt=129.472000, rms=0.681 (0.111%), neg=0, invalid=4512 0139: dt=129.472000, rms=0.681 (0.107%), neg=0, invalid=4512 0140: dt=129.472000, rms=0.680 (0.102%), neg=0, invalid=4512 0141: dt=129.472000, rms=0.679 (0.101%), neg=0, invalid=4512 0142: dt=129.472000, rms=0.679 (0.089%), neg=0, invalid=4512 0143: dt=129.472000, rms=0.678 (0.084%), neg=0, invalid=4512 0144: dt=129.472000, rms=0.678 (0.078%), neg=0, invalid=4512 0145: dt=129.472000, rms=0.677 (0.073%), neg=0, invalid=4512 0146: dt=129.472000, rms=0.677 (0.070%), neg=0, invalid=4512 0147: dt=129.472000, rms=0.676 (0.066%), neg=0, invalid=4512 0148: dt=129.472000, rms=0.676 (0.062%), neg=0, invalid=4512 0149: dt=129.472000, rms=0.675 (0.061%), neg=0, invalid=4512 0150: dt=129.472000, rms=0.675 (0.063%), neg=0, invalid=4512 0151: dt=129.472000, rms=0.674 (0.057%), neg=0, invalid=4512 0152: dt=129.472000, rms=0.674 (0.049%), neg=0, invalid=4512 0153: dt=129.472000, rms=0.674 (0.053%), neg=0, invalid=4512 0154: dt=129.472000, rms=0.673 (0.054%), neg=0, invalid=4512 0155: dt=129.472000, rms=0.673 (0.051%), neg=0, invalid=4512 0156: dt=129.472000, rms=0.673 (0.045%), neg=0, invalid=4512 0157: dt=129.472000, rms=0.672 (0.041%), neg=0, invalid=4512 0158: dt=129.472000, rms=0.672 (0.044%), neg=0, invalid=4512 0159: dt=129.472000, rms=0.672 (0.037%), neg=0, invalid=4512 0160: dt=129.472000, rms=0.672 (0.036%), neg=0, invalid=4512 0161: dt=129.472000, rms=0.671 (0.035%), neg=0, invalid=4512 0162: dt=129.472000, rms=0.671 (0.035%), neg=0, invalid=4512 0163: dt=129.472000, rms=0.671 (0.035%), neg=0, invalid=4512 0164: dt=129.472000, rms=0.671 (0.032%), neg=0, invalid=4512 0165: dt=129.472000, rms=0.671 (0.029%), neg=0, invalid=4512 0166: dt=129.472000, rms=0.670 (0.027%), neg=0, invalid=4512 0167: dt=129.472000, rms=0.670 (0.025%), neg=0, invalid=4512 0168: dt=129.472000, rms=0.670 (0.031%), neg=0, invalid=4512 0169: dt=129.472000, rms=0.670 (0.027%), neg=0, invalid=4512 0170: dt=129.472000, rms=0.670 (0.026%), neg=0, invalid=4512 0171: dt=129.472000, rms=0.670 (0.025%), neg=0, invalid=4512 0172: dt=129.472000, rms=0.669 (0.026%), neg=0, invalid=4512 0173: dt=129.472000, rms=0.669 (0.023%), neg=0, invalid=4512 0174: dt=129.472000, rms=0.669 (0.024%), neg=0, invalid=4512 0175: dt=129.472000, rms=0.669 (0.022%), neg=0, invalid=4512 0176: dt=0.014450, rms=0.669 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=4512 0177: dt=129.472000, rms=0.668 (0.213%), neg=0, invalid=4512 0178: dt=517.888000, rms=0.666 (0.251%), neg=0, invalid=4512 0179: dt=73.984000, rms=0.666 (0.030%), neg=0, invalid=4512 0180: dt=73.984000, rms=0.666 (0.018%), neg=0, invalid=4512 0181: dt=73.984000, rms=0.666 (0.022%), neg=0, invalid=4512 0182: dt=73.984000, rms=0.666 (0.030%), neg=0, invalid=4512 0183: dt=73.984000, rms=0.665 (0.040%), neg=0, invalid=4512 0184: dt=73.984000, rms=0.665 (0.041%), neg=0, invalid=4512 0185: dt=73.984000, rms=0.665 (0.039%), neg=0, invalid=4512 0186: dt=73.984000, rms=0.665 (0.031%), neg=0, invalid=4512 0187: dt=73.984000, rms=0.664 (0.028%), neg=0, invalid=4512 0188: dt=73.984000, rms=0.664 (0.029%), neg=0, invalid=4512 0189: dt=73.984000, rms=0.664 (0.028%), neg=0, invalid=4512 0190: dt=73.984000, rms=0.664 (0.032%), neg=0, invalid=4512 0191: dt=73.984000, rms=0.664 (0.025%), neg=0, invalid=4512 0192: dt=73.984000, rms=0.664 (0.017%), neg=0, invalid=4512 0193: dt=73.984000, rms=0.664 (0.001%), neg=0, invalid=4512 0194: dt=73.984000, rms=0.663 (0.004%), neg=0, invalid=4512 0195: dt=73.984000, rms=0.663 (0.005%), neg=0, invalid=4512 0196: dt=73.984000, rms=0.663 (0.006%), neg=0, invalid=4512 0197: dt=73.984000, rms=0.663 (0.009%), neg=0, invalid=4512 0198: dt=73.984000, rms=0.663 (0.008%), neg=0, invalid=4512 0199: dt=73.984000, rms=0.663 (0.006%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=4512 0200: dt=86.441558, rms=0.662 (0.436%), neg=0, invalid=4512 0201: dt=145.152000, rms=0.657 (0.635%), neg=0, invalid=4512 0202: dt=68.210526, rms=0.655 (0.353%), neg=0, invalid=4512 0203: dt=144.225352, rms=0.652 (0.434%), neg=0, invalid=4512 0204: dt=36.288000, rms=0.650 (0.327%), neg=0, invalid=4512 0205: dt=580.608000, rms=0.644 (0.945%), neg=0, invalid=4512 0206: dt=76.444444, rms=0.640 (0.583%), neg=0, invalid=4512 0207: dt=36.288000, rms=0.639 (0.195%), neg=0, invalid=4512 0208: dt=414.720000, rms=0.636 (0.414%), neg=0, invalid=4512 0209: dt=36.288000, rms=0.635 (0.282%), neg=0, invalid=4512 0210: dt=145.152000, rms=0.633 (0.186%), neg=0, invalid=4512 0211: dt=62.208000, rms=0.633 (0.109%), neg=0, invalid=4512 0212: dt=331.776000, rms=0.631 (0.204%), neg=0, invalid=4512 0213: dt=36.288000, rms=0.630 (0.194%), neg=0, invalid=4512 0214: dt=145.152000, rms=0.629 (0.127%), neg=0, invalid=4512 0215: dt=82.944000, rms=0.629 (0.078%), neg=0, invalid=4512 0216: dt=36.288000, rms=0.629 (0.053%), neg=0, invalid=4512 0217: dt=36.288000, rms=0.628 (0.031%), neg=0, invalid=4512 0218: dt=36.288000, rms=0.628 (0.031%), neg=0, invalid=4512 0219: dt=0.567000, rms=0.628 (0.000%), neg=0, invalid=4512 0220: dt=0.283500, rms=0.628 (0.000%), neg=0, invalid=4512 0221: dt=0.141750, rms=0.628 (0.000%), neg=0, invalid=4512 0222: dt=0.070875, rms=0.628 (0.000%), neg=0, invalid=4512 0223: dt=0.035437, rms=0.628 (0.000%), neg=0, invalid=4512 0224: dt=0.017719, rms=0.628 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.629, neg=0, invalid=4512 0225: dt=133.565217, rms=0.625 (0.598%), neg=0, invalid=4512 0226: dt=95.762963, rms=0.624 (0.234%), neg=0, invalid=4512 0227: dt=62.208000, rms=0.623 (0.110%), neg=0, invalid=4512 0228: dt=145.152000, rms=0.622 (0.158%), neg=0, invalid=4512 0229: dt=82.944000, rms=0.621 (0.082%), neg=0, invalid=4512 0230: dt=82.944000, rms=0.621 (0.077%), neg=0, invalid=4512 0231: dt=82.944000, rms=0.621 (0.064%), neg=0, invalid=4512 0232: dt=62.208000, rms=0.620 (0.063%), neg=0, invalid=4512 0233: dt=145.152000, rms=0.620 (0.085%), neg=0, invalid=4512 0234: dt=36.288000, rms=0.619 (0.060%), neg=0, invalid=4512 0235: dt=2.268000, rms=0.619 (0.002%), neg=0, invalid=4512 0236: dt=2.268000, rms=0.619 (0.002%), neg=0, invalid=4512 0237: dt=0.567000, rms=0.619 (0.001%), neg=0, invalid=4512 0238: dt=0.283500, rms=0.619 (0.000%), neg=0, invalid=4512 0239: dt=0.035437, rms=0.619 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=4512 0240: dt=0.001953, rms=0.623 (0.098%), neg=0, invalid=4512 0241: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=4512 0242: dt=0.000122, rms=0.623 (0.000%), neg=0, invalid=4512 0243: dt=0.000061, rms=0.623 (0.000%), neg=0, invalid=4512 0244: dt=0.000031, rms=0.623 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.624, neg=0, invalid=4512 0245: dt=153.600000, rms=0.596 (4.452%), neg=0, invalid=4512 0246: dt=0.700000, rms=0.596 (0.040%), neg=0, invalid=4512 0247: dt=0.175000, rms=0.596 (0.008%), neg=0, invalid=4512 0248: dt=0.010937, rms=0.596 (0.001%), neg=0, invalid=4512 0249: dt=0.005469, rms=0.596 (0.000%), neg=0, invalid=4512 0250: dt=0.002344, rms=0.596 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.608, neg=0, invalid=4512 0251: dt=0.000246, rms=0.608 (0.112%), neg=0, invalid=4512 0252: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=4512 0253: dt=0.000073, rms=0.608 (0.000%), neg=0, invalid=4512 0254: dt=0.000037, rms=0.608 (0.000%), neg=0, invalid=4512 0255: dt=0.000037, rms=0.608 (0.000%), neg=0, invalid=4512 0256: dt=0.000009, rms=0.608 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.608, neg=0, invalid=4512 0257: dt=0.000000, rms=0.608 (0.112%), neg=0, invalid=4512 0258: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=4512 0259: dt=0.000001, rms=0.608 (0.000%), neg=0, invalid=4512 0260: dt=0.000001, rms=0.608 (0.000%), neg=0, invalid=4512 0261: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.632, neg=0, invalid=4512 0262: dt=4.348315, rms=0.617 (2.384%), neg=0, invalid=4512 0263: dt=0.000000, rms=0.617 (0.005%), neg=0, invalid=4512 0264: dt=0.100000, rms=0.617 (-0.006%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.618, neg=0, invalid=4512 0265: dt=1.792000, rms=0.616 (0.283%), neg=0, invalid=4512 0266: dt=4.096000, rms=0.615 (0.188%), neg=0, invalid=4512 0267: dt=5.120000, rms=0.614 (0.103%), neg=0, invalid=4512 0268: dt=5.120000, rms=0.614 (0.049%), neg=0, invalid=4512 0269: dt=5.120000, rms=0.614 (0.020%), neg=0, invalid=4512 0270: dt=5.120000, rms=0.614 (0.029%), neg=0, invalid=4512 0271: dt=5.120000, rms=0.614 (-0.113%), neg=0, invalid=4512 0272: dt=1.792000, rms=0.614 (0.009%), neg=0, invalid=4512 0273: dt=6.144000, rms=0.613 (0.016%), neg=0, invalid=4512 0274: dt=7.168000, rms=0.613 (0.035%), neg=0, invalid=4512 0275: dt=5.120000, rms=0.613 (0.032%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.600, neg=0, invalid=4512 0276: dt=0.448000, rms=0.578 (3.738%), neg=0, invalid=4512 0277: dt=0.448000, rms=0.571 (1.172%), neg=0, invalid=4512 0278: dt=0.448000, rms=0.567 (0.627%), neg=0, invalid=4512 0279: dt=0.448000, rms=0.565 (0.392%), neg=0, invalid=4512 0280: dt=0.448000, rms=0.563 (0.293%), neg=0, invalid=4512 0281: dt=0.448000, rms=0.562 (0.221%), neg=0, invalid=4512 0282: dt=0.448000, rms=0.561 (0.181%), neg=0, invalid=4512 0283: dt=0.448000, rms=0.560 (0.145%), neg=0, invalid=4512 0284: dt=0.448000, rms=0.560 (0.126%), neg=0, invalid=4512 0285: dt=0.448000, rms=0.559 (0.102%), neg=0, invalid=4512 0286: dt=0.448000, rms=0.558 (0.094%), neg=0, invalid=4512 0287: dt=0.448000, rms=0.558 (0.076%), neg=0, invalid=4512 0288: dt=0.448000, rms=0.558 (0.073%), neg=0, invalid=4512 0289: dt=0.448000, rms=0.557 (0.060%), neg=0, invalid=4512 0290: dt=0.448000, rms=0.557 (0.058%), neg=0, invalid=4512 0291: dt=0.448000, rms=0.557 (0.045%), neg=0, invalid=4512 0292: dt=0.448000, rms=0.556 (0.048%), neg=0, invalid=4512 0293: dt=0.448000, rms=0.556 (0.078%), neg=0, invalid=4512 0294: dt=0.448000, rms=0.555 (0.101%), neg=0, invalid=4512 0295: dt=0.448000, rms=0.555 (0.109%), neg=0, invalid=4512 0296: dt=0.224000, rms=0.555 (0.010%), neg=0, invalid=4512 0297: dt=0.224000, rms=0.555 (0.015%), neg=0, invalid=4512 0298: dt=0.224000, rms=0.555 (0.007%), neg=0, invalid=4512 0299: dt=0.448000, rms=0.555 (0.014%), neg=0, invalid=4512 0300: dt=0.448000, rms=0.554 (0.009%), neg=0, invalid=4512 0301: dt=0.448000, rms=0.554 (0.015%), neg=0, invalid=4512 0302: dt=0.448000, rms=0.554 (0.018%), neg=0, invalid=4512 0303: dt=0.224000, rms=0.554 (0.006%), neg=0, invalid=4512 0304: dt=0.224000, rms=0.554 (0.013%), neg=0, invalid=4512 0305: dt=0.224000, rms=0.554 (0.005%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=4512 0306: dt=0.448000, rms=0.546 (1.540%), neg=0, invalid=4512 0307: dt=0.320000, rms=0.546 (0.089%), neg=0, invalid=4512 0308: dt=0.384000, rms=0.545 (0.051%), neg=0, invalid=4512 0309: dt=0.320000, rms=0.545 (0.001%), neg=0, invalid=4512 0310: dt=0.320000, rms=0.545 (-0.008%), neg=0, invalid=4512 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.543, neg=0, invalid=4512 0311: dt=2.023000, rms=0.542 (0.104%), neg=0, invalid=4512 0312: dt=0.867000, rms=0.542 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.543, neg=0, invalid=4512 0313: dt=73.984000, rms=0.542 (0.126%), neg=0, invalid=4512 0314: dt=129.472000, rms=0.542 (0.035%), neg=0, invalid=4512 0315: dt=129.472000, rms=0.542 (-0.002%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.543, neg=0, invalid=4512 0316: dt=22.666667, rms=0.541 (0.203%), neg=0, invalid=4512 0317: dt=15.552000, rms=0.541 (0.025%), neg=0, invalid=4512 0318: dt=15.552000, rms=0.541 (0.006%), neg=0, invalid=4512 0319: dt=15.552000, rms=0.541 (-0.038%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=4512 0320: dt=36.288000, rms=0.539 (0.474%), neg=0, invalid=4512 0321: dt=95.319149, rms=0.538 (0.265%), neg=0, invalid=4512 0322: dt=31.104000, rms=0.537 (0.144%), neg=0, invalid=4512 0323: dt=31.104000, rms=0.537 (0.072%), neg=0, invalid=4512 0324: dt=31.104000, rms=0.536 (0.094%), neg=0, invalid=4512 0325: dt=31.104000, rms=0.535 (0.127%), neg=0, invalid=4512 0326: dt=31.104000, rms=0.535 (0.121%), neg=0, invalid=4512 0327: dt=31.104000, rms=0.534 (0.127%), neg=0, invalid=4512 0328: dt=31.104000, rms=0.534 (0.105%), neg=0, invalid=4512 0329: dt=31.104000, rms=0.533 (0.103%), neg=0, invalid=4512 0330: dt=36.288000, rms=0.533 (0.025%), neg=0, invalid=4512 0331: dt=36.288000, rms=0.533 (0.021%), neg=0, invalid=4512 0332: dt=36.288000, rms=0.533 (0.035%), neg=0, invalid=4512 0333: dt=36.288000, rms=0.532 (0.056%), neg=0, invalid=4512 0334: dt=36.288000, rms=0.532 (0.058%), neg=0, invalid=4512 0335: dt=36.288000, rms=0.532 (0.067%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0336: dt=36.288000, rms=0.531 (0.060%), neg=0, invalid=4512 0337: dt=36.288000, rms=0.531 (0.066%), neg=0, invalid=4512 0338: dt=36.288000, rms=0.531 (0.062%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0339: dt=25.600000, rms=0.529 (0.518%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0340: dt=44.800000, rms=0.527 (0.307%), neg=0, invalid=4512 0341: dt=25.600000, rms=0.526 (0.165%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0342: dt=25.600000, rms=0.525 (0.247%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0343: dt=25.600000, rms=0.524 (0.302%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 4 iterations, nbhd size=0, neg = 0 0344: dt=25.600000, rms=0.522 (0.216%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=1, neg = 0 0345: dt=25.600000, rms=0.521 (0.271%), neg=0, invalid=4512 iter 0, gcam->neg = 23 after 13 iterations, nbhd size=1, neg = 0 0346: dt=25.600000, rms=0.520 (0.234%), neg=0, invalid=4512 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0347: dt=25.600000, rms=0.519 (0.249%), neg=0, invalid=4512 iter 0, gcam->neg = 26 after 13 iterations, nbhd size=1, neg = 0 0348: dt=25.600000, rms=0.518 (0.172%), neg=0, invalid=4512 iter 0, gcam->neg = 17 after 11 iterations, nbhd size=1, neg = 0 0349: dt=25.600000, rms=0.516 (0.257%), neg=0, invalid=4512 iter 0, gcam->neg = 24 after 13 iterations, nbhd size=1, neg = 0 0350: dt=25.600000, rms=0.515 (0.211%), neg=0, invalid=4512 iter 0, gcam->neg = 18 after 14 iterations, nbhd size=1, neg = 0 0351: dt=25.600000, rms=0.514 (0.245%), neg=0, invalid=4512 iter 0, gcam->neg = 17 after 14 iterations, nbhd size=1, neg = 0 0352: dt=25.600000, rms=0.514 (0.056%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 0353: dt=25.600000, rms=0.513 (0.129%), neg=0, invalid=4512 iter 0, gcam->neg = 15 after 11 iterations, nbhd size=1, neg = 0 0354: dt=25.600000, rms=0.512 (0.148%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 12 iterations, nbhd size=1, neg = 0 0355: dt=25.600000, rms=0.512 (0.138%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 14 iterations, nbhd size=1, neg = 0 0356: dt=25.600000, rms=0.511 (0.079%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 11 iterations, nbhd size=1, neg = 0 0357: dt=25.600000, rms=0.511 (0.084%), neg=0, invalid=4512 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0358: dt=25.600000, rms=0.510 (0.160%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 0359: dt=25.600000, rms=0.509 (0.125%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 0360: dt=25.600000, rms=0.509 (0.066%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0361: dt=32.000000, rms=0.508 (0.102%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0362: dt=11.200000, rms=0.508 (0.046%), neg=0, invalid=4512 0363: dt=11.200000, rms=0.508 (0.022%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0364: dt=11.200000, rms=0.508 (0.029%), neg=0, invalid=4512 0365: dt=11.200000, rms=0.508 (0.034%), neg=0, invalid=4512 0366: dt=11.200000, rms=0.508 (0.043%), neg=0, invalid=4512 0367: dt=11.200000, rms=0.507 (0.036%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0368: dt=11.200000, rms=0.507 (0.027%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.508, neg=0, invalid=4512 0369: dt=60.783920, rms=0.502 (1.068%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0370: dt=32.000000, rms=0.501 (0.285%), neg=0, invalid=4512 0371: dt=25.600000, rms=0.500 (0.115%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0372: dt=25.600000, rms=0.500 (0.078%), neg=0, invalid=4512 0373: dt=25.600000, rms=0.499 (0.171%), neg=0, invalid=4512 0374: dt=25.600000, rms=0.498 (0.127%), neg=0, invalid=4512 0375: dt=25.600000, rms=0.498 (0.111%), neg=0, invalid=4512 0376: dt=25.600000, rms=0.498 (0.054%), neg=0, invalid=4512 0377: dt=11.200000, rms=0.497 (0.060%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0378: dt=76.800000, rms=0.497 (0.119%), neg=0, invalid=4512 0379: dt=11.200000, rms=0.497 (0.044%), neg=0, invalid=4512 0380: dt=11.200000, rms=0.496 (0.022%), neg=0, invalid=4512 0381: dt=11.200000, rms=0.496 (0.020%), neg=0, invalid=4512 0382: dt=11.200000, rms=0.496 (0.026%), neg=0, invalid=4512 0383: dt=11.200000, rms=0.496 (0.036%), neg=0, invalid=4512 0384: dt=11.200000, rms=0.496 (0.042%), neg=0, invalid=4512 0385: dt=11.200000, rms=0.496 (0.046%), neg=0, invalid=4512 0386: dt=11.200000, rms=0.495 (0.041%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.505, neg=0, invalid=4512 0387: dt=0.063000, rms=0.505 (0.110%), neg=0, invalid=4512 0388: dt=0.013500, rms=0.505 (0.000%), neg=0, invalid=4512 0389: dt=0.013500, rms=0.505 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=4512 0390: dt=1.008000, rms=0.505 (0.123%), neg=0, invalid=4512 0391: dt=0.864000, rms=0.505 (0.006%), neg=0, invalid=4512 0392: dt=0.864000, rms=0.505 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.523, neg=0, invalid=4512 0393: dt=1.280000, rms=0.520 (0.544%), neg=0, invalid=4512 0394: dt=0.448000, rms=0.520 (0.022%), neg=0, invalid=4512 0395: dt=0.448000, rms=0.520 (-0.010%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=4512 0396: dt=1.536000, rms=0.519 (0.364%), neg=0, invalid=4512 0397: dt=1.024000, rms=0.519 (0.042%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=1.024000, rms=0.519 (0.002%), neg=0, invalid=4512 0399: dt=1.024000, rms=0.519 (-0.104%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.508, neg=0, invalid=4512 iter 0, gcam->neg = 1573 after 15 iterations, nbhd size=1, neg = 0 0400: dt=2.679228, rms=0.465 (8.389%), neg=0, invalid=4512 0401: dt=0.192000, rms=0.464 (0.415%), neg=0, invalid=4512 0402: dt=0.020000, rms=0.463 (0.008%), neg=0, invalid=4512 0403: dt=0.020000, rms=0.463 (-0.003%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=4512 0404: dt=0.112000, rms=0.463 (0.245%), neg=0, invalid=4512 0405: dt=0.016000, rms=0.463 (0.004%), neg=0, invalid=4512 0406: dt=0.016000, rms=0.463 (-0.001%), neg=0, invalid=4512 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 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=4512 0407: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=4512 0408: dt=73.984000, rms=0.444 (0.010%), neg=0, invalid=4512 0409: dt=129.472000, rms=0.444 (0.010%), neg=0, invalid=4512 0410: dt=23.120000, rms=0.444 (0.000%), neg=0, invalid=4512 0411: dt=23.120000, rms=0.444 (0.000%), neg=0, invalid=4512 0412: dt=23.120000, rms=0.444 (0.000%), neg=0, invalid=4512 0413: dt=23.120000, rms=0.444 (0.001%), neg=0, invalid=4512 0414: dt=23.120000, rms=0.444 (0.001%), neg=0, invalid=4512 0415: dt=23.120000, rms=0.444 (0.001%), neg=0, invalid=4512 0416: dt=23.120000, rms=0.444 (0.001%), neg=0, invalid=4512 0417: dt=23.120000, rms=0.444 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=4512 0418: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=4512 0419: dt=145.152000, rms=0.444 (0.085%), neg=0, invalid=4512 0420: dt=145.152000, rms=0.444 (0.074%), neg=0, invalid=4512 0421: dt=145.152000, rms=0.444 (-0.198%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=4512 0422: dt=11.200000, rms=0.444 (0.122%), neg=0, invalid=4512 0423: dt=8.000000, rms=0.444 (0.021%), neg=0, invalid=4512 0424: dt=8.000000, rms=0.444 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=4512 0425: dt=60.527132, rms=0.441 (0.699%), neg=0, invalid=4512 0426: dt=25.600000, rms=0.439 (0.328%), neg=0, invalid=4512 0427: dt=44.800000, rms=0.439 (0.158%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0428: dt=44.800000, rms=0.439 (0.050%), neg=0, invalid=4512 0429: dt=44.800000, rms=0.437 (0.416%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0430: dt=44.800000, rms=0.436 (0.234%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0431: dt=44.800000, rms=0.435 (0.253%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0432: dt=44.800000, rms=0.433 (0.315%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0433: dt=44.800000, rms=0.432 (0.210%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0434: dt=44.800000, rms=0.431 (0.189%), neg=0, invalid=4512 0435: dt=44.800000, rms=0.431 (0.132%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0436: dt=44.800000, rms=0.431 (0.087%), neg=0, invalid=4512 0437: dt=44.800000, rms=0.430 (0.115%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0438: dt=44.800000, rms=0.430 (0.055%), neg=0, invalid=4512 0439: dt=19.200000, rms=0.430 (0.070%), neg=0, invalid=4512 0440: dt=38.400000, rms=0.429 (0.012%), neg=0, invalid=4512 0441: dt=38.400000, rms=0.429 (0.013%), neg=0, invalid=4512 0442: dt=38.400000, rms=0.429 (0.019%), neg=0, invalid=4512 0443: dt=38.400000, rms=0.429 (0.001%), neg=0, invalid=4512 0444: dt=38.400000, rms=0.429 (0.010%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0445: dt=38.400000, rms=0.429 (-0.003%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.435, neg=0, invalid=4512 0446: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=4512 0447: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.446, neg=0, invalid=4512 0448: dt=0.000000, rms=0.446 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=4512 0449: dt=0.112000, rms=0.446 (0.006%), neg=0, invalid=4512 0450: dt=0.096000, rms=0.446 (0.002%), neg=0, invalid=4512 0451: dt=0.096000, rms=0.446 (-0.001%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.428, neg=0, invalid=4512 iter 0, gcam->neg = 836 after 14 iterations, nbhd size=1, neg = 0 0452: dt=1.608207, rms=0.415 (3.042%), neg=0, invalid=4512 0453: dt=0.000013, rms=0.415 (0.000%), neg=0, invalid=4512 0454: dt=0.000013, rms=0.415 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=4512 0455: dt=0.096000, rms=0.415 (0.071%), neg=0, invalid=4512 0456: dt=0.028000, rms=0.414 (0.005%), neg=0, invalid=4512 0457: dt=0.028000, rms=0.414 (0.000%), neg=0, invalid=4512 0458: dt=0.028000, rms=0.414 (-0.016%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 4 hours, 45 minutes and 14 seconds. mri_ca_register utimesec 17099.348503 mri_ca_register stimesec 11.246290 mri_ca_register ru_maxrss 1328096 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4965688 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 98 mri_ca_register ru_nivcsw 34983 FSRUNTIME@ mri_ca_register 4.7540 hours 1 threads #-------------------------------------- #@# SubCort Seg Tue Jun 14 21:32:38 EDT 2016 mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-49 machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 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/stable6//average/RB_all_2016-05-10.vc700.gca... reading input volume from norm.mgz... average std[0] = 7.3 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 6.65 Atlas used for the 3D morph was /usr/local/freesurfer/stable6//average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.09920 (14) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (5094 voxels, overlap=0.446) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (5094 voxels, peak = 14), gca=14.1 gca peak = 0.17677 (13) mri peak = 0.09985 (15) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4801 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (4801 voxels, peak = 13), gca=13.5 gca peak = 0.28129 (95) mri peak = 0.08215 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (591 voxels, overlap=1.021) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (591 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.10382 (95) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (605 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (605 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.07969 (62) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (664 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (664 voxels, peak = 57), gca=57.5 gca peak = 0.30264 (59) mri peak = 0.09053 (60) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (457 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (457 voxels, peak = 58), gca=58.1 gca peak = 0.07580 (103) mri peak = 0.08415 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41115 voxels, overlap=0.781) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41115 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.07802 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (34990 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (34990 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.03019 (70) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (9447 voxels, overlap=0.169) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (9447 voxels, peak = 70), gca=70.5 gca peak = 0.11620 (58) mri peak = 0.03343 (70) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (10383 voxels, overlap=0.082) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (10383 voxels, peak = 71), gca=71.1 gca peak = 0.30970 (66) mri peak = 0.07298 (71) Right_Caudate (50): linear fit = 1.07 x + 0.0 (910 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.07 x + 0.0 (910 voxels, peak = 70), gca=70.3 gca peak = 0.15280 (69) mri peak = 0.08381 (74) Left_Caudate (11): linear fit = 0.98 x + 0.0 (701 voxels, overlap=1.006) Left_Caudate (11): linear fit = 0.98 x + 0.0 (701 voxels, peak = 67), gca=67.3 gca peak = 0.13902 (56) mri peak = 0.04154 (46) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (6955 voxels, overlap=0.670) Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (6955 voxels, peak = 48), gca=47.9 gca peak = 0.14777 (55) mri peak = 0.04553 (55) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7270 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7270 voxels, peak = 54), gca=54.2 gca peak = 0.16765 (84) mri peak = 0.08351 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5546 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5546 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.09026 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5859 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5859 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.07379 (65) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (257 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (257 voxels, peak = 62), gca=62.4 gca peak = 0.33601 (57) mri peak = 0.08060 (65) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (342 voxels, overlap=1.035) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (342 voxels, peak = 64), gca=63.6 gca peak = 0.11131 (90) mri peak = 0.06614 (89) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3470 voxels, overlap=0.953) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3470 voxels, peak = 92), gca=92.2 gca peak = 0.11793 (83) mri peak = 0.06843 (88) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3496 voxels, overlap=0.921) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3496 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.07413 (83) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1226 voxels, overlap=0.798) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1226 voxels, peak = 85), gca=85.5 gca peak = 0.10360 (77) mri peak = 0.05923 (79) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1452 voxels, overlap=0.951) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1452 voxels, peak = 78), gca=78.2 gca peak = 0.08424 (78) mri peak = 0.07090 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (10126 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (10126 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.07787 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1200 voxels, overlap=0.685) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1200 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.08451 (93) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1199 voxels, overlap=0.791) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1199 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.14545 (16) Third_Ventricle (14): linear fit = 0.58 x + 0.0 (157 voxels, overlap=0.276) Third_Ventricle (14): linear fit = 0.58 x + 0.0 (157 voxels, peak = 14), gca=14.0 gca peak = 0.19357 (14) mri peak = 0.14428 (14) Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (600 voxels, overlap=0.784) Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (600 voxels, peak = 12), gca=11.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19905 (14) mri peak = 0.09920 (14) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (5094 voxels, overlap=0.955) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (5094 voxels, peak = 14), gca=14.5 gca peak = 0.19108 (13) mri peak = 0.09985 (15) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (4801 voxels, overlap=0.730) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (4801 voxels, peak = 11), gca=11.2 gca peak = 0.25707 (97) mri peak = 0.08215 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (591 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (591 voxels, peak = 97), gca=96.5 gca peak = 0.16258 (97) mri peak = 0.10382 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (605 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (605 voxels, peak = 97), gca=97.5 gca peak = 0.27678 (58) mri peak = 0.07969 (62) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (664 voxels, peak = 58), gca=58.0 gca peak = 0.30810 (58) mri peak = 0.09053 (60) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (457 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (457 voxels, peak = 58), gca=58.0 gca peak = 0.07830 (102) mri peak = 0.08415 (102) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (41115 voxels, overlap=0.763) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (41115 voxels, peak = 104), gca=103.5 gca peak = 0.07854 (106) mri peak = 0.07802 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34990 voxels, overlap=0.811) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34990 voxels, peak = 105), gca=105.5 gca peak = 0.08108 (70) mri peak = 0.03019 (70) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (9447 voxels, overlap=0.775) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (9447 voxels, peak = 69), gca=69.0 gca peak = 0.09457 (71) mri peak = 0.03343 (70) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (10383 voxels, overlap=0.909) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (10383 voxels, peak = 73), gca=73.5 gca peak = 0.26033 (71) mri peak = 0.07298 (71) Right_Caudate (50): linear fit = 0.99 x + 0.0 (910 voxels, overlap=1.010) Right_Caudate (50): linear fit = 0.99 x + 0.0 (910 voxels, peak = 70), gca=69.9 gca peak = 0.13821 (68) mri peak = 0.08381 (74) Left_Caudate (11): linear fit = 1.00 x + 0.0 (701 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.00 x + 0.0 (701 voxels, peak = 68), gca=68.0 gca peak = 0.16495 (47) mri peak = 0.04154 (46) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (6955 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (6955 voxels, peak = 51), gca=50.5 gca peak = 0.14576 (54) mri peak = 0.04553 (55) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7270 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7270 voxels, peak = 53), gca=53.2 gca peak = 0.15975 (87) mri peak = 0.08351 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5546 voxels, overlap=0.971) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5546 voxels, peak = 87), gca=86.6 gca peak = 0.15241 (90) mri peak = 0.09026 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5859 voxels, overlap=0.943) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5859 voxels, peak = 91), gca=91.3 gca peak = 0.29649 (64) mri peak = 0.07379 (65) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (257 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (257 voxels, peak = 66), gca=65.6 gca peak = 0.31087 (64) mri peak = 0.08060 (65) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (342 voxels, overlap=1.018) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (342 voxels, peak = 65), gca=65.0 gca peak = 0.10551 (92) mri peak = 0.06614 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3470 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3470 voxels, peak = 92), gca=91.5 gca peak = 0.09502 (87) mri peak = 0.06843 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3496 voxels, overlap=0.994) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3496 voxels, peak = 87), gca=86.6 gca peak = 0.08452 (87) mri peak = 0.07413 (83) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1226 voxels, overlap=0.908) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1226 voxels, peak = 87), gca=86.6 gca peak = 0.08217 (78) mri peak = 0.05923 (79) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1452 voxels, overlap=0.993) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1452 voxels, peak = 78), gca=77.6 gca peak = 0.07855 (88) mri peak = 0.07090 (88) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10126 voxels, overlap=0.825) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10126 voxels, peak = 87), gca=86.7 gca peak = 0.11798 (92) mri peak = 0.07787 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1200 voxels, overlap=0.861) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1200 voxels, peak = 92), gca=91.5 gca peak = 0.14670 (91) mri peak = 0.08451 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1199 voxels, overlap=0.922) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1199 voxels, peak = 91), gca=90.5 gca peak = 0.21239 (22) mri peak = 0.14545 (16) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (157 voxels, overlap=0.735) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (157 voxels, peak = 15), gca=15.3 gca peak = 0.24326 (13) mri peak = 0.14428 (14) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (600 voxels, overlap=0.870) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (600 voxels, peak = 13), gca=13.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18140 (33) gca peak Left_Thalamus = 0.64095 (102) gca peak CSF = 0.26139 (31) gca peak Left_Accumbens_area = 0.58674 (61) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (24) gca peak Right_Accumbens_area = 0.33550 (70) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.51881 (28) gca peak WM_hypointensities = 0.08571 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.70894 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.91 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 76880 voxels changed in iteration 0 of unlikely voxel relabeling 221 voxels changed in iteration 1 of unlikely voxel relabeling 25 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 50183 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels) 375 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 80846 changed. image ll: -2.152, PF=0.500 pass 2: 21119 changed. image ll: -2.151, PF=0.500 pass 3: 6007 changed. pass 4: 2094 changed. 48163 voxels changed in iteration 0 of unlikely voxel relabeling 246 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7788 voxels changed in iteration 0 of unlikely voxel relabeling 173 voxels changed in iteration 1 of unlikely voxel relabeling 36 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7163 voxels changed in iteration 0 of unlikely voxel relabeling 87 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6561 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... mri_ca_label utimesec 4602.352336 mri_ca_label stimesec 2.206664 mri_ca_label ru_maxrss 2092824 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 793462 mri_ca_label ru_majflt 1 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 48 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 126 mri_ca_label ru_nivcsw 7551 auto-labeling took 76 minutes and 46 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/cc_up.lta AD08 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/norm.mgz 20048 voxels in left wm, 31822 in right wm, xrange [122, 131] searching rotation angles z=[-9 5], y=[-9 5] searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 global minimum found at slice 126.0, rotations (-1.63, -2.35) final transformation (x=126.0, yr=-1.632, zr=-2.351): 0.99875 0.04101 -0.02845 0.22891; -0.04100 0.99916 0.00117 18.14805; 0.02848 -0.00000 0.99959 26.45150; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 115 98 eigenvectors: 0.00110 0.00267 1.00000; 0.03997 -0.99920 0.00262; 0.99920 0.03997 -0.00120; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Tue Jun 14 22:50:07 EDT 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Jun 14 22:50:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 618 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 110 white matter peak found at 108 gm peak at 74 (74), valley at 30 (30) csf peak at 11, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 69 (69), valley at 30 (30) csf peak at 10, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Tue Jun 14 22:54:08 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1552401 voxels in mask (pct= 9.25) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Jun 14 22:54:10 EDT 2016 mri_segment -mprage 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): 106.0 +- 5.4 [79.0 --> 125.0] GM (68.0) : 65.9 +- 11.4 [30.0 --> 95.0] setting bottom of white matter range to 77.3 setting top of gray matter range to 88.7 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... 12200 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6555 filled 2505 bright non-wm voxels segmented. 5971 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.56 minutes reading wm segmentation from wm.seg.mgz... 77 voxels added to wm to prevent paths from MTL structures to cortex 2470 additional wm voxels added 0 additional wm voxels added SEG EDIT: 67303 voxels turned on, 32148 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 91 new 91 115,126,128 old 91 new 91 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 33 found - 33 modified | TOTAL: 33 pass 2 (xy+): 0 found - 33 modified | TOTAL: 33 pass 1 (xy-): 31 found - 31 modified | TOTAL: 64 pass 2 (xy-): 0 found - 31 modified | TOTAL: 64 pass 1 (yz+): 28 found - 28 modified | TOTAL: 92 pass 2 (yz+): 0 found - 28 modified | TOTAL: 92 pass 1 (yz-): 26 found - 26 modified | TOTAL: 118 pass 2 (yz-): 0 found - 26 modified | TOTAL: 118 pass 1 (xz+): 20 found - 20 modified | TOTAL: 138 pass 2 (xz+): 0 found - 20 modified | TOTAL: 138 pass 1 (xz-): 36 found - 36 modified | TOTAL: 174 pass 2 (xz-): 0 found - 36 modified | TOTAL: 174 Iteration Number : 1 pass 1 (+++): 64 found - 64 modified | TOTAL: 64 pass 2 (+++): 0 found - 64 modified | TOTAL: 64 pass 1 (+++): 37 found - 37 modified | TOTAL: 101 pass 2 (+++): 0 found - 37 modified | TOTAL: 101 pass 1 (+++): 53 found - 53 modified | TOTAL: 154 pass 2 (+++): 0 found - 53 modified | TOTAL: 154 pass 1 (+++): 53 found - 53 modified | TOTAL: 207 pass 2 (+++): 0 found - 53 modified | TOTAL: 207 Iteration Number : 1 pass 1 (++): 187 found - 187 modified | TOTAL: 187 pass 2 (++): 0 found - 187 modified | TOTAL: 187 pass 1 (+-): 155 found - 155 modified | TOTAL: 342 pass 2 (+-): 1 found - 156 modified | TOTAL: 343 pass 3 (+-): 0 found - 156 modified | TOTAL: 343 pass 1 (--): 161 found - 161 modified | TOTAL: 504 pass 2 (--): 0 found - 161 modified | TOTAL: 504 pass 1 (-+): 167 found - 167 modified | TOTAL: 671 pass 2 (-+): 0 found - 167 modified | TOTAL: 671 Iteration Number : 2 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 17 found - 17 modified | TOTAL: 31 pass 2 (xy-): 0 found - 17 modified | TOTAL: 31 pass 1 (yz+): 17 found - 17 modified | TOTAL: 48 pass 2 (yz+): 0 found - 17 modified | TOTAL: 48 pass 1 (yz-): 17 found - 17 modified | TOTAL: 65 pass 2 (yz-): 0 found - 17 modified | TOTAL: 65 pass 1 (xz+): 19 found - 19 modified | TOTAL: 84 pass 2 (xz+): 0 found - 19 modified | TOTAL: 84 pass 1 (xz-): 10 found - 10 modified | TOTAL: 94 pass 2 (xz-): 0 found - 10 modified | TOTAL: 94 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 13 found - 13 modified | TOTAL: 21 pass 2 (+-): 1 found - 14 modified | TOTAL: 22 pass 3 (+-): 0 found - 14 modified | TOTAL: 22 pass 1 (--): 6 found - 6 modified | TOTAL: 28 pass 2 (--): 0 found - 6 modified | TOTAL: 28 pass 1 (-+): 5 found - 5 modified | TOTAL: 33 pass 2 (-+): 0 found - 5 modified | TOTAL: 33 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 2 found - 2 modified | TOTAL: 9 pass 2 (yz+): 0 found - 2 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 0 found - 0 modified | TOTAL: 10 pass 1 (xz-): 1 found - 1 modified | TOTAL: 11 pass 2 (xz-): 0 found - 1 modified | TOTAL: 11 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1195 (out of 583143: 0.204924) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Jun 14 22:56:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04843; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03079 0.03753 0.00215 -10.10178; -0.03309 1.11025 0.16254 -36.04843; 0.00334 -0.19031 1.02170 11.53719; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1410 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) need search nearby using seed (125, 108, 97), TAL = (3.0, -31.0, 20.0) talairach voxel to voxel transform 0.96909 -0.03222 0.00309 8.59217; 0.02857 0.87584 -0.13940 33.46938; 0.00216 0.16324 0.95279 -5.08606; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 108, 97) --> (3.0, -31.0, 20.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, -31.00, 20.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -31.00, 20.00) SRC: (109.10, 117.59, 105.20) search lh wm seed point around talairach space (-15.00, -31.00, 20.00), SRC: (143.99, 118.62, 105.27) 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 Jun 14 22:57:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 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 = 9 (out of 271866: 0.003310) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ slice 50: 1781 vertices, 1911 faces slice 60: 7596 vertices, 7873 faces slice 70: 17779 vertices, 18155 faces slice 80: 30214 vertices, 30631 faces slice 90: 42415 vertices, 42799 faces slice 100: 53494 vertices, 53935 faces slice 110: 66039 vertices, 66473 faces slice 120: 78118 vertices, 78575 faces slice 130: 89403 vertices, 89823 faces slice 140: 100667 vertices, 101077 faces slice 150: 109870 vertices, 110231 faces slice 160: 117409 vertices, 117744 faces slice 170: 124791 vertices, 125115 faces slice 180: 131462 vertices, 131768 faces slice 190: 136819 vertices, 137074 faces slice 200: 140674 vertices, 140835 faces slice 210: 141256 vertices, 141352 faces slice 220: 141256 vertices, 141352 faces slice 230: 141256 vertices, 141352 faces slice 240: 141256 vertices, 141352 faces slice 250: 141256 vertices, 141352 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 141256 voxel in cpt #1: X=-96 [v=141256,e=424056,f=282704] located at (-26.007793, -12.364778, 8.295385) For the whole surface: X=-96 [v=141256,e=424056,f=282704] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Jun 14 22:57:30 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 4 found - 4 modified | TOTAL: 4 pass 2 (yz+): 0 found - 4 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 293438: 0.002045) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ slice 50: 1816 vertices, 1973 faces slice 60: 9378 vertices, 9714 faces slice 70: 21542 vertices, 21976 faces slice 80: 35016 vertices, 35480 faces slice 90: 47459 vertices, 47840 faces slice 100: 59723 vertices, 60169 faces slice 110: 72796 vertices, 73261 faces slice 120: 86576 vertices, 87098 faces slice 130: 99353 vertices, 99856 faces slice 140: 110784 vertices, 111255 faces slice 150: 121174 vertices, 121589 faces slice 160: 129336 vertices, 129730 faces slice 170: 136850 vertices, 137239 faces slice 180: 143657 vertices, 144011 faces slice 190: 149422 vertices, 149735 faces slice 200: 153510 vertices, 153755 faces slice 210: 154138 vertices, 154276 faces slice 220: 154138 vertices, 154276 faces slice 230: 154138 vertices, 154276 faces slice 240: 154138 vertices, 154276 faces slice 250: 154138 vertices, 154276 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 154138 voxel in cpt #1: X=-138 [v=154138,e=462828,f=308552] located at (30.604076, -13.395094, 10.624629) For the whole surface: X=-138 [v=154138,e=462828,f=308552] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Jun 14 22:57:38 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Tue Jun 14 22:57:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 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 Jun 14 22:57:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.1 mm, total surface area = 72256 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes step 000: RMS=0.163 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.043 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 56.004486 mris_inflate stimesec 0.075988 mris_inflate ru_maxrss 182132 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23969 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 36 mris_inflate ru_nivcsw 69 #-------------------------------------------- #@# Inflation1 rh Tue Jun 14 22:58:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.7 mm, total surface area = 78797 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.2 minutes step 000: RMS=0.165 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.059 (target=0.015) step 035: RMS=0.055 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.048 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 70.039352 mris_inflate stimesec 0.143978 mris_inflate ru_maxrss 198464 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25500 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 36 mris_inflate ru_nivcsw 222 #-------------------------------------------- #@# QSphere lh Tue Jun 14 22:59:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->7.21) (max @ vno 76086 --> 76103) face area 0.03 +- 0.03 (-0.29-->0.63) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.142, avgs=0 005/300: dt: 0.9000, rms radial error=175.885, avgs=0 010/300: dt: 0.9000, rms radial error=175.333, avgs=0 015/300: dt: 0.9000, rms radial error=174.607, avgs=0 020/300: dt: 0.9000, rms radial error=173.780, avgs=0 025/300: dt: 0.9000, rms radial error=172.895, avgs=0 030/300: dt: 0.9000, rms radial error=171.977, avgs=0 035/300: dt: 0.9000, rms radial error=171.043, avgs=0 040/300: dt: 0.9000, rms radial error=170.102, avgs=0 045/300: dt: 0.9000, rms radial error=169.157, avgs=0 050/300: dt: 0.9000, rms radial error=168.214, avgs=0 055/300: dt: 0.9000, rms radial error=167.272, avgs=0 060/300: dt: 0.9000, rms radial error=166.335, avgs=0 065/300: dt: 0.9000, rms radial error=165.402, avgs=0 070/300: dt: 0.9000, rms radial error=164.474, avgs=0 075/300: dt: 0.9000, rms radial error=163.550, avgs=0 080/300: dt: 0.9000, rms radial error=162.631, avgs=0 085/300: dt: 0.9000, rms radial error=161.717, avgs=0 090/300: dt: 0.9000, rms radial error=160.807, avgs=0 095/300: dt: 0.9000, rms radial error=159.903, avgs=0 100/300: dt: 0.9000, rms radial error=159.003, avgs=0 105/300: dt: 0.9000, rms radial error=158.108, avgs=0 110/300: dt: 0.9000, rms radial error=157.218, avgs=0 115/300: dt: 0.9000, rms radial error=156.333, avgs=0 120/300: dt: 0.9000, rms radial error=155.452, avgs=0 125/300: dt: 0.9000, rms radial error=154.577, avgs=0 130/300: dt: 0.9000, rms radial error=153.706, avgs=0 135/300: dt: 0.9000, rms radial error=152.840, avgs=0 140/300: dt: 0.9000, rms radial error=151.978, avgs=0 145/300: dt: 0.9000, rms radial error=151.122, avgs=0 150/300: dt: 0.9000, rms radial error=150.270, avgs=0 155/300: dt: 0.9000, rms radial error=149.423, avgs=0 160/300: dt: 0.9000, rms radial error=148.580, avgs=0 165/300: dt: 0.9000, rms radial error=147.743, avgs=0 170/300: dt: 0.9000, rms radial error=146.909, avgs=0 175/300: dt: 0.9000, rms radial error=146.081, avgs=0 180/300: dt: 0.9000, rms radial error=145.257, avgs=0 185/300: dt: 0.9000, rms radial error=144.437, avgs=0 190/300: dt: 0.9000, rms radial error=143.623, avgs=0 195/300: dt: 0.9000, rms radial error=142.813, avgs=0 200/300: dt: 0.9000, rms radial error=142.007, avgs=0 205/300: dt: 0.9000, rms radial error=141.206, avgs=0 210/300: dt: 0.9000, rms radial error=140.410, avgs=0 215/300: dt: 0.9000, rms radial error=139.618, avgs=0 220/300: dt: 0.9000, rms radial error=138.830, avgs=0 225/300: dt: 0.9000, rms radial error=138.047, avgs=0 230/300: dt: 0.9000, rms radial error=137.269, avgs=0 235/300: dt: 0.9000, rms radial error=136.494, avgs=0 240/300: dt: 0.9000, rms radial error=135.724, avgs=0 245/300: dt: 0.9000, rms radial error=134.959, avgs=0 250/300: dt: 0.9000, rms radial error=134.198, avgs=0 255/300: dt: 0.9000, rms radial error=133.441, avgs=0 260/300: dt: 0.9000, rms radial error=132.688, avgs=0 265/300: dt: 0.9000, rms radial error=131.939, avgs=0 270/300: dt: 0.9000, rms radial error=131.195, avgs=0 275/300: dt: 0.9000, rms radial error=130.455, avgs=0 280/300: dt: 0.9000, rms radial error=129.719, avgs=0 285/300: dt: 0.9000, rms radial error=128.987, avgs=0 290/300: dt: 0.9000, rms radial error=128.259, avgs=0 295/300: dt: 0.9000, rms radial error=127.536, avgs=0 300/300: dt: 0.9000, rms radial error=126.816, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16518.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 2766.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 296.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00947 epoch 4 (K=640.0), pass 1, starting sse = 18.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/12 = 0.00511 final distance error %25.90 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours mris_sphere utimesec 353.590246 mris_sphere stimesec 0.090986 mris_sphere ru_maxrss 182308 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24010 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 38 mris_sphere ru_nivcsw 387 FSRUNTIME@ mris_sphere 0.0983 hours 1 threads #-------------------------------------------- #@# QSphere rh Tue Jun 14 23:05:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.55 (0.00-->7.70) (max @ vno 54180 --> 55423) face area 0.02 +- 0.03 (-0.11-->0.59) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.992, avgs=0 005/300: dt: 0.9000, rms radial error=175.735, avgs=0 010/300: dt: 0.9000, rms radial error=175.182, avgs=0 015/300: dt: 0.9000, rms radial error=174.455, avgs=0 020/300: dt: 0.9000, rms radial error=173.628, avgs=0 025/300: dt: 0.9000, rms radial error=172.743, avgs=0 030/300: dt: 0.9000, rms radial error=171.826, avgs=0 035/300: dt: 0.9000, rms radial error=170.893, avgs=0 040/300: dt: 0.9000, rms radial error=169.952, avgs=0 045/300: dt: 0.9000, rms radial error=169.008, avgs=0 050/300: dt: 0.9000, rms radial error=168.065, avgs=0 055/300: dt: 0.9000, rms radial error=167.125, avgs=0 060/300: dt: 0.9000, rms radial error=166.188, avgs=0 065/300: dt: 0.9000, rms radial error=165.255, avgs=0 070/300: dt: 0.9000, rms radial error=164.327, avgs=0 075/300: dt: 0.9000, rms radial error=163.403, avgs=0 080/300: dt: 0.9000, rms radial error=162.485, avgs=0 085/300: dt: 0.9000, rms radial error=161.571, avgs=0 090/300: dt: 0.9000, rms radial error=160.662, avgs=0 095/300: dt: 0.9000, rms radial error=159.758, avgs=0 100/300: dt: 0.9000, rms radial error=158.858, avgs=0 105/300: dt: 0.9000, rms radial error=157.964, avgs=0 110/300: dt: 0.9000, rms radial error=157.075, avgs=0 115/300: dt: 0.9000, rms radial error=156.191, avgs=0 120/300: dt: 0.9000, rms radial error=155.311, avgs=0 125/300: dt: 0.9000, rms radial error=154.436, avgs=0 130/300: dt: 0.9000, rms radial error=153.566, avgs=0 135/300: dt: 0.9000, rms radial error=152.701, avgs=0 140/300: dt: 0.9000, rms radial error=151.841, avgs=0 145/300: dt: 0.9000, rms radial error=150.985, avgs=0 150/300: dt: 0.9000, rms radial error=150.134, avgs=0 155/300: dt: 0.9000, rms radial error=149.289, avgs=0 160/300: dt: 0.9000, rms radial error=148.449, avgs=0 165/300: dt: 0.9000, rms radial error=147.613, avgs=0 170/300: dt: 0.9000, rms radial error=146.783, avgs=0 175/300: dt: 0.9000, rms radial error=145.956, avgs=0 180/300: dt: 0.9000, rms radial error=145.135, avgs=0 185/300: dt: 0.9000, rms radial error=144.317, avgs=0 190/300: dt: 0.9000, rms radial error=143.505, avgs=0 195/300: dt: 0.9000, rms radial error=142.696, avgs=0 200/300: dt: 0.9000, rms radial error=141.892, avgs=0 205/300: dt: 0.9000, rms radial error=141.093, avgs=0 210/300: dt: 0.9000, rms radial error=140.298, avgs=0 215/300: dt: 0.9000, rms radial error=139.507, avgs=0 220/300: dt: 0.9000, rms radial error=138.721, avgs=0 225/300: dt: 0.9000, rms radial error=137.939, avgs=0 230/300: dt: 0.9000, rms radial error=137.162, avgs=0 235/300: dt: 0.9000, rms radial error=136.390, avgs=0 240/300: dt: 0.9000, rms radial error=135.622, avgs=0 245/300: dt: 0.9000, rms radial error=134.858, avgs=0 250/300: dt: 0.9000, rms radial error=134.098, avgs=0 255/300: dt: 0.9000, rms radial error=133.343, avgs=0 260/300: dt: 0.9000, rms radial error=132.592, avgs=0 265/300: dt: 0.9000, rms radial error=131.845, avgs=0 270/300: dt: 0.9000, rms radial error=131.102, avgs=0 275/300: dt: 0.9000, rms radial error=130.363, avgs=0 280/300: dt: 0.9000, rms radial error=129.629, avgs=0 285/300: dt: 0.9000, rms radial error=128.899, avgs=0 290/300: dt: 0.9000, rms radial error=128.173, avgs=0 295/300: dt: 0.9000, rms radial error=127.451, avgs=0 300/300: dt: 0.9000, rms radial error=126.733, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18197.30 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 = 3100.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 343.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00621 epoch 4 (K=640.0), pass 1, starting sse = 27.67 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00639 final distance error %26.13 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.11 hours mris_sphere utimesec 393.058246 mris_sphere stimesec 0.097985 mris_sphere ru_maxrss 198648 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 25545 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 37 mris_sphere ru_nivcsw 819 FSRUNTIME@ mris_sphere 0.1093 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue Jun 14 23:12:26 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Tue Jun 14 23:12:26 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Tue Jun 14 23:12:26 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD08 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 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ before topology correction, eno=-96 (nv=141256, nf=282704, ne=424056, g=49) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4000 ambiguous faces found in tessellation segmenting defects... 66 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 31 into 35 65 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5994 (-4.7997) -vertex loglikelihood: -6.8926 (-3.4463) -normal dot loglikelihood: -3.6450 (-3.6450) -quad curv loglikelihood: -6.6447 (-3.3223) Total Loglikelihood : -26.7817 CORRECTING DEFECT 0 (vertices=39, convex hull=73) After retessellation of defect 0, euler #=-62 (138639,414481,275780) : difference with theory (-62) = 0 CORRECTING DEFECT 1 (vertices=8, convex hull=35) After retessellation of defect 1, euler #=-61 (138640,414494,275793) : difference with theory (-61) = 0 CORRECTING DEFECT 2 (vertices=45, convex hull=79) After retessellation of defect 2, euler #=-60 (138653,414565,275852) : difference with theory (-60) = 0 CORRECTING DEFECT 3 (vertices=18, convex hull=46) After retessellation of defect 3, euler #=-59 (138655,414591,275877) : difference with theory (-59) = 0 CORRECTING DEFECT 4 (vertices=24, convex hull=51) After retessellation of defect 4, euler #=-58 (138668,414648,275922) : difference with theory (-58) = 0 CORRECTING DEFECT 5 (vertices=10, convex hull=22) After retessellation of defect 5, euler #=-57 (138670,414661,275934) : difference with theory (-57) = 0 CORRECTING DEFECT 6 (vertices=32, convex hull=55) After retessellation of defect 6, euler #=-56 (138687,414733,275990) : difference with theory (-56) = 0 CORRECTING DEFECT 7 (vertices=5, convex hull=26) After retessellation of defect 7, euler #=-55 (138687,414741,275999) : difference with theory (-55) = 0 CORRECTING DEFECT 8 (vertices=20, convex hull=49) After retessellation of defect 8, euler #=-54 (138696,414786,276036) : difference with theory (-54) = 0 CORRECTING DEFECT 9 (vertices=43, convex hull=79) After retessellation of defect 9, euler #=-53 (138723,414899,276123) : difference with theory (-53) = 0 CORRECTING DEFECT 10 (vertices=46, convex hull=69) After retessellation of defect 10, euler #=-52 (138748,415002,276202) : difference with theory (-52) = 0 CORRECTING DEFECT 11 (vertices=28, convex hull=70) After retessellation of defect 11, euler #=-51 (138757,415054,276246) : difference with theory (-51) = 0 CORRECTING DEFECT 12 (vertices=59, convex hull=82) After retessellation of defect 12, euler #=-50 (138785,415170,276335) : difference with theory (-50) = 0 CORRECTING DEFECT 13 (vertices=32, convex hull=39) After retessellation of defect 13, euler #=-49 (138792,415203,276362) : difference with theory (-49) = 0 CORRECTING DEFECT 14 (vertices=74, convex hull=95) After retessellation of defect 14, euler #=-49 (138828,415359,276482) : difference with theory (-48) = 1 CORRECTING DEFECT 15 (vertices=97, convex hull=117) After retessellation of defect 15, euler #=-48 (138889,415595,276658) : difference with theory (-47) = 1 CORRECTING DEFECT 16 (vertices=19, convex hull=15) After retessellation of defect 16, euler #=-47 (138889,415597,276661) : difference with theory (-46) = 1 CORRECTING DEFECT 17 (vertices=10, convex hull=19) After retessellation of defect 17, euler #=-46 (138891,415609,276672) : difference with theory (-45) = 1 CORRECTING DEFECT 18 (vertices=42, convex hull=82) After retessellation of defect 18, euler #=-45 (138912,415706,276749) : difference with theory (-44) = 1 CORRECTING DEFECT 19 (vertices=210, convex hull=92) After retessellation of defect 19, euler #=-44 (138926,415791,276821) : difference with theory (-43) = 1 CORRECTING DEFECT 20 (vertices=97, convex hull=67) After retessellation of defect 20, euler #=-43 (138940,415860,276877) : difference with theory (-42) = 1 CORRECTING DEFECT 21 (vertices=31, convex hull=72) After retessellation of defect 21, euler #=-42 (138958,415940,276940) : difference with theory (-41) = 1 CORRECTING DEFECT 22 (vertices=7, convex hull=18) After retessellation of defect 22, euler #=-41 (138959,415946,276946) : difference with theory (-40) = 1 CORRECTING DEFECT 23 (vertices=11, convex hull=15) After retessellation of defect 23, euler #=-40 (138960,415953,276953) : difference with theory (-39) = 1 CORRECTING DEFECT 24 (vertices=5, convex hull=11) After retessellation of defect 24, euler #=-39 (138960,415955,276956) : difference with theory (-38) = 1 CORRECTING DEFECT 25 (vertices=26, convex hull=44) After retessellation of defect 25, euler #=-38 (138969,416001,276994) : difference with theory (-37) = 1 CORRECTING DEFECT 26 (vertices=24, convex hull=78) After retessellation of defect 26, euler #=-37 (138982,416073,277054) : difference with theory (-36) = 1 CORRECTING DEFECT 27 (vertices=5, convex hull=15) After retessellation of defect 27, euler #=-36 (138982,416076,277058) : difference with theory (-35) = 1 CORRECTING DEFECT 28 (vertices=53, convex hull=63) After retessellation of defect 28, euler #=-35 (139001,416157,277121) : difference with theory (-34) = 1 CORRECTING DEFECT 29 (vertices=130, convex hull=128) After retessellation of defect 29, euler #=-34 (139070,416429,277325) : difference with theory (-33) = 1 CORRECTING DEFECT 30 (vertices=53, convex hull=47) After retessellation of defect 30, euler #=-33 (139079,416472,277360) : difference with theory (-32) = 1 CORRECTING DEFECT 31 (vertices=81, convex hull=64) After retessellation of defect 31, euler #=-32 (139097,416556,277427) : difference with theory (-31) = 1 CORRECTING DEFECT 32 (vertices=78, convex hull=109) After retessellation of defect 32, euler #=-31 (139129,416699,277539) : difference with theory (-30) = 1 CORRECTING DEFECT 33 (vertices=63, convex hull=102) After retessellation of defect 33, euler #=-30 (139167,416857,277660) : difference with theory (-29) = 1 CORRECTING DEFECT 34 (vertices=60, convex hull=71) After retessellation of defect 34, euler #=-28 (139190,416961,277743) : difference with theory (-28) = 0 CORRECTING DEFECT 35 (vertices=63, convex hull=56) After retessellation of defect 35, euler #=-27 (139215,417057,277815) : difference with theory (-27) = 0 CORRECTING DEFECT 36 (vertices=23, convex hull=19) After retessellation of defect 36, euler #=-26 (139220,417076,277830) : difference with theory (-26) = 0 CORRECTING DEFECT 37 (vertices=14, convex hull=17) After retessellation of defect 37, euler #=-25 (139223,417088,277840) : difference with theory (-25) = 0 CORRECTING DEFECT 38 (vertices=21, convex hull=48) After retessellation of defect 38, euler #=-24 (139232,417136,277880) : difference with theory (-24) = 0 CORRECTING DEFECT 39 (vertices=21, convex hull=47) After retessellation of defect 39, euler #=-23 (139242,417186,277921) : difference with theory (-23) = 0 CORRECTING DEFECT 40 (vertices=58, convex hull=79) After retessellation of defect 40, euler #=-22 (139263,417277,277992) : difference with theory (-22) = 0 CORRECTING DEFECT 41 (vertices=149, convex hull=37) After retessellation of defect 41, euler #=-21 (139273,417320,278026) : difference with theory (-21) = 0 CORRECTING DEFECT 42 (vertices=49, convex hull=49) After retessellation of defect 42, euler #=-20 (139291,417391,278080) : difference with theory (-20) = 0 CORRECTING DEFECT 43 (vertices=13, convex hull=21) After retessellation of defect 43, euler #=-19 (139293,417407,278095) : difference with theory (-19) = 0 CORRECTING DEFECT 44 (vertices=8, convex hull=27) After retessellation of defect 44, euler #=-18 (139297,417427,278112) : difference with theory (-18) = 0 CORRECTING DEFECT 45 (vertices=23, convex hull=65) After retessellation of defect 45, euler #=-17 (139310,417492,278165) : difference with theory (-17) = 0 CORRECTING DEFECT 46 (vertices=5, convex hull=9) After retessellation of defect 46, euler #=-16 (139310,417494,278168) : difference with theory (-16) = 0 CORRECTING DEFECT 47 (vertices=30, convex hull=64) After retessellation of defect 47, euler #=-15 (139321,417550,278214) : difference with theory (-15) = 0 CORRECTING DEFECT 48 (vertices=88, convex hull=107) After retessellation of defect 48, euler #=-14 (139352,417691,278325) : difference with theory (-14) = 0 CORRECTING DEFECT 49 (vertices=15, convex hull=23) After retessellation of defect 49, euler #=-13 (139355,417709,278341) : difference with theory (-13) = 0 CORRECTING DEFECT 50 (vertices=28, convex hull=37) After retessellation of defect 50, euler #=-12 (139362,417743,278369) : difference with theory (-12) = 0 CORRECTING DEFECT 51 (vertices=28, convex hull=65) After retessellation of defect 51, euler #=-11 (139379,417821,278431) : difference with theory (-11) = 0 CORRECTING DEFECT 52 (vertices=60, convex hull=95) After retessellation of defect 52, euler #=-10 (139398,417916,278508) : difference with theory (-10) = 0 CORRECTING DEFECT 53 (vertices=9, convex hull=24) After retessellation of defect 53, euler #=-9 (139400,417929,278520) : difference with theory (-9) = 0 CORRECTING DEFECT 54 (vertices=8, convex hull=27) After retessellation of defect 54, euler #=-8 (139402,417943,278533) : difference with theory (-8) = 0 CORRECTING DEFECT 55 (vertices=36, convex hull=59) After retessellation of defect 55, euler #=-7 (139420,418025,278598) : difference with theory (-7) = 0 CORRECTING DEFECT 56 (vertices=16, convex hull=51) After retessellation of defect 56, euler #=-6 (139428,418069,278635) : difference with theory (-6) = 0 CORRECTING DEFECT 57 (vertices=37, convex hull=66) After retessellation of defect 57, euler #=-5 (139438,418125,278682) : difference with theory (-5) = 0 CORRECTING DEFECT 58 (vertices=39, convex hull=69) After retessellation of defect 58, euler #=-4 (139451,418193,278738) : difference with theory (-4) = 0 CORRECTING DEFECT 59 (vertices=37, convex hull=67) After retessellation of defect 59, euler #=-3 (139473,418291,278815) : difference with theory (-3) = 0 CORRECTING DEFECT 60 (vertices=44, convex hull=85) After retessellation of defect 60, euler #=-2 (139499,418403,278902) : difference with theory (-2) = 0 CORRECTING DEFECT 61 (vertices=32, convex hull=61) After retessellation of defect 61, euler #=-1 (139517,418481,278963) : difference with theory (-1) = 0 CORRECTING DEFECT 62 (vertices=24, convex hull=30) After retessellation of defect 62, euler #=0 (139521,418503,278982) : difference with theory (0) = 0 CORRECTING DEFECT 63 (vertices=31, convex hull=67) After retessellation of defect 63, euler #=1 (139535,418573,279039) : difference with theory (1) = 0 CORRECTING DEFECT 64 (vertices=38, convex hull=69) After retessellation of defect 64, euler #=2 (139545,418629,279086) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.23 (0.07-->10.29) (max @ vno 102361 --> 105086) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.23 (0.07-->10.29) (max @ vno 102361 --> 105086) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 214 mutations (37.4%), 358 crossovers (62.6%), 156 vertices were eliminated building final representation... 1711 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139545, nf=279086, ne=418629, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 38.1 minutes 0 defective edges removing intersecting faces 000: 309 intersecting 001: 2 intersecting mris_fix_topology utimesec 2284.054770 mris_fix_topology stimesec 0.274958 mris_fix_topology ru_maxrss 436624 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55986 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 64 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 69 mris_fix_topology ru_nivcsw 5107 FSRUNTIME@ mris_fix_topology lh 0.6347 hours 1 threads #@# Fix Topology rh Tue Jun 14 23:50:31 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD08 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 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ before topology correction, eno=-138 (nv=154138, nf=308552, ne=462828, g=70) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 9888 ambiguous faces found in tessellation segmenting defects... 67 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 33 into 32 66 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5655 (-4.7828) -vertex loglikelihood: -6.8093 (-3.4046) -normal dot loglikelihood: -3.5383 (-3.5383) -quad curv loglikelihood: -6.5146 (-3.2573) Total Loglikelihood : -26.4276 CORRECTING DEFECT 0 (vertices=58, convex hull=99) After retessellation of defect 0, euler #=-64 (148442,443676,295170) : difference with theory (-63) = 1 CORRECTING DEFECT 1 (vertices=20, convex hull=57) After retessellation of defect 1, euler #=-63 (148452,443723,295208) : difference with theory (-62) = 1 CORRECTING DEFECT 2 (vertices=27, convex hull=59) After retessellation of defect 2, euler #=-62 (148469,443793,295262) : difference with theory (-61) = 1 CORRECTING DEFECT 3 (vertices=5, convex hull=23) After retessellation of defect 3, euler #=-61 (148470,443802,295271) : difference with theory (-60) = 1 CORRECTING DEFECT 4 (vertices=31, convex hull=70) After retessellation of defect 4, euler #=-60 (148484,443875,295331) : difference with theory (-59) = 1 CORRECTING DEFECT 5 (vertices=15, convex hull=17) After retessellation of defect 5, euler #=-59 (148485,443882,295338) : difference with theory (-58) = 1 CORRECTING DEFECT 6 (vertices=11, convex hull=25) After retessellation of defect 6, euler #=-58 (148488,443900,295354) : difference with theory (-57) = 1 CORRECTING DEFECT 7 (vertices=21, convex hull=34) After retessellation of defect 7, euler #=-57 (148497,443939,295385) : difference with theory (-56) = 1 CORRECTING DEFECT 8 (vertices=645, convex hull=262) After retessellation of defect 8, euler #=-56 (148669,444587,295862) : difference with theory (-55) = 1 CORRECTING DEFECT 9 (vertices=12, convex hull=27) After retessellation of defect 9, euler #=-55 (148670,444599,295874) : difference with theory (-54) = 1 CORRECTING DEFECT 10 (vertices=661, convex hull=66) After retessellation of defect 10, euler #=-54 (148678,444646,295914) : difference with theory (-53) = 1 CORRECTING DEFECT 11 (vertices=222, convex hull=152) After retessellation of defect 11, euler #=-53 (148771,444997,296173) : difference with theory (-52) = 1 CORRECTING DEFECT 12 (vertices=23, convex hull=51) After retessellation of defect 12, euler #=-52 (148785,445059,296222) : difference with theory (-51) = 1 CORRECTING DEFECT 13 (vertices=31, convex hull=53) After retessellation of defect 13, euler #=-51 (148797,445115,296267) : difference with theory (-50) = 1 CORRECTING DEFECT 14 (vertices=27, convex hull=45) After retessellation of defect 14, euler #=-50 (148803,445149,296296) : difference with theory (-49) = 1 CORRECTING DEFECT 15 (vertices=1416, convex hull=168) normal vector of length zero at vertex 151158 with 4 faces After retessellation of defect 15, euler #=-49 (148815,445263,296399) : difference with theory (-48) = 1 CORRECTING DEFECT 16 (vertices=83, convex hull=113) After retessellation of defect 16, euler #=-48 (148831,445362,296483) : difference with theory (-47) = 1 CORRECTING DEFECT 17 (vertices=15, convex hull=24) After retessellation of defect 17, euler #=-47 (148835,445378,296496) : difference with theory (-46) = 1 CORRECTING DEFECT 18 (vertices=24, convex hull=29) After retessellation of defect 18, euler #=-46 (148837,445392,296509) : difference with theory (-45) = 1 CORRECTING DEFECT 19 (vertices=30, convex hull=69) After retessellation of defect 19, euler #=-45 (148852,445464,296567) : difference with theory (-44) = 1 CORRECTING DEFECT 20 (vertices=216, convex hull=82) After retessellation of defect 20, euler #=-44 (148900,445645,296701) : difference with theory (-43) = 1 CORRECTING DEFECT 21 (vertices=121, convex hull=138) After retessellation of defect 21, euler #=-43 (148965,445904,296896) : difference with theory (-42) = 1 CORRECTING DEFECT 22 (vertices=20, convex hull=52) After retessellation of defect 22, euler #=-42 (148977,445961,296942) : difference with theory (-41) = 1 CORRECTING DEFECT 23 (vertices=30, convex hull=66) After retessellation of defect 23, euler #=-41 (148995,446039,297003) : difference with theory (-40) = 1 CORRECTING DEFECT 24 (vertices=35, convex hull=47) After retessellation of defect 24, euler #=-40 (149010,446103,297053) : difference with theory (-39) = 1 CORRECTING DEFECT 25 (vertices=7, convex hull=22) After retessellation of defect 25, euler #=-39 (149012,446116,297065) : difference with theory (-38) = 1 CORRECTING DEFECT 26 (vertices=25, convex hull=51) After retessellation of defect 26, euler #=-38 (149025,446177,297114) : difference with theory (-37) = 1 CORRECTING DEFECT 27 (vertices=24, convex hull=25) After retessellation of defect 27, euler #=-37 (149031,446201,297133) : difference with theory (-36) = 1 CORRECTING DEFECT 28 (vertices=57, convex hull=56) After retessellation of defect 28, euler #=-36 (149054,446286,297196) : difference with theory (-35) = 1 CORRECTING DEFECT 29 (vertices=20, convex hull=54) After retessellation of defect 29, euler #=-35 (149063,446332,297234) : difference with theory (-34) = 1 CORRECTING DEFECT 30 (vertices=43, convex hull=81) After retessellation of defect 30, euler #=-34 (149089,446444,297321) : difference with theory (-33) = 1 CORRECTING DEFECT 31 (vertices=10, convex hull=29) After retessellation of defect 31, euler #=-33 (149092,446463,297338) : difference with theory (-32) = 1 CORRECTING DEFECT 32 (vertices=95, convex hull=110) After retessellation of defect 32, euler #=-31 (149127,446621,297463) : difference with theory (-31) = 0 CORRECTING DEFECT 33 (vertices=24, convex hull=27) After retessellation of defect 33, euler #=-30 (149131,446645,297484) : difference with theory (-30) = 0 CORRECTING DEFECT 34 (vertices=303, convex hull=149) After retessellation of defect 34, euler #=-29 (149161,446806,297616) : difference with theory (-29) = 0 CORRECTING DEFECT 35 (vertices=82, convex hull=101) After retessellation of defect 35, euler #=-28 (149209,446999,297762) : difference with theory (-28) = 0 CORRECTING DEFECT 36 (vertices=34, convex hull=64) After retessellation of defect 36, euler #=-27 (149229,447086,297830) : difference with theory (-27) = 0 CORRECTING DEFECT 37 (vertices=25, convex hull=35) After retessellation of defect 37, euler #=-26 (149236,447121,297859) : difference with theory (-26) = 0 CORRECTING DEFECT 38 (vertices=48, convex hull=48) After retessellation of defect 38, euler #=-25 (149241,447157,297891) : difference with theory (-25) = 0 CORRECTING DEFECT 39 (vertices=14, convex hull=22) After retessellation of defect 39, euler #=-24 (149245,447174,297905) : difference with theory (-24) = 0 CORRECTING DEFECT 40 (vertices=30, convex hull=75) After retessellation of defect 40, euler #=-23 (149266,447261,297972) : difference with theory (-23) = 0 CORRECTING DEFECT 41 (vertices=34, convex hull=78) After retessellation of defect 41, euler #=-22 (149277,447323,298024) : difference with theory (-22) = 0 CORRECTING DEFECT 42 (vertices=20, convex hull=29) After retessellation of defect 42, euler #=-21 (149281,447346,298044) : difference with theory (-21) = 0 CORRECTING DEFECT 43 (vertices=6, convex hull=14) After retessellation of defect 43, euler #=-20 (149283,447357,298054) : difference with theory (-20) = 0 CORRECTING DEFECT 44 (vertices=69, convex hull=103) After retessellation of defect 44, euler #=-19 (149324,447524,298181) : difference with theory (-19) = 0 CORRECTING DEFECT 45 (vertices=35, convex hull=25) After retessellation of defect 45, euler #=-18 (149334,447562,298210) : difference with theory (-18) = 0 CORRECTING DEFECT 46 (vertices=8, convex hull=29) After retessellation of defect 46, euler #=-17 (149335,447574,298222) : difference with theory (-17) = 0 CORRECTING DEFECT 47 (vertices=54, convex hull=33) After retessellation of defect 47, euler #=-16 (149342,447606,298248) : difference with theory (-16) = 0 CORRECTING DEFECT 48 (vertices=75, convex hull=100) After retessellation of defect 48, euler #=-15 (149384,447775,298376) : difference with theory (-15) = 0 CORRECTING DEFECT 49 (vertices=100, convex hull=88) After retessellation of defect 49, euler #=-14 (149408,447884,298462) : difference with theory (-14) = 0 CORRECTING DEFECT 50 (vertices=18, convex hull=43) After retessellation of defect 50, euler #=-13 (149418,447926,298495) : difference with theory (-13) = 0 CORRECTING DEFECT 51 (vertices=33, convex hull=33) After retessellation of defect 51, euler #=-12 (149422,447949,298515) : difference with theory (-12) = 0 CORRECTING DEFECT 52 (vertices=31, convex hull=44) After retessellation of defect 52, euler #=-11 (149424,447972,298537) : difference with theory (-11) = 0 CORRECTING DEFECT 53 (vertices=9, convex hull=28) After retessellation of defect 53, euler #=-10 (149426,447985,298549) : difference with theory (-10) = 0 CORRECTING DEFECT 54 (vertices=28, convex hull=58) After retessellation of defect 54, euler #=-9 (149440,448052,298603) : difference with theory (-9) = 0 CORRECTING DEFECT 55 (vertices=45, convex hull=84) After retessellation of defect 55, euler #=-8 (149465,448159,298686) : difference with theory (-8) = 0 CORRECTING DEFECT 56 (vertices=41, convex hull=65) After retessellation of defect 56, euler #=-7 (149484,448242,298751) : difference with theory (-7) = 0 CORRECTING DEFECT 57 (vertices=38, convex hull=68) After retessellation of defect 57, euler #=-6 (149503,448325,298816) : difference with theory (-6) = 0 CORRECTING DEFECT 58 (vertices=109, convex hull=48) After retessellation of defect 58, euler #=-5 (149508,448355,298842) : difference with theory (-5) = 0 CORRECTING DEFECT 59 (vertices=50, convex hull=76) After retessellation of defect 59, euler #=-4 (149529,448446,298913) : difference with theory (-4) = 0 CORRECTING DEFECT 60 (vertices=28, convex hull=42) After retessellation of defect 60, euler #=-3 (149539,448493,298951) : difference with theory (-3) = 0 CORRECTING DEFECT 61 (vertices=33, convex hull=57) After retessellation of defect 61, euler #=-2 (149545,448534,298987) : difference with theory (-2) = 0 CORRECTING DEFECT 62 (vertices=158, convex hull=94) After retessellation of defect 62, euler #=-1 (149582,448684,299101) : difference with theory (-1) = 0 CORRECTING DEFECT 63 (vertices=16, convex hull=51) After retessellation of defect 63, euler #=0 (149591,448730,299139) : difference with theory (0) = 0 CORRECTING DEFECT 64 (vertices=6, convex hull=29) After retessellation of defect 64, euler #=1 (149594,448747,299154) : difference with theory (1) = 0 CORRECTING DEFECT 65 (vertices=36, convex hull=74) After retessellation of defect 65, euler #=2 (149612,448830,299220) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.06-->29.41) (max @ vno 74549 --> 88545) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.24 (0.06-->29.41) (max @ vno 74549 --> 88545) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 219 mutations (34.4%), 417 crossovers (65.6%), 331 vertices were eliminated building final representation... 4526 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=149612, nf=299220, ne=448830, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 61.5 minutes 0 defective edges removing intersecting faces 000: 345 intersecting 001: 19 intersecting mris_fix_topology utimesec 3689.796065 mris_fix_topology stimesec 0.308953 mris_fix_topology ru_maxrss 476696 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 52761 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 65 mris_fix_topology ru_nivcsw 9217 FSRUNTIME@ mris_fix_topology rh 1.0253 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 139545 - 418629 + 279086 = 2 --> 0 holes F =2V-4: 279086 = 279090-4 (0) 2E=3F: 837258 = 837258 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 149612 - 448830 + 299220 = 2 --> 0 holes F =2V-4: 299220 = 299224-4 (0) 2E=3F: 897660 = 897660 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 22 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 49 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jun 15 00:52:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD08 lh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.164 2016/05/13 18:03:58 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 35984 bright wm thresholded. 2661 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 279527 voxels (1.67%) border gray 308339 voxels (1.84%) WM (96.0): 96.0 +- 9.3 [70.0 --> 110.0] GM (68.0) : 66.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.9 (was 70) setting MAX_BORDER_WHITE to 109.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 36.8 (was 40) setting MAX_GRAY to 90.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.02-->3.14) (max @ vno 50708 --> 60542) face area 0.27 +- 0.13 (0.00-->1.84) mean absolute distance = 0.90 +- 1.23 5085 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-9.6, GM=63+-13.0 mean inside = 90.4, mean outside = 68.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=77.4, 137 (137) missing vertices, mean dist 0.0 [1.1 (%40.6)->0.8 (%59.4))] %36 local maxima, %60 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 0.90 +- 0.26 (0.09-->3.89) (max @ vno 60061 --> 64922) face area 0.27 +- 0.13 (0.00-->2.57) mean absolute distance = 0.48 +- 0.85 5226 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4400316.5, rms=11.960 001: dt: 0.5000, sse=2315529.5, rms=8.159 (31.782%) 002: dt: 0.5000, sse=1493127.9, rms=5.993 (26.538%) 003: dt: 0.5000, sse=1168102.9, rms=4.894 (18.342%) 004: dt: 0.5000, sse=1036312.6, rms=4.353 (11.056%) 005: dt: 0.5000, sse=983575.4, rms=4.099 (5.847%) 006: dt: 0.5000, sse=963534.1, rms=3.985 (2.778%) 007: dt: 0.5000, sse=945477.1, rms=3.919 (1.637%) rms = 3.90, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=937024.8, rms=3.897 (0.584%) 009: dt: 0.2500, sse=743083.5, rms=2.705 (30.576%) 010: dt: 0.2500, sse=692848.1, rms=2.340 (13.514%) 011: dt: 0.2500, sse=682633.2, rms=2.250 (3.811%) 012: dt: 0.2500, sse=676033.4, rms=2.191 (2.636%) rms = 2.16, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=674069.9, rms=2.165 (1.198%) 014: dt: 0.1250, sse=656143.9, rms=2.013 (7.022%) rms = 1.99, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=654009.6, rms=1.986 (1.309%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.0, 163 (48) missing vertices, mean dist -0.3 [0.6 (%60.2)->0.3 (%39.8))] %48 local maxima, %47 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 +- 0.26 (0.10-->4.32) (max @ vno 60061 --> 64922) face area 0.34 +- 0.17 (0.00-->3.71) mean absolute distance = 0.36 +- 0.52 4458 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1256885.8, rms=4.638 016: dt: 0.5000, sse=1001946.2, rms=3.436 (25.908%) rms = 3.67, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=867482.6, rms=2.633 (23.368%) 018: dt: 0.2500, sse=807264.6, rms=2.165 (17.764%) 019: dt: 0.2500, sse=791925.4, rms=1.941 (10.356%) 020: dt: 0.2500, sse=774951.7, rms=1.855 (4.460%) rms = 1.81, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=770478.5, rms=1.805 (2.647%) 022: dt: 0.1250, sse=756789.9, rms=1.676 (7.146%) rms = 1.66, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=759372.2, rms=1.662 (0.858%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=82.8, 145 (32) missing vertices, mean dist -0.2 [0.4 (%65.9)->0.2 (%34.1))] %68 local maxima, %27 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 0.88 +- 0.26 (0.03-->4.48) (max @ vno 60061 --> 64922) face area 0.33 +- 0.16 (0.00-->3.79) mean absolute distance = 0.28 +- 0.41 3671 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1120268.4, rms=4.105 024: dt: 0.5000, sse=955570.5, rms=3.231 (21.299%) rms = 3.56, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=810566.2, rms=2.276 (29.538%) 026: dt: 0.2500, sse=766078.7, rms=1.841 (19.118%) 027: dt: 0.2500, sse=747831.5, rms=1.683 (8.611%) rms = 1.66, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=747446.2, rms=1.662 (1.199%) 029: dt: 0.1250, sse=730706.6, rms=1.495 (10.061%) rms = 1.47, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=727636.2, rms=1.473 (1.465%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.0, 147 (19) missing vertices, mean dist -0.1 [0.3 (%57.5)->0.2 (%42.5))] %77 local maxima, %19 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=793516.8, rms=2.253 rms = 2.46, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=721787.7, rms=1.551 (31.171%) 032: dt: 0.2500, sse=710355.7, rms=1.133 (26.919%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.12, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=697508.1, rms=1.118 (1.387%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 8185 vertices erasing segment 1 (vno[0] = 55058) erasing segment 2 (vno[0] = 55107) erasing segment 3 (vno[0] = 78464) erasing segment 4 (vno[0] = 101392) erasing segment 5 (vno[0] = 103171) erasing segment 6 (vno[0] = 104148) erasing segment 7 (vno[0] = 138889) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area vertex spacing 0.88 +- 0.26 (0.03-->4.53) (max @ vno 60061 --> 64922) face area 0.33 +- 0.16 (0.00-->3.81) refinement took 5.9 minutes #-------------------------------------------- #@# Make White Surf rh Wed Jun 15 00:58:12 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD08 rh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.164 2016/05/13 18:03:58 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 35984 bright wm thresholded. 2661 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 279527 voxels (1.67%) border gray 308339 voxels (1.84%) WM (96.0): 96.0 +- 9.3 [70.0 --> 110.0] GM (68.0) : 66.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.9 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 37.8 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.01-->4.58) (max @ vno 73211 --> 74352) face area 0.27 +- 0.13 (0.00-->3.56) mean absolute distance = 0.87 +- 1.19 4916 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-10.4, GM=64+-12.2 mean inside = 90.8, mean outside = 70.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=78.5, 95 (95) missing vertices, mean dist 0.1 [1.0 (%39.6)->0.8 (%60.4))] %42 local maxima, %53 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 0.90 +- 0.26 (0.08-->4.47) (max @ vno 73211 --> 73224) face area 0.27 +- 0.13 (0.00-->3.15) mean absolute distance = 0.49 +- 0.84 5233 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4155041.2, rms=11.076 001: dt: 0.5000, sse=2215023.0, rms=7.541 (31.915%) 002: dt: 0.5000, sse=1463424.4, rms=5.558 (26.298%) 003: dt: 0.5000, sse=1176142.0, rms=4.581 (17.580%) 004: dt: 0.5000, sse=1063859.6, rms=4.125 (9.937%) 005: dt: 0.5000, sse=1006369.4, rms=3.879 (5.976%) 006: dt: 0.5000, sse=984622.3, rms=3.777 (2.618%) 007: dt: 0.5000, sse=967476.3, rms=3.687 (2.386%) rms = 3.67, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=963314.4, rms=3.671 (0.431%) 009: dt: 0.2500, sse=774147.4, rms=2.507 (31.720%) 010: dt: 0.2500, sse=724039.6, rms=2.153 (14.099%) 011: dt: 0.2500, sse=715026.6, rms=2.081 (3.375%) 012: dt: 0.2500, sse=708213.8, rms=2.024 (2.705%) rms = 2.00, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=707259.2, rms=2.004 (1.002%) 014: dt: 0.1250, sse=691501.6, rms=1.867 (6.860%) rms = 1.85, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=690289.1, rms=1.852 (0.802%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... mean border=81.2, 83 (27) missing vertices, mean dist -0.3 [0.6 (%61.5)->0.3 (%38.5))] %55 local maxima, %41 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 0.88 +- 0.25 (0.08-->4.40) (max @ vno 73211 --> 74352) face area 0.34 +- 0.16 (0.00-->4.53) mean absolute distance = 0.38 +- 0.51 4743 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1376561.5, rms=4.747 016: dt: 0.5000, sse=1088784.2, rms=3.525 (25.752%) rms = 3.59, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=954427.6, rms=2.794 (20.734%) 018: dt: 0.2500, sse=879860.9, rms=2.291 (17.993%) 019: dt: 0.2500, sse=847733.9, rms=2.014 (12.099%) 020: dt: 0.2500, sse=835774.3, rms=1.868 (7.267%) 021: dt: 0.2500, sse=824049.2, rms=1.776 (4.923%) rms = 1.73, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=819573.3, rms=1.727 (2.753%) 023: dt: 0.1250, sse=808298.4, rms=1.619 (6.261%) rms = 1.61, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=805175.6, rms=1.605 (0.815%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.2, 90 (19) missing vertices, mean dist -0.2 [0.4 (%68.7)->0.2 (%31.3))] %74 local maxima, %21 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 0.87 +- 0.26 (0.04-->4.53) (max @ vno 76317 --> 75042) face area 0.33 +- 0.16 (0.00-->4.62) mean absolute distance = 0.28 +- 0.40 4126 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1272554.9, rms=4.435 025: dt: 0.5000, sse=1029642.6, rms=3.258 (26.533%) rms = 3.43, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=874406.2, rms=2.354 (27.761%) 027: dt: 0.2500, sse=809731.6, rms=1.809 (23.150%) 028: dt: 0.2500, sse=796593.5, rms=1.631 (9.837%) rms = 1.59, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=787025.3, rms=1.586 (2.716%) 030: dt: 0.1250, sse=775277.9, rms=1.446 (8.828%) rms = 1.43, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=773607.4, rms=1.428 (1.248%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.5, 104 (14) missing vertices, mean dist -0.1 [0.3 (%59.2)->0.2 (%40.8))] %82 local maxima, %14 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=849757.1, rms=2.288 rms = 2.37, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=771795.1, rms=1.597 (30.188%) 033: dt: 0.2500, sse=753880.1, rms=1.129 (29.313%) rms = 1.14, time step reduction 2 of 3 to 0.125... rms = 1.11, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=736590.4, rms=1.111 (1.584%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8014 vertices erasing segment 1 (vno[0] = 65139) erasing segment 2 (vno[0] = 111510) erasing segment 3 (vno[0] = 112512) erasing segment 4 (vno[0] = 113319) erasing segment 5 (vno[0] = 113343) erasing segment 6 (vno[0] = 113395) erasing segment 7 (vno[0] = 117919) erasing segment 8 (vno[0] = 149094) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area vertex spacing 0.88 +- 0.26 (0.05-->4.55) (max @ vno 75042 --> 76317) face area 0.32 +- 0.16 (0.00-->4.38) refinement took 6.4 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jun 15 01:04:37 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm 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... #-------------------------------------------- #@# Smooth2 rh Wed Jun 15 01:04:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm 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 Wed Jun 15 01:04:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.2 mm, total surface area = 81727 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.184 (target=0.015) step 005: RMS=0.128 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 1.2 minutes mris_inflate utimesec 70.002358 mris_inflate stimesec 0.100984 mris_inflate ru_maxrss 180024 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23577 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 96 mris_inflate ru_nivcsw 119 #-------------------------------------------- #@# Inflation2 rh Wed Jun 15 01:06:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 47.8 mm, total surface area = 86621 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 1.0 minutes mris_inflate utimesec 58.512104 mris_inflate stimesec 0.120981 mris_inflate ru_maxrss 192792 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25232 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 45 mris_inflate ru_nivcsw 1460 #-------------------------------------------- #@# Curv .H and .K lh Wed Jun 15 01:07:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_curvature -w lh.white total integrated curvature = 5.584*4pi (70.177) --> -5 handles ICI = 207.6, FI = 1991.0, variation=31972.978 writing Gaussian curvature to ./lh.white.K...done. writing mean curvature to ./lh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 154 vertices thresholded to be in k1 ~ [-0.33 0.56], k2 ~ [-0.10 0.13] total integrated curvature = 0.474*4pi (5.959) --> 1 handles ICI = 1.4, FI = 8.9, variation=154.326 114 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 149 vertices thresholded to be in [-0.16 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Jun 15 01:08:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_curvature -w rh.white total integrated curvature = 0.442*4pi (5.549) --> 1 handles ICI = 204.7, FI = 1978.1, variation=31794.042 writing Gaussian curvature to ./rh.white.K...done. writing mean curvature to ./rh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 196 vertices thresholded to be in k1 ~ [-0.34 0.53], k2 ~ [-0.11 0.08] total integrated curvature = 0.479*4pi (6.019) --> 1 handles ICI = 1.5, FI = 9.2, variation=161.786 135 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 144 vertices thresholded to be in [-0.16 0.26] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Wed Jun 15 01:10:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm AD08 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 [ AD08/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 [ 248 ] Gb_filter = 0 #----------------------------------------- #@# Curvature Stats rh Wed Jun 15 01:10:23 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm AD08 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 [ AD08/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 [ 273 ] Gb_filter = 0 WARN: S lookup min: -0.499299 WARN: S explicit min: 0.000000 vertex = 102 #-------------------------------------------- #@# Sphere lh Wed Jun 15 01:10:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.295... 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 %19.11 pass 1: epoch 2 of 3 starting distance error %19.08 unfolding complete - removing small folds... starting distance error %19.00 removing remaining folds... final distance error %19.02 MRISunfold() return, current seed 1234 -01: dt=0.0000, 237 negative triangles 188: dt=0.9900, 237 negative triangles 189: dt=0.9900, 90 negative triangles 190: dt=0.9900, 68 negative triangles 191: dt=0.9900, 46 negative triangles 192: dt=0.9900, 47 negative triangles 193: dt=0.9900, 30 negative triangles 194: dt=0.9900, 25 negative triangles 195: dt=0.9900, 24 negative triangles 196: dt=0.9900, 18 negative triangles 197: dt=0.9900, 13 negative triangles 198: dt=0.9900, 12 negative triangles 199: dt=0.9900, 9 negative triangles 200: dt=0.9900, 6 negative triangles 201: dt=0.9900, 6 negative triangles 202: dt=0.9900, 5 negative triangles 203: dt=0.9900, 3 negative triangles 204: dt=0.9900, 2 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 3 negative triangles 207: dt=0.9900, 2 negative triangles 208: dt=0.9900, 1 negative triangles 209: dt=0.9900, 2 negative triangles 210: dt=0.9900, 1 negative triangles 211: dt=0.9900, 3 negative triangles 212: dt=0.9900, 1 negative triangles 213: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.18 hours mris_sphere utimesec 4241.765153 mris_sphere stimesec 0.801878 mris_sphere ru_maxrss 246796 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 40565 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 94 mris_sphere ru_nivcsw 14482 FSRUNTIME@ mris_sphere 1.1788 hours 1 threads #-------------------------------------------- #@# Sphere rh Wed Jun 15 02:21:13 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.290... 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 %19.85 pass 1: epoch 2 of 3 starting distance error %19.76 unfolding complete - removing small folds... starting distance error %19.65 removing remaining folds... final distance error %19.66 MRISunfold() return, current seed 1234 -01: dt=0.0000, 244 negative triangles 179: dt=0.9900, 244 negative triangles 180: dt=0.9900, 132 negative triangles 181: dt=0.9900, 106 negative triangles 182: dt=0.9900, 90 negative triangles 183: dt=0.9900, 76 negative triangles 184: dt=0.9900, 72 negative triangles 185: dt=0.9900, 69 negative triangles 186: dt=0.9900, 76 negative triangles 187: dt=0.9900, 72 negative triangles 188: dt=0.9900, 58 negative triangles 189: dt=0.9900, 64 negative triangles 190: dt=0.9900, 58 negative triangles 191: dt=0.9900, 61 negative triangles 192: dt=0.9900, 60 negative triangles 193: dt=0.9900, 55 negative triangles 194: dt=0.9900, 51 negative triangles 195: dt=0.9900, 55 negative triangles 196: dt=0.9900, 61 negative triangles 197: dt=0.9900, 53 negative triangles 198: dt=0.9900, 49 negative triangles 199: dt=0.9900, 49 negative triangles 200: dt=0.9900, 52 negative triangles 201: dt=0.9900, 55 negative triangles 202: dt=0.9900, 44 negative triangles 203: dt=0.9900, 46 negative triangles 204: dt=0.9900, 50 negative triangles 205: dt=0.9900, 43 negative triangles 206: dt=0.9900, 45 negative triangles 207: dt=0.9900, 40 negative triangles 208: dt=0.9900, 45 negative triangles 209: dt=0.9900, 46 negative triangles 210: dt=0.9900, 42 negative triangles 211: dt=0.9900, 39 negative triangles 212: dt=0.9900, 37 negative triangles 213: dt=0.9900, 43 negative triangles 214: dt=0.9900, 42 negative triangles 215: dt=0.9900, 43 negative triangles 216: dt=0.9900, 38 negative triangles 217: dt=0.9900, 32 negative triangles 218: dt=0.9900, 40 negative triangles 219: dt=0.9900, 38 negative triangles 220: dt=0.9900, 33 negative triangles 221: dt=0.9900, 32 negative triangles 222: dt=0.9900, 29 negative triangles 223: dt=0.9900, 27 negative triangles 224: dt=0.9900, 28 negative triangles 225: dt=0.9900, 23 negative triangles 226: dt=0.9900, 21 negative triangles 227: dt=0.9900, 21 negative triangles 228: dt=0.9900, 18 negative triangles 229: dt=0.9900, 21 negative triangles 230: dt=0.9900, 19 negative triangles 231: dt=0.9900, 23 negative triangles 232: dt=0.9900, 22 negative triangles 233: dt=0.9900, 24 negative triangles 234: dt=0.9900, 21 negative triangles 235: dt=0.9900, 17 negative triangles 236: dt=0.9900, 16 negative triangles 237: dt=0.9900, 19 negative triangles 238: dt=0.9900, 13 negative triangles 239: dt=0.9900, 12 negative triangles 240: dt=0.9900, 13 negative triangles 241: dt=0.9900, 13 negative triangles 242: dt=0.9900, 10 negative triangles 243: dt=0.9900, 13 negative triangles 244: dt=0.9900, 14 negative triangles 245: dt=0.9900, 11 negative triangles 246: dt=0.9900, 6 negative triangles 247: dt=0.9900, 5 negative triangles 248: dt=0.9900, 6 negative triangles 249: dt=0.9900, 6 negative triangles 250: dt=0.9900, 3 negative triangles 251: dt=0.9900, 4 negative triangles 252: dt=0.9900, 3 negative triangles 253: dt=0.9900, 1 negative triangles 254: dt=0.9900, 3 negative triangles 255: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.17 hours mris_sphere utimesec 4197.007957 mris_sphere stimesec 0.459930 mris_sphere ru_maxrss 264360 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 43415 mris_sphere ru_majflt 9 mris_sphere ru_nswap 0 mris_sphere ru_inblock 720 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 107 mris_sphere ru_nivcsw 6363 FSRUNTIME@ mris_sphere 1.1694 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Wed Jun 15 03:31:23 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/stable6//average/lh.curvature.buckner40.2016-03-20.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/stable6//average/lh.curvature.buckner40.2016-03-20.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable6//average/lh.curvature.buckner40.2016-03-20.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 = 5.335 curvature mean = 0.016, std = 0.817 curvature mean = 0.027, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 350017.8, tmin=1.4674 d=32.00 min @ (0.00, -8.00, -8.00) sse = 211599.5, tmin=2.9232 d=16.00 min @ (0.00, 4.00, 0.00) sse = 209590.0, tmin=4.3758 d=8.00 min @ (0.00, -2.00, 2.00) sse = 194214.2, tmin=5.8465 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 191243.1, tmin=7.3255 d=2.00 min @ (0.00, -0.50, 0.50) sse = 190442.2, tmin=8.8098 d=0.50 min @ (0.00, 0.12, -0.12) sse = 190367.1, tmin=11.7770 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 11.78 min curvature mean = -0.024, std = 0.833 curvature mean = 0.010, std = 0.948 curvature mean = -0.028, std = 0.844 curvature mean = 0.003, std = 0.979 curvature mean = -0.030, std = 0.846 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.036, std = 0.369 curvature mean = 0.032, std = 0.250 curvature mean = 0.071, std = 0.269 curvature mean = 0.027, std = 0.309 curvature mean = 0.041, std = 0.425 curvature mean = 0.025, std = 0.337 curvature mean = 0.024, std = 0.549 curvature mean = 0.025, std = 0.349 curvature mean = 0.009, std = 0.657 MRISregister() return, current seed 0 -01: dt=0.0000, 37 negative triangles 114: dt=0.9900, 37 negative triangles expanding nbhd size to 1 115: dt=0.9900, 53 negative triangles 116: dt=0.9900, 37 negative triangles 117: dt=0.9900, 35 negative triangles 118: dt=0.9900, 39 negative triangles 119: dt=0.9900, 36 negative triangles 120: dt=0.9900, 38 negative triangles 121: dt=0.9900, 32 negative triangles 122: dt=0.9900, 29 negative triangles 123: dt=0.9900, 30 negative triangles 124: dt=0.9900, 24 negative triangles 125: dt=0.9900, 17 negative triangles 126: dt=0.9900, 15 negative triangles 127: dt=0.9900, 20 negative triangles 128: dt=0.9900, 17 negative triangles 129: dt=0.9900, 16 negative triangles 130: dt=0.9900, 17 negative triangles 131: dt=0.9900, 13 negative triangles 132: dt=0.9900, 9 negative triangles 133: dt=0.9900, 9 negative triangles 134: dt=0.9900, 9 negative triangles 135: dt=0.9900, 11 negative triangles 136: dt=0.9900, 7 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 6 negative triangles 139: dt=0.9900, 4 negative triangles 140: dt=0.9900, 3 negative triangles 141: dt=0.9900, 3 negative triangles 142: dt=0.9900, 3 negative triangles 143: dt=0.9900, 3 negative triangles 144: dt=0.9900, 3 negative triangles 145: dt=0.9900, 3 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 3 negative triangles 148: dt=0.9900, 1 negative triangles 149: dt=0.9900, 1 negative triangles 150: dt=0.9900, 1 negative triangles 151: dt=0.9900, 1 negative triangles 152: dt=0.9900, 1 negative triangles 153: dt=0.9900, 1 negative triangles 154: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.48 hours mris_register utimesec 5319.029384 mris_register stimesec 0.833873 mris_register ru_maxrss 231328 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 32510 mris_register ru_majflt 5 mris_register ru_nswap 0 mris_register ru_inblock 760 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 139 mris_register ru_nivcsw 9599 FSRUNTIME@ mris_register 1.4781 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Wed Jun 15 05:00:05 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/stable6//average/rh.curvature.buckner40.2016-03-20.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/stable6//average/rh.curvature.buckner40.2016-03-20.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable6//average/rh.curvature.buckner40.2016-03-20.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 = 5.499 curvature mean = 0.003, std = 0.811 curvature mean = 0.029, std = 0.856 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, 0.00, 8.00) sse = 270449.2, tmin=3.4867 d=16.00 min @ (4.00, 4.00, 0.00) sse = 240064.9, tmin=5.1125 d=4.00 min @ (-1.00, -1.00, -1.00) sse = 237693.7, tmin=8.6226 d=2.00 min @ (0.00, 0.50, 0.50) sse = 236305.5, tmin=10.3627 d=1.00 min @ (0.00, 0.00, -0.25) sse = 236273.8, tmin=12.1070 d=0.50 min @ (0.00, 0.00, 0.12) sse = 236243.4, tmin=13.8475 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 13.85 min curvature mean = -0.020, std = 0.827 curvature mean = 0.011, std = 0.945 curvature mean = -0.023, std = 0.836 curvature mean = 0.004, std = 0.978 curvature mean = -0.025, std = 0.837 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.034, std = 0.306 curvature mean = 0.030, std = 0.242 curvature mean = 0.083, std = 0.318 curvature mean = 0.026, std = 0.300 curvature mean = 0.044, std = 0.508 curvature mean = 0.025, std = 0.326 curvature mean = 0.024, std = 0.654 curvature mean = 0.025, std = 0.337 curvature mean = 0.009, std = 0.770 MRISregister() return, current seed 0 -01: dt=0.0000, 112 negative triangles 118: dt=0.9900, 112 negative triangles expanding nbhd size to 1 119: dt=0.9900, 135 negative triangles 120: dt=0.9405, 114 negative triangles 121: dt=0.9405, 113 negative triangles 122: dt=0.9405, 106 negative triangles 123: dt=0.9405, 107 negative triangles 124: dt=0.9405, 103 negative triangles 125: dt=0.9405, 99 negative triangles 126: dt=0.9405, 93 negative triangles 127: dt=0.9405, 87 negative triangles 128: dt=0.9405, 84 negative triangles 129: dt=0.9405, 84 negative triangles 130: dt=0.9405, 84 negative triangles 131: dt=0.9405, 74 negative triangles 132: dt=0.9405, 77 negative triangles 133: dt=0.9405, 74 negative triangles 134: dt=0.9405, 71 negative triangles 135: dt=0.9405, 73 negative triangles 136: dt=0.9405, 72 negative triangles 137: dt=0.9405, 71 negative triangles 138: dt=0.9405, 71 negative triangles 139: dt=0.9405, 68 negative triangles 140: dt=0.9405, 66 negative triangles 141: dt=0.9405, 69 negative triangles 142: dt=0.9405, 66 negative triangles 143: dt=0.9405, 67 negative triangles 144: dt=0.9405, 67 negative triangles 145: dt=0.9405, 66 negative triangles 146: dt=0.9405, 62 negative triangles 147: dt=0.9405, 62 negative triangles 148: dt=0.9405, 60 negative triangles 149: dt=0.9405, 61 negative triangles 150: dt=0.9405, 60 negative triangles 151: dt=0.9405, 61 negative triangles 152: dt=0.9405, 62 negative triangles 153: dt=0.9405, 61 negative triangles 154: dt=0.9405, 59 negative triangles 155: dt=0.9405, 59 negative triangles 156: dt=0.9405, 60 negative triangles 157: dt=0.9405, 55 negative triangles 158: dt=0.9405, 55 negative triangles 159: dt=0.9405, 54 negative triangles 160: dt=0.9405, 55 negative triangles 161: dt=0.9405, 55 negative triangles 162: dt=0.9405, 52 negative triangles 163: dt=0.9405, 51 negative triangles 164: dt=0.9405, 50 negative triangles 165: dt=0.9405, 49 negative triangles 166: dt=0.9405, 50 negative triangles 167: dt=0.9405, 49 negative triangles 168: dt=0.9405, 48 negative triangles 169: dt=0.9405, 49 negative triangles 170: dt=0.9405, 47 negative triangles 171: dt=0.9405, 46 negative triangles 172: dt=0.9405, 46 negative triangles 173: dt=0.9405, 45 negative triangles 174: dt=0.9405, 44 negative triangles 175: dt=0.9405, 44 negative triangles 176: dt=0.9405, 42 negative triangles 177: dt=0.9405, 45 negative triangles 178: dt=0.9405, 38 negative triangles 179: dt=0.9405, 36 negative triangles 180: dt=0.9405, 37 negative triangles 181: dt=0.9405, 35 negative triangles 182: dt=0.9405, 34 negative triangles 183: dt=0.9405, 34 negative triangles 184: dt=0.9405, 33 negative triangles 185: dt=0.9405, 31 negative triangles 186: dt=0.9405, 30 negative triangles 187: dt=0.9405, 28 negative triangles 188: dt=0.9405, 28 negative triangles 189: dt=0.9405, 22 negative triangles 190: dt=0.9405, 19 negative triangles 191: dt=0.9405, 18 negative triangles 192: dt=0.9405, 14 negative triangles 193: dt=0.9405, 14 negative triangles 194: dt=0.9405, 16 negative triangles 195: dt=0.9405, 16 negative triangles 196: dt=0.9405, 13 negative triangles 197: dt=0.9405, 15 negative triangles 198: dt=0.9405, 18 negative triangles 199: dt=0.9405, 13 negative triangles 200: dt=0.9405, 11 negative triangles 201: dt=0.9405, 10 negative triangles 202: dt=0.9405, 11 negative triangles 203: dt=0.9405, 12 negative triangles 204: dt=0.9405, 14 negative triangles 205: dt=0.9405, 11 negative triangles 206: dt=0.9405, 11 negative triangles 207: dt=0.9405, 9 negative triangles 208: dt=0.9405, 9 negative triangles 209: dt=0.9405, 9 negative triangles 210: dt=0.9405, 9 negative triangles 211: dt=0.9405, 5 negative triangles 212: dt=0.9405, 3 negative triangles 213: dt=0.9405, 2 negative triangles 214: dt=0.9405, 3 negative triangles 215: dt=0.9405, 1 negative triangles 216: dt=0.9405, 1 negative triangles 217: dt=0.9405, 1 negative triangles 218: dt=0.9405, 3 negative triangles 219: dt=0.9405, 2 negative triangles 220: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.87 hours mris_register utimesec 6737.898683 mris_register stimesec 1.141826 mris_register ru_maxrss 246016 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 32295 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 107 mris_register ru_nivcsw 14278 FSRUNTIME@ mris_register 1.8725 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Wed Jun 15 06:52:26 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts 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 #-------------------------------------------- #@# Jacobian white rh Wed Jun 15 06:52:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts 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 lh Wed Jun 15 06:52:32 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable6//average/lh.curvature.buckner40.2016-03-20.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/stable6//average/lh.curvature.buckner40.2016-03-20.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Wed Jun 15 06:52:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable6//average/rh.curvature.buckner40.2016-03-20.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/stable6//average/rh.curvature.buckner40.2016-03-20.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Jun 15 06:52:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable6//average/lh.DKatlas.2016-03-20.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/lh.DKatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.007 0 singular and 325 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: 3124 changed, 139545 examined... 001: 724 changed, 13241 examined... 002: 187 changed, 3990 examined... 003: 61 changed, 1072 examined... 004: 24 changed, 401 examined... 005: 11 changed, 138 examined... 006: 3 changed, 67 examined... 007: 3 changed, 24 examined... 008: 1 changed, 18 examined... 009: 0 changed, 6 examined... 291 labels changed using aseg 000: 154 total segments, 106 labels (360 vertices) changed 001: 51 total segments, 1 labels (3 vertices) changed 002: 50 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1990 vertices marked for relabeling... 1990 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc rh Wed Jun 15 06:52:55 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable6//average/rh.DKatlas.2016-03-20.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/rh.DKatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.005 0 singular and 351 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1240 labels changed using aseg relabeling using gibbs priors... 000: 2931 changed, 149612 examined... 001: 710 changed, 12476 examined... 002: 180 changed, 3914 examined... 003: 56 changed, 1082 examined... 004: 29 changed, 345 examined... 005: 15 changed, 166 examined... 006: 7 changed, 86 examined... 007: 3 changed, 46 examined... 008: 2 changed, 17 examined... 009: 1 changed, 13 examined... 010: 2 changed, 7 examined... 011: 0 changed, 11 examined... 184 labels changed using aseg 000: 109 total segments, 71 labels (258 vertices) changed 001: 39 total segments, 1 labels (1 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1743 vertices marked for relabeling... 1743 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 19 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Jun 15 06:53:14 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD08 lh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 35984 bright wm thresholded. 2661 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 279527 voxels (1.67%) border gray 308339 voxels (1.84%) WM (96.0): 96.0 +- 9.3 [70.0 --> 110.0] GM (68.0) : 66.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.9 (was 70) setting MAX_BORDER_WHITE to 109.3 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 36.8 (was 40) setting MAX_GRAY to 90.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 23.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100+-9.6, GM=63+-13.0 mean inside = 90.4, mean outside = 68.8 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... reading initial pial vertex positions from white... mean border=46.6, 174 (174) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.2 (%100.0))] %17 local maxima, %61 large gradients and %18 min vals, 73 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 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 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=39018780.0, rms=37.978 001: dt: 0.0500, sse=34676684.0, rms=35.765 (5.829%) 002: dt: 0.0500, sse=31708420.0, rms=34.169 (4.462%) 003: dt: 0.0500, sse=29433382.0, rms=32.893 (3.734%) 004: dt: 0.0500, sse=27581690.0, rms=31.817 (3.272%) 005: dt: 0.0500, sse=26015882.0, rms=30.877 (2.952%) 006: dt: 0.0500, sse=24650384.0, rms=30.034 (2.731%) 007: dt: 0.0500, sse=23434308.0, rms=29.263 (2.568%) 008: dt: 0.0500, sse=22334448.0, rms=28.547 (2.446%) 009: dt: 0.0500, sse=21327088.0, rms=27.875 (2.353%) 010: dt: 0.0500, sse=20396418.0, rms=27.240 (2.279%) positioning took 1.0 minutes mean border=46.5, 137 (84) missing vertices, mean dist 1.4 [0.1 (%0.0)->1.7 (%100.0))] %17 local maxima, %61 large gradients and %17 min vals, 71 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21339606.0, rms=27.882 011: dt: 0.0500, sse=20470416.0, rms=27.290 (2.124%) 012: dt: 0.0500, sse=19657908.0, rms=26.725 (2.072%) 013: dt: 0.0500, sse=18894470.0, rms=26.182 (2.030%) 014: dt: 0.0500, sse=18176250.0, rms=25.661 (1.990%) 015: dt: 0.0500, sse=17499458.0, rms=25.160 (1.952%) 016: dt: 0.0500, sse=16861102.0, rms=24.679 (1.915%) 017: dt: 0.0500, sse=16257240.0, rms=24.214 (1.882%) 018: dt: 0.0500, sse=15687370.0, rms=23.767 (1.845%) 019: dt: 0.0500, sse=15146771.0, rms=23.336 (1.817%) 020: dt: 0.0500, sse=14634944.0, rms=22.919 (1.784%) positioning took 1.0 minutes mean border=46.2, 142 (58) missing vertices, mean dist 1.1 [0.1 (%1.8)->1.4 (%98.2))] %17 local maxima, %61 large gradients and %17 min vals, 63 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14784669.0, rms=23.046 021: dt: 0.0500, sse=14269216.0, rms=22.621 (1.842%) 022: dt: 0.0500, sse=13780984.0, rms=22.212 (1.811%) 023: dt: 0.0500, sse=13307092.0, rms=21.807 (1.823%) 024: dt: 0.0500, sse=12858143.0, rms=21.416 (1.792%) 025: dt: 0.0500, sse=12436200.0, rms=21.042 (1.746%) 026: dt: 0.0500, sse=12039283.0, rms=20.684 (1.701%) 027: dt: 0.0500, sse=11655869.0, rms=20.332 (1.701%) 028: dt: 0.0500, sse=11278926.0, rms=19.980 (1.731%) 029: dt: 0.0500, sse=10910744.0, rms=19.630 (1.752%) 030: dt: 0.0500, sse=10551168.0, rms=19.282 (1.772%) positioning took 1.0 minutes mean border=46.1, 220 (51) missing vertices, mean dist 0.8 [0.1 (%15.0)->1.2 (%85.0))] %18 local maxima, %61 large gradients and %17 min vals, 60 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=10738483.0, rms=19.461 031: dt: 0.5000, sse=8125674.0, rms=16.752 (13.920%) 032: dt: 0.5000, sse=6136545.0, rms=14.340 (14.398%) 033: dt: 0.5000, sse=4643022.5, rms=12.231 (14.712%) 034: dt: 0.5000, sse=3591857.2, rms=10.479 (14.319%) 035: dt: 0.5000, sse=2917482.2, rms=9.191 (12.292%) 036: dt: 0.5000, sse=2478262.5, rms=8.232 (10.437%) 037: dt: 0.5000, sse=2242023.8, rms=7.676 (6.755%) 038: dt: 0.5000, sse=2076239.9, rms=7.247 (5.580%) 039: dt: 0.5000, sse=2001072.5, rms=7.054 (2.674%) 040: dt: 0.5000, sse=1932410.1, rms=6.858 (2.776%) 041: dt: 0.5000, sse=1903543.9, rms=6.784 (1.081%) 042: dt: 0.5000, sse=1865297.5, rms=6.667 (1.723%) rms = 6.63, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1850549.9, rms=6.631 (0.537%) 044: dt: 0.2500, sse=1517748.9, rms=5.552 (16.267%) 045: dt: 0.2500, sse=1404954.0, rms=5.162 (7.031%) rms = 5.22, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1355055.1, rms=4.970 (3.722%) 047: dt: 0.1250, sse=1290434.1, rms=4.707 (5.296%) rms = 4.66, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1279627.8, rms=4.660 (0.989%) positioning took 2.1 minutes mean border=44.4, 1200 (9) missing vertices, mean dist 0.1 [0.1 (%49.4)->0.4 (%50.6))] %30 local maxima, %49 large gradients and %16 min vals, 33 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=1792577.9, rms=5.887 rms = 6.28, time step reduction 1 of 3 to 0.250... 049: dt: 0.2500, sse=1534356.5, rms=4.974 (15.501%) 050: dt: 0.2500, sse=1410248.2, rms=4.468 (10.186%) rms = 4.42, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=1397811.0, rms=4.425 (0.963%) 052: dt: 0.1250, sse=1273419.8, rms=3.836 (13.294%) 053: dt: 0.1250, sse=1246707.8, rms=3.704 (3.461%) rms = 3.65, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1236854.6, rms=3.654 (1.343%) positioning took 0.7 minutes mean border=43.3, 1245 (9) missing vertices, mean dist 0.1 [0.1 (%54.7)->0.3 (%45.3))] %46 local maxima, %33 large gradients and %16 min vals, 30 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=1343657.0, rms=4.180 rms = 5.34, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1259427.6, rms=3.778 (9.629%) 056: dt: 0.2500, sse=1238762.6, rms=3.679 (2.608%) rms = 3.69, time step reduction 2 of 3 to 0.125... 057: dt: 0.1250, sse=1223115.6, rms=3.595 (2.278%) 058: dt: 0.1250, sse=1198808.6, rms=3.465 (3.622%) 059: dt: 0.1250, sse=1188604.0, rms=3.411 (1.567%) rms = 3.37, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1181597.6, rms=3.375 (1.055%) positioning took 0.8 minutes mean border=42.2, 2005 (9) missing vertices, mean dist 0.0 [0.1 (%53.6)->0.3 (%46.4))] %51 local maxima, %28 large gradients and %15 min vals, 24 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1232719.1, rms=3.640 rms = 5.04, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1179845.8, rms=3.350 (7.978%) 062: dt: 0.2500, sse=1165582.4, rms=3.284 (1.983%) rms = 3.33, time step reduction 2 of 3 to 0.125... 063: dt: 0.1250, sse=1154173.0, rms=3.214 (2.109%) 064: dt: 0.1250, sse=1137375.4, rms=3.113 (3.141%) rms = 3.07, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1129130.8, rms=3.067 (1.489%) positioning took 0.7 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area.pial vertex spacing 0.99 +- 0.41 (0.09-->5.79) (max @ vno 93571 --> 94642) face area 0.39 +- 0.29 (0.00-->4.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139545 vertices processed 25000 of 139545 vertices processed 50000 of 139545 vertices processed 75000 of 139545 vertices processed 100000 of 139545 vertices processed 125000 of 139545 vertices processed 0 of 139545 vertices processed 25000 of 139545 vertices processed 50000 of 139545 vertices processed 75000 of 139545 vertices processed 100000 of 139545 vertices processed 125000 of 139545 vertices processed thickness calculation complete, 62:194 truncations. 44627 vertices at 0 distance 108252 vertices at 1 distance 78929 vertices at 2 distance 26123 vertices at 3 distance 6229 vertices at 4 distance 1465 vertices at 5 distance 386 vertices at 6 distance 145 vertices at 7 distance 65 vertices at 8 distance 23 vertices at 9 distance 29 vertices at 10 distance 17 vertices at 11 distance 5 vertices at 12 distance 3 vertices at 13 distance 5 vertices at 14 distance 8 vertices at 15 distance 3 vertices at 16 distance 3 vertices at 17 distance 2 vertices at 18 distance 2 vertices at 19 distance 3 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.thickness positioning took 9.8 minutes #-------------------------------------------- #@# Make Pial Surf rh Wed Jun 15 07:03:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD08 rh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 35984 bright wm thresholded. 2661 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 279527 voxels (1.67%) border gray 308339 voxels (1.84%) WM (96.0): 96.0 +- 9.3 [70.0 --> 110.0] GM (68.0) : 66.2 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.9 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 37.8 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 24.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-10.4, GM=64+-12.2 mean inside = 90.8, mean outside = 70.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=48.5, 177 (177) missing vertices, mean dist 1.8 [0.8 (%0.0)->2.4 (%100.0))] %14 local maxima, %60 large gradients and %21 min vals, 107 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 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 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=41104404.0, rms=37.573 001: dt: 0.0500, sse=36544300.0, rms=35.389 (5.811%) 002: dt: 0.0500, sse=33480706.0, rms=33.844 (4.368%) 003: dt: 0.0500, sse=31148550.0, rms=32.617 (3.623%) 004: dt: 0.0500, sse=29261452.0, rms=31.590 (3.149%) 005: dt: 0.0500, sse=27669338.0, rms=30.697 (2.827%) 006: dt: 0.0500, sse=26286464.0, rms=29.900 (2.598%) 007: dt: 0.0500, sse=25058734.0, rms=29.173 (2.429%) 008: dt: 0.0500, sse=23952722.0, rms=28.503 (2.297%) 009: dt: 0.0500, sse=22941628.0, rms=27.877 (2.199%) 010: dt: 0.0500, sse=22008522.0, rms=27.285 (2.121%) positioning took 1.2 minutes mean border=48.4, 121 (89) missing vertices, mean dist 1.4 [0.2 (%0.0)->1.8 (%100.0))] %15 local maxima, %60 large gradients and %20 min vals, 104 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22775532.0, rms=27.770 011: dt: 0.0500, sse=21901920.0, rms=27.215 (1.999%) 012: dt: 0.0500, sse=21085608.0, rms=26.685 (1.944%) 013: dt: 0.0500, sse=20318076.0, rms=26.178 (1.901%) 014: dt: 0.0500, sse=19595002.0, rms=25.691 (1.861%) 015: dt: 0.0500, sse=18911674.0, rms=25.222 (1.825%) 016: dt: 0.0500, sse=18265762.0, rms=24.771 (1.790%) 017: dt: 0.0500, sse=17652650.0, rms=24.334 (1.762%) 018: dt: 0.0500, sse=17070794.0, rms=23.913 (1.732%) 019: dt: 0.0500, sse=16515730.0, rms=23.504 (1.711%) 020: dt: 0.0500, sse=15986849.0, rms=23.107 (1.688%) positioning took 1.1 minutes mean border=48.2, 129 (66) missing vertices, mean dist 1.1 [0.1 (%1.3)->1.5 (%98.7))] %15 local maxima, %60 large gradients and %20 min vals, 102 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=16089414.0, rms=23.188 021: dt: 0.0500, sse=15563324.0, rms=22.788 (1.725%) 022: dt: 0.0500, sse=15060660.0, rms=22.399 (1.707%) 023: dt: 0.0500, sse=14571631.0, rms=22.014 (1.719%) 024: dt: 0.0500, sse=14103150.0, rms=21.639 (1.705%) 025: dt: 0.0500, sse=13655761.0, rms=21.274 (1.685%) 026: dt: 0.0500, sse=13227525.0, rms=20.919 (1.668%) 027: dt: 0.0500, sse=12808838.0, rms=20.566 (1.687%) 028: dt: 0.0500, sse=12396824.0, rms=20.213 (1.719%) 029: dt: 0.0500, sse=11992198.0, rms=19.859 (1.748%) 030: dt: 0.0500, sse=11594082.0, rms=19.506 (1.782%) positioning took 1.1 minutes mean border=48.0, 188 (54) missing vertices, mean dist 0.9 [0.1 (%11.1)->1.3 (%88.9))] %15 local maxima, %60 large gradients and %20 min vals, 92 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=11764133.0, rms=19.655 031: dt: 0.5000, sse=8868819.0, rms=16.888 (14.077%) 032: dt: 0.5000, sse=6576670.0, rms=14.316 (15.229%) 033: dt: 0.5000, sse=4828051.5, rms=11.997 (16.202%) 034: dt: 0.5000, sse=3593165.0, rms=10.030 (16.395%) 035: dt: 0.5000, sse=2867802.5, rms=8.675 (13.511%) 036: dt: 0.5000, sse=2421324.5, rms=7.713 (11.085%) 037: dt: 0.5000, sse=2201734.5, rms=7.200 (6.659%) 038: dt: 0.5000, sse=2051306.9, rms=6.816 (5.325%) 039: dt: 0.5000, sse=1995039.2, rms=6.672 (2.119%) 040: dt: 0.5000, sse=1929038.6, rms=6.489 (2.742%) rms = 6.45, time step reduction 1 of 3 to 0.250... 041: dt: 0.5000, sse=1915268.5, rms=6.455 (0.527%) 042: dt: 0.2500, sse=1556591.2, rms=5.341 (17.255%) 043: dt: 0.2500, sse=1456288.2, rms=5.004 (6.309%) rms = 5.01, time step reduction 2 of 3 to 0.125... 044: dt: 0.1250, sse=1406279.0, rms=4.819 (3.695%) 045: dt: 0.1250, sse=1337398.8, rms=4.550 (5.582%) 046: dt: 0.1250, sse=1323424.1, rms=4.493 (1.256%) rms = 4.48, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=1320958.0, rms=4.482 (0.248%) positioning took 2.2 minutes mean border=46.6, 1605 (14) missing vertices, mean dist 0.1 [0.1 (%48.0)->0.4 (%52.0))] %29 local maxima, %47 large gradients and %18 min vals, 39 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=1718571.6, rms=5.332 rms = 5.84, time step reduction 1 of 3 to 0.250... 048: dt: 0.2500, sse=1522589.4, rms=4.628 (13.196%) 049: dt: 0.2500, sse=1423553.6, rms=4.226 (8.693%) 050: dt: 0.2500, sse=1402662.6, rms=4.147 (1.878%) rms = 4.16, time step reduction 2 of 3 to 0.125... 051: dt: 0.1250, sse=1362279.8, rms=3.965 (4.387%) 052: dt: 0.1250, sse=1302877.9, rms=3.683 (7.105%) 053: dt: 0.1250, sse=1285220.5, rms=3.597 (2.336%) rms = 3.55, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1276416.8, rms=3.555 (1.177%) positioning took 1.0 minutes mean border=45.5, 1759 (13) missing vertices, mean dist 0.1 [0.1 (%52.4)->0.3 (%47.6))] %46 local maxima, %31 large gradients and %18 min vals, 46 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=1391171.9, rms=4.090 rms = 5.11, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1310097.6, rms=3.723 (8.993%) 056: dt: 0.2500, sse=1290502.6, rms=3.635 (2.354%) rms = 3.65, time step reduction 2 of 3 to 0.125... 057: dt: 0.1250, sse=1276610.2, rms=3.564 (1.942%) 058: dt: 0.1250, sse=1255809.4, rms=3.459 (2.966%) rms = 3.41, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1245934.9, rms=3.410 (1.409%) positioning took 0.8 minutes mean border=44.5, 2849 (13) missing vertices, mean dist 0.1 [0.1 (%51.7)->0.3 (%48.3))] %51 local maxima, %26 large gradients and %18 min vals, 40 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1299607.2, rms=3.672 rms = 4.81, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1248203.9, rms=3.413 (7.044%) 061: dt: 0.2500, sse=1230136.2, rms=3.334 (2.335%) rms = 3.36, time step reduction 2 of 3 to 0.125... 062: dt: 0.1250, sse=1218913.4, rms=3.271 (1.877%) 063: dt: 0.1250, sse=1201605.1, rms=3.175 (2.919%) rms = 3.13, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1192235.2, rms=3.126 (1.554%) positioning took 0.8 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area.pial vertex spacing 0.97 +- 0.40 (0.07-->5.47) (max @ vno 148738 --> 148715) face area 0.38 +- 0.28 (0.00-->4.37) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 149612 vertices processed 25000 of 149612 vertices processed 50000 of 149612 vertices processed 75000 of 149612 vertices processed 100000 of 149612 vertices processed 125000 of 149612 vertices processed 0 of 149612 vertices processed 25000 of 149612 vertices processed 50000 of 149612 vertices processed 75000 of 149612 vertices processed 100000 of 149612 vertices processed 125000 of 149612 vertices processed thickness calculation complete, 41:268 truncations. 46104 vertices at 0 distance 117970 vertices at 1 distance 84094 vertices at 2 distance 28168 vertices at 3 distance 7371 vertices at 4 distance 1894 vertices at 5 distance 553 vertices at 6 distance 212 vertices at 7 distance 83 vertices at 8 distance 45 vertices at 9 distance 31 vertices at 10 distance 23 vertices at 11 distance 17 vertices at 12 distance 10 vertices at 13 distance 3 vertices at 14 distance 4 vertices at 15 distance 1 vertices at 16 distance 2 vertices at 17 distance 2 vertices at 18 distance 2 vertices at 19 distance 5 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume lh Wed Jun 15 07:13:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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_convert --volume AD08 lh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label Total face volume 205775 Total vertex volume 202380 (mask=0) #@# AD08 lh 202380 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed Jun 15 07:13:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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_convert --volume AD08 rh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label Total face volume 222498 Total vertex volume 219294 (mask=0) #@# AD08 rh 219294 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed Jun 15 07:13:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD08 SUBJECTS_DIR is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc 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 = 58 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Wed Jun 15 07:29:13 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab AD08 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally 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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1493 948 1913 1.910 0.437 0.120 0.037 19 2.0 bankssts 1090 722 1947 2.645 0.690 0.147 0.035 22 1.5 caudalanteriorcingulate 2868 1977 4892 2.148 0.472 0.137 0.043 46 5.0 caudalmiddlefrontal 2457 1509 2577 1.683 0.376 0.132 0.033 37 3.2 cuneus 651 468 1538 2.733 0.815 0.131 0.034 6 1.0 entorhinal 3959 2672 7965 2.531 0.551 0.142 0.041 64 6.8 fusiform 6449 3966 7738 1.791 0.485 0.118 0.031 84 7.7 inferiorparietal 4515 3141 8154 2.223 0.538 0.145 0.039 81 7.0 inferiortemporal 1876 1236 2181 1.705 0.618 0.130 0.039 35 2.8 isthmuscingulate 7633 4917 10492 1.982 0.446 0.142 0.037 111 11.2 lateraloccipital 4192 2788 7011 2.247 0.536 0.140 0.048 71 8.2 lateralorbitofrontal 5157 3388 7067 1.917 0.540 0.146 0.042 85 8.7 lingual 2781 1788 4231 2.131 0.678 0.139 0.054 66 5.9 medialorbitofrontal 4825 3270 8290 2.161 0.515 0.126 0.033 73 6.3 middletemporal 884 601 1933 2.662 0.677 0.107 0.031 9 1.0 parahippocampal 2114 1260 3119 2.329 0.465 0.106 0.031 19 2.4 paracentral 2838 2019 5098 2.226 0.421 0.132 0.034 41 4.1 parsopercularis 1199 817 2452 2.268 0.470 0.170 0.053 30 2.5 parsorbitalis 1875 1283 2830 2.018 0.412 0.131 0.035 30 2.4 parstriangularis 1877 1205 2009 1.840 0.440 0.123 0.032 19 2.5 pericalcarine 7542 4511 10439 2.061 0.592 0.106 0.027 86 8.0 postcentral 2076 1384 2950 2.039 0.632 0.134 0.029 36 2.5 posteriorcingulate 7914 4918 11902 2.306 0.513 0.116 0.037 82 12.9 precentral 6514 4122 7602 1.787 0.434 0.125 0.033 87 8.5 precuneus 1416 937 2696 2.590 0.577 0.137 0.045 29 2.5 rostralanteriorcingulate 7677 5304 12510 2.024 0.488 0.148 0.048 149 15.1 rostralmiddlefrontal 10471 7251 19236 2.259 0.546 0.142 0.050 172 23.3 superiorfrontal 8453 4973 10057 1.898 0.475 0.111 0.030 104 9.5 superiorparietal 5839 3898 10707 2.387 0.501 0.108 0.026 60 6.2 superiortemporal 6345 3968 9006 2.094 0.581 0.117 0.029 72 7.2 supramarginal 434 300 963 2.268 0.432 0.176 0.068 10 1.5 frontalpole 654 462 2345 3.349 0.713 0.141 0.049 11 1.1 temporalpole 797 468 1135 2.311 0.314 0.130 0.038 10 1.0 transversetemporal 4115 2706 7398 2.663 0.795 0.126 0.040 57 6.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab AD08 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally 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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1493 1050 1913 1.910 0.437 0.125 0.032 17 1.8 bankssts 1090 823 1947 2.645 0.690 0.159 0.040 70 1.6 caudalanteriorcingulate 2868 2449 4892 2.148 0.472 0.147 0.032 36 3.9 caudalmiddlefrontal 2457 1703 2577 1.683 0.376 0.124 0.025 30 2.9 cuneus 651 692 1538 2.733 0.815 0.170 0.038 13 1.3 entorhinal 3959 3483 7965 2.531 0.551 0.166 0.045 63 8.3 fusiform 6449 4754 7738 1.791 0.485 0.128 0.024 75 6.8 inferiorparietal 4515 3955 8154 2.223 0.538 0.164 0.043 77 8.0 inferiortemporal 1876 1396 2181 1.705 0.618 0.170 0.052 60 4.8 isthmuscingulate 7633 5753 10492 1.982 0.446 0.138 0.032 109 11.3 lateraloccipital 4192 3293 7011 2.247 0.536 0.156 0.042 68 7.9 lateralorbitofrontal 5157 4079 7067 1.917 0.540 0.145 0.038 81 8.4 lingual 2781 2171 4231 2.131 0.678 0.156 0.041 66 5.0 medialorbitofrontal 4825 4244 8290 2.161 0.515 0.146 0.030 55 6.4 middletemporal 884 864 1933 2.662 0.677 0.168 0.037 11 1.5 parahippocampal 2114 1434 3119 2.329 0.465 0.103 0.020 17 1.7 paracentral 2838 2580 5098 2.226 0.421 0.151 0.028 31 3.5 parsopercularis 1199 1318 2452 2.268 0.470 0.217 0.045 20 2.6 parsorbitalis 1875 1510 2830 2.018 0.412 0.153 0.031 25 2.4 parstriangularis 1877 1041 2009 1.840 0.440 0.106 0.032 30 2.3 pericalcarine 7542 5668 10439 2.061 0.592 0.111 0.020 56 6.8 postcentral 2076 1531 2950 2.039 0.632 0.156 0.038 63 3.3 posteriorcingulate 7914 5386 11902 2.306 0.513 0.104 0.021 74 6.9 precentral 6514 4438 7602 1.787 0.434 0.128 0.028 89 8.0 precuneus 1416 1221 2696 2.590 0.577 0.170 0.043 23 2.5 rostralanteriorcingulate 7677 6953 12510 2.024 0.488 0.177 0.042 121 15.1 rostralmiddlefrontal 10471 9560 19236 2.259 0.546 0.170 0.041 190 18.7 superiorfrontal 8453 5778 10057 1.898 0.475 0.118 0.023 92 7.9 superiorparietal 5839 4904 10707 2.387 0.501 0.134 0.028 59 7.3 superiortemporal 6345 4578 9006 2.094 0.581 0.123 0.026 66 6.6 supramarginal 434 540 963 2.268 0.432 0.228 0.042 7 1.0 frontalpole 654 897 2345 3.349 0.713 0.213 0.043 7 1.4 temporalpole 797 537 1135 2.311 0.314 0.107 0.025 10 0.8 transversetemporal 4115 2711 7398 2.663 0.795 0.135 0.033 58 5.7 insula #----------------------------------------- #@# Parcellation Stats rh Wed Jun 15 07:30:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab AD08 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally 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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1316 886 1743 1.980 0.399 0.099 0.023 10 1.0 bankssts 978 685 1923 2.502 0.600 0.127 0.027 11 1.0 caudalanteriorcingulate 2801 1849 4079 2.105 0.385 0.122 0.033 32 3.6 caudalmiddlefrontal 2390 1472 2731 1.651 0.506 0.139 0.032 37 3.1 cuneus 477 341 1540 3.234 0.799 0.134 0.045 5 0.9 entorhinal 4210 2827 8094 2.588 0.551 0.129 0.030 55 4.8 fusiform 9324 5224 11218 1.972 0.493 0.107 0.029 119 10.8 inferiorparietal 5268 3525 10314 2.488 0.639 0.140 0.045 100 9.1 inferiortemporal 1768 1125 2522 2.037 0.790 0.132 0.048 29 3.3 isthmuscingulate 7663 4809 11232 2.104 0.550 0.139 0.036 106 11.1 lateraloccipital 4330 2874 7428 2.344 0.633 0.139 0.042 69 6.8 lateralorbitofrontal 4977 3252 6582 1.848 0.607 0.146 0.038 80 7.7 lingual 2823 1891 4408 2.100 0.633 0.136 0.035 48 3.8 medialorbitofrontal 5525 3724 9891 2.323 0.538 0.121 0.028 77 6.2 middletemporal 1202 783 2294 2.497 0.658 0.097 0.032 14 1.7 parahippocampal 2643 1510 4009 2.347 0.573 0.113 0.036 32 3.9 paracentral 2242 1515 3937 2.330 0.374 0.121 0.032 29 2.6 parsopercularis 1439 963 2766 2.318 0.574 0.129 0.038 22 1.9 parsorbitalis 2718 1859 4321 2.128 0.422 0.141 0.036 41 3.8 parstriangularis 2490 1644 2157 1.486 0.361 0.154 0.040 39 4.3 pericalcarine 7646 4766 9584 1.895 0.509 0.109 0.031 86 10.1 postcentral 1872 1257 3202 2.355 0.633 0.131 0.035 31 2.4 posteriorcingulate 8512 5249 12955 2.360 0.484 0.111 0.033 85 12.5 precentral 6679 4225 9337 2.134 0.498 0.119 0.031 75 8.0 precuneus 1120 729 2002 2.387 0.437 0.129 0.030 20 1.3 rostralanteriorcingulate 8813 6154 13956 2.009 0.459 0.146 0.041 151 15.2 rostralmiddlefrontal 10338 7018 18862 2.311 0.521 0.133 0.041 141 16.5 superiorfrontal 9712 5478 12111 2.027 0.450 0.102 0.027 110 10.0 superiorparietal 6584 4213 12041 2.554 0.554 0.113 0.031 71 8.7 superiortemporal 7571 4706 10814 2.181 0.467 0.110 0.030 87 8.9 supramarginal 498 326 988 2.253 0.510 0.176 0.057 15 1.2 frontalpole 644 433 2281 3.678 0.612 0.145 0.059 13 1.5 temporalpole 701 328 1030 2.640 0.395 0.105 0.037 8 1.0 transversetemporal 3806 2511 6938 2.712 0.659 0.131 0.043 56 6.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab AD08 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally 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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1316 878 1743 1.980 0.399 0.107 0.025 14 1.3 bankssts 978 855 1923 2.502 0.600 0.166 0.043 20 1.6 caudalanteriorcingulate 2801 2026 4079 2.105 0.385 0.121 0.027 31 3.1 caudalmiddlefrontal 2390 1880 2731 1.651 0.506 0.142 0.031 43 3.6 cuneus 477 585 1540 3.234 0.799 0.181 0.041 6 0.9 entorhinal 4210 3360 8094 2.588 0.551 0.155 0.039 93 7.5 fusiform 9324 6123 11218 1.972 0.493 0.115 0.026 162 10.5 inferiorparietal 5268 4622 10314 2.488 0.639 0.161 0.041 107 9.7 inferiortemporal 1768 1328 2522 2.037 0.790 0.157 0.043 47 3.4 isthmuscingulate 7663 5887 11232 2.104 0.550 0.140 0.035 105 12.2 lateraloccipital 4330 3486 7428 2.344 0.633 0.166 0.046 68 9.0 lateralorbitofrontal 4977 3888 6582 1.848 0.607 0.142 0.037 97 8.4 lingual 2823 2315 4408 2.100 0.633 0.168 0.045 51 5.7 medialorbitofrontal 5525 4678 9891 2.323 0.538 0.142 0.030 59 7.7 middletemporal 1202 1055 2294 2.497 0.658 0.154 0.040 23 2.2 parahippocampal 2643 1818 4009 2.347 0.573 0.106 0.020 25 2.2 paracentral 2242 1851 3937 2.330 0.374 0.141 0.027 26 2.6 parsopercularis 1439 1400 2766 2.318 0.574 0.165 0.034 17 2.1 parsorbitalis 2718 2250 4321 2.128 0.422 0.151 0.032 33 3.6 parstriangularis 2490 1395 2157 1.486 0.361 0.114 0.034 49 3.5 pericalcarine 7646 5457 9584 1.895 0.509 0.107 0.020 59 6.7 postcentral 1872 1424 3202 2.355 0.633 0.154 0.035 65 2.5 posteriorcingulate 8512 5695 12955 2.360 0.484 0.105 0.022 108 8.2 precentral 6679 4471 9337 2.134 0.498 0.126 0.029 101 8.0 precuneus 1120 971 2002 2.387 0.437 0.165 0.038 16 1.8 rostralanteriorcingulate 8813 7609 13956 2.009 0.459 0.167 0.038 138 15.1 rostralmiddlefrontal 10338 8940 18862 2.311 0.521 0.152 0.036 141 16.0 superiorfrontal 9712 6523 12111 2.027 0.450 0.107 0.019 105 7.9 superiorparietal 6584 5145 12041 2.554 0.554 0.134 0.031 85 9.4 superiortemporal 7571 5225 10814 2.181 0.467 0.115 0.025 73 7.7 supramarginal 498 525 988 2.253 0.510 0.211 0.049 9 1.1 frontalpole 644 775 2281 3.678 0.612 0.196 0.048 7 1.4 temporalpole 701 428 1030 2.640 0.395 0.083 0.020 3 0.5 transversetemporal 3806 2483 6938 2.712 0.659 0.144 0.043 76 6.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Jun 15 07:32:10 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable6//average/lh.CDatlas.2016-03-20.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/lh.CDatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 2.8 using min determinant for regularization = 0.078 0 singular and 728 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 9 labels changed using aseg relabeling using gibbs priors... 000: 9228 changed, 139545 examined... 001: 2214 changed, 35535 examined... 002: 670 changed, 11467 examined... 003: 269 changed, 3843 examined... 004: 128 changed, 1518 examined... 005: 55 changed, 736 examined... 006: 35 changed, 328 examined... 007: 15 changed, 177 examined... 008: 7 changed, 82 examined... 009: 3 changed, 36 examined... 010: 0 changed, 14 examined... 2 labels changed using aseg 000: 278 total segments, 191 labels (2715 vertices) changed 001: 100 total segments, 16 labels (110 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1420 vertices marked for relabeling... 1420 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Wed Jun 15 07:32:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable6//average/rh.CDatlas.2016-03-20.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/rh.CDatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 1.5 using min determinant for regularization = 0.022 0 singular and 721 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 10 labels changed using aseg relabeling using gibbs priors... 000: 10170 changed, 149612 examined... 001: 2375 changed, 39361 examined... 002: 694 changed, 12497 examined... 003: 286 changed, 3827 examined... 004: 131 changed, 1604 examined... 005: 76 changed, 729 examined... 006: 46 changed, 448 examined... 007: 23 changed, 251 examined... 008: 19 changed, 118 examined... 009: 9 changed, 92 examined... 010: 5 changed, 54 examined... 011: 3 changed, 23 examined... 012: 1 changed, 11 examined... 013: 1 changed, 9 examined... 014: 0 changed, 7 examined... 10 labels changed using aseg 000: 281 total segments, 195 labels (2964 vertices) changed 001: 97 total segments, 13 labels (101 vertices) changed 002: 85 total segments, 1 labels (2 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 46 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1252 vertices marked for relabeling... 1252 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 23 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jun 15 07:32:54 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1473 1030 2359 2.052 0.483 0.154 0.047 23 3.1 G&S_frontomargin 1744 1159 2904 2.183 0.444 0.140 0.032 24 2.3 G&S_occipital_inf 1850 990 2646 2.234 0.509 0.114 0.041 28 2.9 G&S_paracentral 1679 1099 3267 2.553 0.478 0.128 0.029 21 1.7 G&S_subcentral 1019 683 2010 2.176 0.475 0.178 0.069 30 3.2 G&S_transv_frontopol 2200 1495 3761 2.362 0.512 0.133 0.038 34 3.4 G&S_cingul-Ant 1429 967 2367 2.431 0.485 0.125 0.030 19 1.8 G&S_cingul-Mid-Ant 1718 1132 2746 2.261 0.478 0.131 0.033 25 2.4 G&S_cingul-Mid-Post 765 513 1278 2.019 0.640 0.151 0.050 14 1.5 G_cingul-Post-dorsal 346 229 553 2.050 0.646 0.155 0.053 9 0.6 G_cingul-Post-ventral 2325 1412 2541 1.667 0.392 0.143 0.037 42 3.5 G_cuneus 1992 1375 3912 2.305 0.423 0.138 0.039 36 3.3 G_front_inf-Opercular 385 251 837 2.353 0.438 0.157 0.053 10 0.7 G_front_inf-Orbital 1049 716 2113 2.253 0.404 0.157 0.048 28 1.8 G_front_inf-Triangul 3714 2522 7184 2.183 0.503 0.165 0.062 104 9.3 G_front_middle 7134 4860 14834 2.391 0.567 0.155 0.064 151 20.2 G_front_sup 818 513 1647 3.138 0.671 0.157 0.061 16 2.0 G_Ins_lg&S_cent_ins 880 588 2430 3.224 0.581 0.144 0.044 16 1.5 G_insular_short 2455 1531 4278 2.225 0.458 0.144 0.039 43 3.7 G_occipital_middle 1533 877 2088 1.984 0.483 0.105 0.024 15 1.3 G_occipital_sup 1478 991 3400 2.637 0.514 0.148 0.042 29 2.5 G_oc-temp_lat-fusifor 4021 2549 5608 1.910 0.566 0.152 0.050 78 7.7 G_oc-temp_med-Lingual 1155 811 2950 2.817 0.773 0.127 0.037 13 1.7 G_oc-temp_med-Parahip 2802 1849 5585 2.231 0.587 0.162 0.066 74 7.4 G_orbital 2357 1233 2746 1.812 0.469 0.132 0.050 46 4.1 G_pariet_inf-Angular 3240 1939 5384 2.293 0.601 0.121 0.033 44 4.1 G_pariet_inf-Supramar 3429 1838 4296 1.954 0.469 0.112 0.041 58 4.9 G_parietal_sup 2902 1537 4069 2.139 0.543 0.102 0.030 41 3.4 G_postcentral 3056 1668 5059 2.485 0.535 0.112 0.047 37 6.9 G_precentral 3649 2171 4464 1.772 0.457 0.129 0.039 64 5.5 G_precuneus 1133 701 1938 2.062 0.619 0.148 0.072 38 3.2 G_rectus 763 462 1072 2.280 1.160 0.125 0.057 16 1.5 G_subcallosal 546 313 898 2.405 0.310 0.129 0.036 8 0.7 G_temp_sup-G_T_transv 2157 1443 5350 2.628 0.520 0.140 0.044 39 3.8 G_temp_sup-Lateral 492 342 1161 2.943 0.644 0.085 0.018 2 0.4 G_temp_sup-Plan_polar 1005 673 1608 2.145 0.440 0.101 0.022 10 0.8 G_temp_sup-Plan_tempo 2124 1464 4678 2.363 0.584 0.168 0.057 61 5.1 G_temporal_inf 2746 1815 5387 2.254 0.514 0.141 0.042 59 4.5 G_temporal_middle 339 235 359 1.712 0.398 0.115 0.023 2 0.3 Lat_Fis-ant-Horizont 276 203 347 1.972 0.355 0.110 0.022 2 0.2 Lat_Fis-ant-Vertical 1137 760 1365 2.177 0.484 0.114 0.024 7 1.2 Lat_Fis-post 2131 1329 2642 1.864 0.448 0.156 0.049 40 4.2 Pole_occipital 1555 1085 4467 2.857 0.757 0.149 0.048 28 2.8 Pole_temporal 2184 1468 2420 1.874 0.483 0.121 0.028 19 2.6 S_calcarine 3075 2155 3579 1.841 0.558 0.106 0.025 18 3.4 S_central 1115 776 1350 1.992 0.403 0.092 0.013 5 0.6 S_cingul-Marginalis 513 344 729 2.371 0.330 0.098 0.022 2 0.5 S_circular_insula_ant 1604 1079 2181 2.287 0.431 0.081 0.013 5 0.9 S_circular_insula_inf 1814 1211 2437 2.353 0.366 0.104 0.023 11 1.6 S_circular_insula_sup 714 495 1287 2.437 0.634 0.133 0.032 8 1.0 S_collat_transv_ant 666 457 650 1.756 0.390 0.154 0.039 9 0.9 S_collat_transv_post 1724 1249 2256 1.854 0.371 0.118 0.030 20 2.2 S_front_inf 1625 1140 2278 1.876 0.466 0.129 0.032 19 2.2 S_front_middle 2707 1901 3814 1.941 0.400 0.119 0.030 23 3.4 S_front_sup 297 193 294 1.649 0.341 0.128 0.028 3 0.4 S_interm_prim-Jensen 2561 1658 2544 1.643 0.390 0.109 0.021 21 2.3 S_intrapariet&P_trans 955 681 1199 1.973 0.327 0.124 0.024 7 0.9 S_oc_middle&Lunatus 1344 880 1518 1.949 0.301 0.102 0.018 8 1.0 S_oc_sup&transversal 598 407 789 2.082 0.422 0.133 0.028 6 0.7 S_occipital_ant 797 544 1102 2.219 0.350 0.116 0.025 5 0.9 S_oc-temp_lat 1962 1375 2878 2.263 0.437 0.118 0.022 15 1.8 S_oc-temp_med&Lingual 332 236 396 1.708 0.300 0.111 0.020 2 0.3 S_orbital_lateral 729 488 935 2.227 0.607 0.121 0.023 6 0.7 S_orbital_med-olfact 1568 1082 2463 2.254 0.470 0.139 0.037 20 2.5 S_orbital-H_Shaped 2346 1472 2446 1.810 0.404 0.116 0.025 22 2.5 S_parieto_occipital 1805 1159 1600 1.804 0.897 0.119 0.023 33 1.6 S_pericallosal 3858 2523 4498 1.861 0.442 0.100 0.018 27 2.8 S_postcentral 1737 1187 2448 2.151 0.369 0.119 0.026 14 1.8 S_precentral-inf-part 1297 872 1706 2.151 0.411 0.116 0.024 10 1.3 S_precentral-sup-part 706 467 842 1.997 0.638 0.133 0.026 9 0.8 S_suborbital 1182 814 1323 1.765 0.352 0.135 0.033 12 1.7 S_subparietal 1818 1264 2312 2.003 0.400 0.127 0.027 17 2.0 S_temporal_inf 5937 3973 6935 1.818 0.443 0.104 0.023 49 5.3 S_temporal_sup 409 276 581 2.320 0.447 0.144 0.032 5 0.5 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jun 15 07:33:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1075 762 1731 1.982 0.469 0.145 0.044 18 1.8 G&S_frontomargin 1330 842 2686 2.498 0.566 0.141 0.037 20 1.9 G&S_occipital_inf 1801 931 2399 2.154 0.527 0.126 0.054 31 4.6 G&S_paracentral 1610 1047 2815 2.369 0.495 0.134 0.045 24 2.9 G&S_subcentral 1222 843 2266 2.163 0.449 0.167 0.048 31 2.6 G&S_transv_frontopol 3292 2233 5448 2.243 0.492 0.126 0.031 43 3.9 G&S_cingul-Ant 1379 971 2509 2.462 0.435 0.114 0.026 12 1.5 G&S_cingul-Mid-Ant 1316 905 2442 2.503 0.540 0.112 0.025 13 1.3 G&S_cingul-Mid-Post 805 491 1421 2.330 0.655 0.164 0.067 17 2.1 G_cingul-Post-dorsal 362 232 740 2.628 0.566 0.128 0.042 5 0.6 G_cingul-Post-ventral 2297 1416 2675 1.646 0.533 0.147 0.035 40 3.1 G_cuneus 1702 1110 3395 2.433 0.430 0.136 0.037 28 2.4 G_front_inf-Opercular 497 336 1159 2.515 0.412 0.155 0.044 10 0.9 G_front_inf-Orbital 1189 810 2058 2.084 0.389 0.163 0.047 25 2.1 G_front_inf-Triangul 3699 2496 6931 2.155 0.449 0.151 0.048 76 7.2 G_front_middle 7034 4667 14403 2.423 0.553 0.142 0.049 125 13.3 G_front_sup 693 458 1436 2.792 0.639 0.148 0.064 18 1.7 G_Ins_lg&S_cent_ins 828 550 2082 2.995 0.676 0.161 0.059 18 2.1 G_insular_short 2575 1440 4205 2.361 0.405 0.127 0.034 42 3.3 G_occipital_middle 1509 858 1913 1.949 0.465 0.131 0.035 24 2.1 G_occipital_sup 1825 1180 4087 2.650 0.566 0.143 0.036 36 2.6 G_oc-temp_lat-fusifor 3356 2144 4625 1.849 0.653 0.151 0.042 60 5.6 G_oc-temp_med-Lingual 1377 882 3398 2.880 0.835 0.125 0.049 21 3.0 G_oc-temp_med-Parahip 3107 2026 6442 2.451 0.642 0.146 0.048 62 5.6 G_orbital 4084 1998 4981 1.995 0.509 0.103 0.034 60 5.4 G_pariet_inf-Angular 3547 2054 5723 2.291 0.480 0.116 0.038 55 5.2 G_pariet_inf-Supramar 3444 1710 4606 2.151 0.438 0.094 0.032 47 4.4 G_parietal_sup 2805 1519 3449 1.897 0.511 0.112 0.038 40 4.6 G_postcentral 3336 1807 5843 2.510 0.447 0.116 0.042 48 5.7 G_precentral 2876 1694 4579 2.162 0.485 0.121 0.042 44 4.6 G_precuneus 846 543 1394 1.970 0.661 0.155 0.053 20 2.0 G_rectus 443 264 653 2.236 0.885 0.104 0.043 9 0.6 G_subcallosal 606 274 993 2.710 0.383 0.112 0.041 8 0.9 G_temp_sup-G_T_transv 2480 1477 5163 2.640 0.495 0.124 0.045 42 4.9 G_temp_sup-Lateral 652 457 1683 3.276 0.693 0.102 0.025 4 0.6 G_temp_sup-Plan_polar 1060 661 1750 2.399 0.543 0.106 0.030 11 1.2 G_temp_sup-Plan_tempo 2890 1894 6625 2.584 0.728 0.149 0.056 72 5.9 G_temporal_inf 3206 2103 6432 2.389 0.505 0.134 0.035 60 4.1 G_temporal_middle 415 287 475 1.987 0.357 0.112 0.018 2 0.3 Lat_Fis-ant-Horizont 173 120 264 2.071 0.403 0.102 0.019 1 0.1 Lat_Fis-ant-Vertical 1394 939 2001 2.466 0.473 0.103 0.024 8 1.2 Lat_Fis-post 3853 2442 4954 1.778 0.566 0.150 0.044 62 6.8 Pole_occipital 1789 1226 5187 3.141 0.623 0.146 0.051 34 3.7 Pole_temporal 2254 1497 2254 1.771 0.597 0.145 0.035 32 3.4 S_calcarine 3561 2466 3942 1.855 0.564 0.104 0.022 19 3.5 S_central 1562 1048 2241 2.123 0.396 0.103 0.021 14 1.3 S_cingul-Marginalis 525 350 796 2.748 0.431 0.119 0.027 4 0.6 S_circular_insula_ant 1593 1062 2311 2.464 0.581 0.093 0.019 7 1.4 S_circular_insula_inf 1609 1106 2255 2.413 0.361 0.107 0.022 9 1.5 S_circular_insula_sup 863 584 1511 2.607 0.598 0.126 0.032 9 0.9 S_collat_transv_ant 510 338 549 2.017 0.334 0.142 0.026 5 0.6 S_collat_transv_post 2498 1757 3180 1.884 0.357 0.125 0.030 25 2.8 S_front_inf 2133 1493 2929 1.947 0.436 0.142 0.038 33 3.3 S_front_middle 2223 1527 3226 2.101 0.412 0.115 0.026 18 2.5 S_front_sup 884 593 937 1.863 0.444 0.108 0.024 6 0.8 S_interm_prim-Jensen 4043 2554 4377 1.818 0.401 0.099 0.018 33 2.8 S_intrapariet&P_trans 929 620 1014 1.960 0.406 0.141 0.032 9 1.3 S_oc_middle&Lunatus 1265 824 1528 2.022 0.388 0.121 0.022 12 1.1 S_oc_sup&transversal 705 476 1009 2.370 0.289 0.104 0.020 4 0.6 S_occipital_ant 1143 778 1473 2.251 0.352 0.122 0.027 9 1.3 S_oc-temp_lat 2168 1538 2880 2.168 0.507 0.105 0.019 13 1.7 S_oc-temp_med&Lingual 661 456 748 1.941 0.491 0.148 0.037 7 1.1 S_orbital_lateral 836 569 1146 2.092 0.732 0.126 0.038 10 1.0 S_orbital_med-olfact 1517 1041 2248 2.130 0.459 0.136 0.033 18 2.0 S_orbital-H_Shaped 2911 1787 3206 1.990 0.497 0.109 0.021 24 2.5 S_parieto_occipital 1690 1088 1672 1.881 0.780 0.125 0.032 29 2.0 S_pericallosal 4088 2704 4974 2.020 0.395 0.103 0.019 32 3.2 S_postcentral 1482 991 2060 2.272 0.365 0.088 0.015 6 0.9 S_precentral-inf-part 1696 1126 2108 2.240 0.368 0.102 0.020 10 1.6 S_precentral-sup-part 415 289 456 1.814 0.501 0.122 0.019 4 0.3 S_suborbital 1324 908 1835 2.054 0.496 0.136 0.032 14 1.7 S_subparietal 1626 1126 2201 2.201 0.421 0.111 0.022 12 1.5 S_temporal_inf 6351 4194 7890 1.997 0.431 0.102 0.022 50 5.6 S_temporal_sup 236 159 316 2.730 0.367 0.136 0.028 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Jun 15 07:34:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable6//average/lh.DKTatlas.2016-03-20.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/lh.DKTatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1136 labels changed using aseg relabeling using gibbs priors... 000: 1909 changed, 139545 examined... 001: 411 changed, 9119 examined... 002: 118 changed, 2410 examined... 003: 48 changed, 704 examined... 004: 35 changed, 258 examined... 005: 28 changed, 184 examined... 006: 23 changed, 141 examined... 007: 19 changed, 106 examined... 008: 12 changed, 90 examined... 009: 12 changed, 76 examined... 010: 8 changed, 59 examined... 011: 4 changed, 35 examined... 012: 3 changed, 23 examined... 013: 2 changed, 21 examined... 014: 1 changed, 10 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 1 changed, 8 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 1 changed, 7 examined... 024: 1 changed, 11 examined... 025: 1 changed, 4 examined... 026: 1 changed, 10 examined... 027: 2 changed, 5 examined... 028: 2 changed, 8 examined... 029: 2 changed, 12 examined... 030: 4 changed, 13 examined... 031: 3 changed, 14 examined... 032: 2 changed, 14 examined... 033: 4 changed, 14 examined... 034: 3 changed, 25 examined... 035: 5 changed, 19 examined... 036: 3 changed, 26 examined... 037: 0 changed, 16 examined... 342 labels changed using aseg 000: 59 total segments, 25 labels (261 vertices) changed 001: 37 total segments, 3 labels (5 vertices) changed 002: 34 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1084 vertices marked for relabeling... 1084 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Wed Jun 15 07:34:41 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable6//average/rh.DKTatlas.2016-03-20.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.779 2016/06/08 20:03:14 greve Exp $ reading atlas from /usr/local/freesurfer/stable6//average/rh.DKTatlas.2016-03-20.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.007 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1239 labels changed using aseg relabeling using gibbs priors... 000: 2112 changed, 149612 examined... 001: 499 changed, 9649 examined... 002: 132 changed, 2780 examined... 003: 61 changed, 754 examined... 004: 31 changed, 334 examined... 005: 21 changed, 174 examined... 006: 12 changed, 114 examined... 007: 9 changed, 62 examined... 008: 4 changed, 50 examined... 009: 3 changed, 26 examined... 010: 2 changed, 19 examined... 011: 0 changed, 14 examined... 262 labels changed using aseg 000: 57 total segments, 24 labels (325 vertices) changed 001: 35 total segments, 2 labels (7 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 858 vertices marked for relabeling... 858 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jun 15 07:35:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab AD08 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1607 1076 2735 2.545 0.633 0.146 0.034 29 2.2 caudalanteriorcingulate 3043 2102 5159 2.136 0.472 0.137 0.042 50 5.1 caudalmiddlefrontal 3252 1998 3526 1.727 0.399 0.130 0.031 47 4.1 cuneus 555 406 1364 2.740 0.840 0.128 0.032 5 0.8 entorhinal 3715 2510 7096 2.479 0.553 0.139 0.039 57 6.0 fusiform 6488 3951 7642 1.796 0.480 0.122 0.033 89 8.2 inferiorparietal 4493 3112 8708 2.296 0.574 0.149 0.042 86 7.4 inferiortemporal 1833 1200 2160 1.732 0.603 0.132 0.040 34 2.8 isthmuscingulate 7651 4910 10586 1.990 0.450 0.140 0.037 109 11.0 lateraloccipital 4610 3072 8093 2.279 0.571 0.150 0.053 87 10.0 lateralorbitofrontal 5372 3524 7285 1.909 0.535 0.147 0.043 89 9.1 lingual 2489 1566 3717 2.095 0.759 0.138 0.059 63 5.9 medialorbitofrontal 6249 4225 10159 2.102 0.504 0.123 0.032 87 7.6 middletemporal 889 608 1990 2.672 0.678 0.104 0.031 8 1.0 parahippocampal 2504 1503 3817 2.352 0.485 0.113 0.043 28 4.8 paracentral 2619 1852 4604 2.222 0.403 0.131 0.033 37 3.8 parsopercularis 1115 745 1985 2.253 0.420 0.130 0.035 16 1.5 parsorbitalis 2177 1528 3380 2.007 0.456 0.132 0.036 33 3.0 parstriangularis 1856 1189 2005 1.858 0.444 0.122 0.032 19 2.4 pericalcarine 8385 5050 11606 2.065 0.598 0.106 0.027 94 8.7 postcentral 2332 1555 3419 2.062 0.647 0.134 0.031 41 2.9 posteriorcingulate 7862 4878 11840 2.318 0.509 0.115 0.037 80 12.8 precentral 6455 4075 7575 1.786 0.434 0.123 0.033 86 8.3 precuneus 1940 1278 3321 2.489 0.676 0.133 0.042 32 3.0 rostralanteriorcingulate 5574 3851 9298 2.019 0.469 0.151 0.051 118 11.7 rostralmiddlefrontal 11748 8159 21292 2.196 0.545 0.145 0.049 207 24.8 superiorfrontal 6680 3900 7815 1.892 0.458 0.110 0.031 84 7.8 superiorparietal 7602 5074 14511 2.413 0.619 0.114 0.031 86 9.4 superiortemporal 5886 3681 8367 2.102 0.582 0.115 0.028 64 6.6 supramarginal 766 450 1085 2.304 0.318 0.130 0.037 10 1.0 transversetemporal 3233 2151 6238 2.790 0.681 0.121 0.033 38 4.3 insula #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jun 15 07:35:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab AD08 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1071 748 2081 2.491 0.602 0.128 0.028 13 1.1 caudalanteriorcingulate 2977 1959 4291 2.109 0.382 0.121 0.032 33 3.9 caudalmiddlefrontal 3124 1966 3633 1.705 0.519 0.137 0.030 45 3.7 cuneus 439 313 1467 3.265 0.809 0.130 0.040 4 0.8 entorhinal 3779 2543 7039 2.555 0.542 0.129 0.029 50 4.2 fusiform 9380 5249 11373 1.983 0.490 0.108 0.030 122 11.0 inferiorparietal 5745 3842 11472 2.519 0.638 0.139 0.045 106 9.9 inferiortemporal 1739 1110 2474 2.044 0.785 0.134 0.048 29 3.3 isthmuscingulate 7614 4764 11029 2.092 0.551 0.140 0.037 107 11.1 lateraloccipital 4617 3097 8215 2.307 0.608 0.148 0.045 82 8.0 lateralorbitofrontal 4953 3239 6572 1.861 0.611 0.146 0.038 78 7.7 lingual 2219 1455 3384 2.024 0.716 0.136 0.042 41 3.6 medialorbitofrontal 6382 4287 11026 2.280 0.544 0.117 0.027 83 6.8 middletemporal 1177 763 2217 2.483 0.647 0.095 0.031 13 1.7 parahippocampal 2798 1606 4352 2.366 0.576 0.113 0.036 33 4.1 paracentral 2469 1673 4291 2.297 0.384 0.123 0.032 32 2.9 parsopercularis 1215 802 2308 2.410 0.598 0.125 0.033 16 1.5 parsorbitalis 2714 1888 4158 2.077 0.425 0.142 0.036 39 3.8 parstriangularis 2428 1596 2093 1.488 0.365 0.154 0.041 38 4.2 pericalcarine 8565 5289 10725 1.926 0.511 0.109 0.031 94 11.1 postcentral 1886 1266 3185 2.332 0.648 0.129 0.035 30 2.4 posteriorcingulate 8215 5050 12554 2.364 0.488 0.113 0.034 86 12.3 precentral 6876 4250 9625 2.132 0.496 0.117 0.032 81 8.6 precuneus 1525 1000 2660 2.394 0.464 0.130 0.029 25 1.8 rostralanteriorcingulate 6379 4396 9896 2.007 0.459 0.142 0.040 103 10.3 rostralmiddlefrontal 13189 9014 23642 2.267 0.506 0.135 0.041 201 21.4 superiorfrontal 7996 4537 10009 2.021 0.450 0.100 0.026 89 8.0 superiorparietal 8289 5356 15908 2.603 0.648 0.116 0.034 98 11.4 superiortemporal 7144 4449 10109 2.167 0.476 0.108 0.029 80 8.3 supramarginal 709 335 1034 2.629 0.402 0.111 0.039 8 1.0 transversetemporal 3467 2311 6475 2.730 0.637 0.129 0.040 48 5.7 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Jun 15 07:36:26 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts pctsurfcon --s AD08 --lh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts/pctsurfcon.log Wed Jun 15 07:36:26 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts /usr/local/freesurfer/stable6//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-49 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/stable6/ mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.wm.mgh --regheader AD08 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 73734 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.wm.mgh Dim: 139545 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.gm.mgh --projfrac 0.3 --regheader AD08 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 91578 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.gm.mgh Dim: 139545 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9592/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.w-g.pct.mgh --annot AD08 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.w-g.pct.mgh --annot AD08 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.w-g.pct.mgh Vertex Area is 0.650999 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Wed Jun 15 07:36:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts pctsurfcon --s AD08 --rh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts/pctsurfcon.log Wed Jun 15 07:36:34 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts /usr/local/freesurfer/stable6//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-49 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/stable6/ mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.wm.mgh --regheader AD08 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 78609 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.wm.mgh Dim: 149612 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.gm.mgh --projfrac 0.3 --regheader AD08 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 97376 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.gm.mgh Dim: 149612 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/tmp.pctsurfcon.9646/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.w-g.pct.mgh --annot AD08 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.w-g.pct.mgh --annot AD08 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.w-g.pct.mgh Vertex Area is 0.640039 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Wed Jun 15 07:36:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3362 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4011 voxels changed to hypointensity... 7216 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed Jun 15 07:37:08 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 418603 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Wed Jun 15 07:38:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --aseg aseg.presurf.hypos --annot aparc.a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 418603 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed Jun 15 07:40:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --aseg aseg.presurf.hypos --annot aparc.DKTatlas SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 418603 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed Jun 15 07:44:12 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed Jun 15 07:44:12 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri /usr/local/freesurfer/stable6//bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux compute-0-49 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 mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname compute-0-49 machine x86_64 user fdu0 input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Wed Jun 15 07:44:12 EDT 2016 Ended at Wed Jun 15 07:44:20 EDT 2016 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed Jun 15 07:44:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 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/stable6//ASegStatsLUT.txt --subject AD08 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 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/stable6//ASegStatsLUT.txt --subject AD08 sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Computing euler number orig.nofix lheno = -96, rheno = -138 orig.nofix lhholes = 49, rhholes = 70 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 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 Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Wed Jun 15 07:48:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8565 vertices from left hemi Ripped 8532 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 872536 Used brute-force search on 143 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 6.000000 2 k 1221.000000 3 k 6.000000 4 k 1.000000 5 k 4.000000 Fixing Parahip RH WM Found 21 clusters 0 k 236.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 2.000000 7 k 3.000000 8 k 2.000000 9 k 1.000000 10 k 1.000000 11 k 5.000000 12 k 2.000000 13 k 1.000000 14 k 1.000000 15 k 2.000000 16 k 24.000000 17 k 1.000000 18 k 1.000000 19 k 1.000000 20 k 1679.000000 Writing output aseg to mri/wmparc.mgz 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 AD08 --surf-wm-vol --ctab /usr/local/freesurfer/stable6//WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 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 AD08 --surf-wm-vol --ctab /usr/local/freesurfer/stable6//WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-49 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 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 Reporting on 70 segmentations Using PrintSegStat mri_segstats done /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Jun 15 08:00:47 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.label --trgsubject AD08 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 545 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4674 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.label --trgsubject AD08 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 1055 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8964 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.label --trgsubject AD08 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA3a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 358 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4435 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.label --trgsubject AD08 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA3b_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 426 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6409 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.label --trgsubject AD08 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA4a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 558 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6342 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.label --trgsubject AD08 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA4p_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 530 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4600 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.label --trgsubject AD08 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA6_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 1198 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14787 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.label --trgsubject AD08 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA44_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 565 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4746 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.label --trgsubject AD08 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA45_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 637 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4059 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.label --trgsubject AD08 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.V1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 1803 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6444 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.label --trgsubject AD08 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.V2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 3511 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11625 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.label --trgsubject AD08 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.MT_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 342 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2360 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject AD08 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.entorhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 139545 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1478 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject AD08 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.perirhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1101 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 468 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA3a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1616 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA3b_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA4a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA4p_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1756 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA6_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7589 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA44_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 296 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.BA45_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 233 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.V1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 1390 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.V2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 1579 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4913 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.MT_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 139545 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.entorhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 139545 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject AD08 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./lh.perirhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 139545 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 524 mri_label2label: Done mris_label2annot --s AD08 --hemi lh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label cmdline mris_label2annot --s AD08 --hemi lh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname compute-0-49 machine x86_64 user fdu0 subject AD08 hemi lh SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc ColorTable /usr/local/freesurfer/stable6//average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 95171 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.BA_exvivo.annot mris_label2annot --s AD08 --hemi lh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label cmdline mris_label2annot --s AD08 --hemi lh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-49 machine x86_64 user fdu0 subject AD08 hemi lh SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc ColorTable /usr/local/freesurfer/stable6//average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 113118 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab AD08 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/stable6//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1285 774 1435 1.726 0.518 0.106 0.031 18 1.7 BA1_exvivo 5113 2974 6570 2.035 0.514 0.099 0.024 51 4.8 BA2_exvivo 1289 786 1808 2.373 0.642 0.111 0.032 13 1.9 BA3a_exvivo 2380 1614 2879 1.832 0.466 0.108 0.025 17 2.6 BA3b_exvivo 1686 976 2777 2.459 0.460 0.120 0.039 20 2.6 BA4a_exvivo 1730 885 2743 2.550 0.475 0.107 0.057 21 5.0 BA4p_exvivo 8825 6072 15882 2.283 0.527 0.136 0.046 125 18.2 BA6_exvivo 2747 1975 4420 2.120 0.397 0.129 0.032 34 3.8 BA44_exvivo 2895 2022 4800 2.000 0.459 0.138 0.040 52 4.6 BA45_exvivo 4098 2551 4995 1.842 0.490 0.150 0.045 75 7.4 V1_exvivo 9056 5908 11291 1.839 0.453 0.140 0.037 125 13.4 V2_exvivo 1921 1263 2597 1.999 0.454 0.118 0.026 17 2.1 MT_exvivo 607 432 1190 2.545 0.796 0.119 0.031 7 0.7 perirhinal_exvivo 742 515 2109 3.003 0.615 0.174 0.077 20 2.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab AD08 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 205775 Total vertex volume 202380 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/stable6//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 788 510 814 1.560 0.376 0.086 0.021 4 0.6 BA1_exvivo 2156 1108 2880 2.151 0.535 0.099 0.029 28 2.4 BA2_exvivo 1080 683 1469 2.304 0.620 0.110 0.031 11 1.5 BA3a_exvivo 1411 1002 1484 1.660 0.369 0.113 0.027 9 1.7 BA3b_exvivo 1731 949 2816 2.498 0.468 0.123 0.050 24 4.0 BA4a_exvivo 1307 674 2098 2.600 0.480 0.104 0.050 13 3.2 BA4p_exvivo 4930 3380 8797 2.298 0.549 0.132 0.045 60 10.5 BA6_exvivo 1741 1292 2897 2.096 0.398 0.133 0.036 26 2.8 BA44_exvivo 1144 804 2029 2.055 0.484 0.144 0.044 23 2.1 BA45_exvivo 4402 2746 5395 1.828 0.485 0.149 0.045 81 7.9 V1_exvivo 4597 3020 5398 1.749 0.419 0.141 0.036 63 6.7 V2_exvivo 427 290 609 2.023 0.360 0.119 0.025 4 0.4 MT_exvivo 304 217 536 2.481 0.822 0.145 0.039 5 0.4 perirhinal_exvivo 409 280 1021 2.846 0.547 0.153 0.075 10 1.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Wed Jun 15 08:06:28 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.label --trgsubject AD08 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 676 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4638 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.label --trgsubject AD08 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1145 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7832 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.label --trgsubject AD08 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA3a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 529 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.label --trgsubject AD08 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA3b_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 711 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5233 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.label --trgsubject AD08 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA4a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 687 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6434 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.label --trgsubject AD08 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA4p_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 402 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4875 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.label --trgsubject AD08 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA6_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1690 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13946 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.label --trgsubject AD08 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA44_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 834 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7746 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.label --trgsubject AD08 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA45_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1257 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6612 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.label --trgsubject AD08 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.V1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1508 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6235 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.label --trgsubject AD08 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.V2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 2624 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10640 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.label --trgsubject AD08 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.MT_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 674 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2606 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject AD08 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.entorhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 149612 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1111 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject AD08 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.perirhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1099 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 379 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA3a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1976 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA3b_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 306 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA4a_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA4p_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1618 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA6_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1087 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8046 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA44_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1151 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.BA45_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 181 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1359 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.V1_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1028 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.V2_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 1182 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4619 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.MT_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 149612 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 338 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.entorhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 149612 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 751 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject AD08 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = AD08 trglabel = ./rh.perirhinal_exvivo.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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /usr/local/freesurfer/stable6/ Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 149612 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 334 mri_label2label: Done mris_label2annot --s AD08 --hemi rh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label cmdline mris_label2annot --s AD08 --hemi rh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname compute-0-49 machine x86_64 user fdu0 subject AD08 hemi rh SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc ColorTable /usr/local/freesurfer/stable6//average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 104544 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.BA_exvivo.annot mris_label2annot --s AD08 --hemi rh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label cmdline mris_label2annot --s AD08 --hemi rh --ctab /usr/local/freesurfer/stable6//average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-49 machine x86_64 user fdu0 subject AD08 hemi rh SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc ColorTable /usr/local/freesurfer/stable6//average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 123936 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab AD08 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/stable6//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 1289 793 1611 2.054 0.451 0.107 0.024 12 1.2 BA1_exvivo 4472 2850 5883 2.064 0.454 0.107 0.025 44 4.5 BA2_exvivo 1536 972 1882 1.762 0.606 0.103 0.030 14 2.0 BA3a_exvivo 2499 1463 3356 1.997 0.501 0.114 0.033 33 3.6 BA3b_exvivo 1645 1019 2273 2.169 0.585 0.137 0.054 25 4.3 BA4a_exvivo 1458 950 1537 1.691 0.455 0.112 0.034 16 1.9 BA4p_exvivo 9449 5875 15858 2.402 0.482 0.117 0.039 109 14.8 BA6_exvivo 3412 2302 6115 2.442 0.411 0.115 0.027 35 3.6 BA44_exvivo 4679 3187 7962 2.213 0.499 0.135 0.036 68 6.1 BA45_exvivo 3676 2391 3526 1.594 0.502 0.156 0.041 64 6.3 V1_exvivo 7673 4868 10132 1.865 0.615 0.147 0.040 123 12.2 V2_exvivo 2394 1493 3753 2.310 0.465 0.132 0.033 28 3.0 MT_exvivo 538 356 195 2.801 0.892 0.092 0.019 3 0.5 perirhinal_exvivo 348 196 390 2.697 0.910 0.132 0.049 6 0.7 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab AD08 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 222498 Total vertex volume 219294 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/stable6//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.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 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) lhCtxGM: 201908.014 201097.000 diff= 811.0 pctdiff= 0.402 rhCtxGM: 218792.078 217778.000 diff= 1014.1 pctdiff= 0.463 lhCtxWM: 219739.912 220695.500 diff= -955.6 pctdiff=-0.435 rhCtxWM: 234899.260 235403.500 diff= -504.2 pctdiff=-0.215 SubCortGMVol 52987.000 SupraTentVol 964724.264 (962125.000) diff=2599.264 pctdiff=0.269 SupraTentVolNotVent 930697.264 (928098.000) diff=2599.264 pctdiff=0.279 BrainSegVol 1105179.000 (1101214.000) diff=3965.000 pctdiff=0.359 BrainSegVolNotVent 1066094.000 (1066328.264) diff=-234.264 pctdiff=-0.022 BrainSegVolNotVent 1066094.000 CerebellumVol 137865.000 VentChorVol 34027.000 3rd4th5thCSF 5058.000 CSFVol 1093.000, OptChiasmVol 131.000 MaskVol 1606964.000 949 588 1164 2.115 0.372 0.088 0.014 5 0.5 BA1_exvivo 2447 1668 3117 2.035 0.378 0.107 0.021 20 2.0 BA2_exvivo 1467 897 1662 1.721 0.561 0.106 0.032 15 2.2 BA3a_exvivo 1945 1149 2492 1.927 0.475 0.111 0.032 25 2.5 BA3b_exvivo 973 557 1631 2.422 0.579 0.121 0.056 15 2.8 BA4a_exvivo 1175 798 1183 1.601 0.355 0.110 0.028 9 1.3 BA4p_exvivo 6361 3931 10386 2.389 0.477 0.118 0.037 69 9.6 BA6_exvivo 930 609 1771 2.505 0.329 0.120 0.032 11 1.1 BA44_exvivo 1076 707 1869 2.215 0.395 0.130 0.034 16 1.2 BA45_exvivo 3465 2243 3321 1.606 0.523 0.155 0.041 60 6.0 V1_exvivo 3998 2575 5560 1.864 0.649 0.146 0.038 63 6.2 V2_exvivo 309 188 472 2.315 0.362 0.146 0.032 5 0.3 MT_exvivo 327 212 33 2.837 0.737 0.091 0.020 2 0.3 perirhinal_exvivo 254 137 108 2.625 0.827 0.143 0.053 5 0.6 entorhinal_exvivo Started at Tue Jun 14 16:00:22 EDT 2016 Ended at Wed Jun 15 08:12:48 EDT 2016 #@#%# recon-all-run-time-hours 16.207 recon-all -s AD08 finished without error at Wed Jun 15 08:12:48 EDT 2016 New invocation of recon-all Wed Jul 6 13:45:55 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon2 -autorecon3 -no-isrunning -subjid AD08 subjid AD08 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-38 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877324 1509552 31367772 20 69288 447096 -/+ buffers/cache: 993168 31884156 Swap: 67108860 80600 67028260 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:45:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/06-17:46:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-38 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Wed Jul 6 13:46:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (54, 63, 38) --> (195, 195, 207) using (101, 107, 123) as brain centroid... mean wm in atlas = 107, using box (84,91,102) --> (118, 123,143) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -7429.4 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, -10.8, -13.1): log p = -7143.266 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7093.3, old_max_log_p =-7143.3 (thresh=-7136.1) 1.075 0.000 0.000 -10.121; 0.000 1.066 0.140 -35.940; 0.000 -0.140 1.066 -2.666; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7074.7, old_max_log_p =-7093.3 (thresh=-7086.2) 0.994 0.000 0.000 0.148; 0.000 1.146 0.151 -47.550; 0.000 -0.130 0.986 5.434; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7074.7, old_max_log_p =-7074.7 (thresh=-7067.6) 0.994 0.000 0.000 0.148; 0.000 1.146 0.151 -47.550; 0.000 -0.130 0.986 5.434; 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=-6999.5, old_max_log_p =-7074.7 (thresh=-7067.6) 1.012 0.003 -0.030 0.790; 0.002 1.175 0.052 -38.043; 0.031 -0.014 0.977 -12.327; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6999.5, old_max_log_p =-6999.5 (thresh=-6992.5) 1.012 0.003 -0.030 0.790; 0.002 1.175 0.052 -38.043; 0.031 -0.014 0.977 -12.327; 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=-6991.1, old_max_log_p =-6999.5 (thresh=-6992.5) 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.978 -8.631; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6987.6, old_max_log_p =-6991.1 (thresh=-6984.2) 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 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 1.00850 0.01239 -0.01305 -1.93763; -0.00553 1.17594 0.06057 -38.13432; 0.01449 -0.02388 0.98137 -9.03241; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00850 0.01239 -0.01305 -1.93763; -0.00553 1.17594 0.06057 -38.13432; 0.01449 -0.02388 0.98137 -9.03241; 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) = 6987.6 tol 0.000010 Resulting transform: 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6987.6 (old=-7429.4) transform before final EM align: 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 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 1.00850 0.01239 -0.01305 -1.93763; -0.00553 1.17594 0.06057 -38.13432; 0.01449 -0.02388 0.98137 -9.03241; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00850 0.01239 -0.01305 -1.93763; -0.00553 1.17594 0.06057 -38.13432; 0.01449 -0.02388 0.98137 -9.03241; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 840065.5 tol 0.000000 final transform: 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 55 seconds. #-------------------------------------- #@# CA Normalize Wed Jul 6 14:07:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_normalize -f /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/tmp/control.dat -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz reading manually defined control points from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/tmp/control.dat writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (54, 63, 41) --> (195, 195, 207) using (101, 107, 124) as brain centroid... mean wm in atlas = 107, using box (84,91,104) --> (118, 123,144) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 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 (124, 71, 37) --> (192, 171, 208) Left_Cerebral_White_Matter: limiting intensities to 114.0 --> 235.0 16 of 20 (80.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 72, 37) --> (128, 170, 208) Right_Cerebral_White_Matter: limiting intensities to 111.0 --> 235.0 6 of 8 (75.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 143, 60) --> (175, 181, 115) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 235.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (80, 143, 58) --> (126, 180, 116) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 235.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 138, 95) --> (142, 196, 128) Reading 0 control points... Brain_Stem: limiting intensities to 115.0 --> 235.0 6 of 7 (85.7%) samples deleted using 55 total control points for intensity normalization... bias field = 0.843 +- 0.063 0 of 27 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 71, 37) --> (192, 171, 208) Left_Cerebral_White_Matter: limiting intensities to 87.0 --> 198.0 0 of 108 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 72, 37) --> (128, 170, 208) Right_Cerebral_White_Matter: limiting intensities to 79.0 --> 198.0 0 of 98 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 143, 60) --> (175, 181, 115) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (80, 143, 58) --> (126, 180, 116) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 198.0 0 of 20 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 138, 95) --> (142, 196, 128) Reading 0 control points... Brain_Stem: limiting intensities to 82.0 --> 198.0 4 of 28 (14.3%) samples deleted using 254 total control points for intensity normalization... bias field = 1.085 +- 0.079 0 of 250 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 71, 37) --> (192, 171, 208) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 212.0 0 of 189 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 72, 37) --> (128, 170, 208) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 212.0 0 of 167 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 143, 60) --> (175, 181, 115) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (80, 143, 58) --> (126, 180, 116) Right_Cerebellum_White_Matter: limiting intensities to 86.0 --> 212.0 0 of 18 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 138, 95) --> (142, 196, 128) Reading 0 control points... Brain_Stem: limiting intensities to 79.0 --> 212.0 0 of 16 (0.0%) samples deleted using 390 total control points for intensity normalization... bias field = 1.008 +- 0.053 0 of 390 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 Wed Jul 6 14:09:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.17 (predicted orig area = 6.9) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.040, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37583.336 ms 0001: dt=129.472000, rms=0.897 (13.789%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37394.699 ms 0002: dt=129.472000, rms=0.870 (3.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39873.824 ms 0003: dt=295.936000, rms=0.846 (2.712%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37363.867 ms 0004: dt=55.488000, rms=0.841 (0.608%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39841.812 ms 0005: dt=129.472000, rms=0.838 (0.377%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40062.832 ms 0006: dt=517.888000, rms=0.825 (1.534%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37357.273 ms 0007: dt=32.368000, rms=0.822 (0.336%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39836.422 ms 0008: dt=32.368000, rms=0.821 (0.099%), neg=0, invalid=766 0009: dt=32.368000, rms=0.821 (0.054%), neg=0, invalid=766 0010: dt=32.368000, rms=0.820 (0.078%), neg=0, invalid=766 0011: dt=32.368000, rms=0.819 (0.106%), neg=0, invalid=766 0012: dt=32.368000, rms=0.818 (0.187%), neg=0, invalid=766 0013: dt=32.368000, rms=0.815 (0.327%), neg=0, invalid=766 0014: dt=32.368000, rms=0.812 (0.396%), neg=0, invalid=766 0015: dt=32.368000, rms=0.809 (0.428%), neg=0, invalid=766 0016: dt=32.368000, rms=0.805 (0.404%), neg=0, invalid=766 0017: dt=32.368000, rms=0.802 (0.374%), neg=0, invalid=766 0018: dt=32.368000, rms=0.800 (0.327%), neg=0, invalid=766 0019: dt=32.368000, rms=0.797 (0.277%), neg=0, invalid=766 0020: dt=32.368000, rms=0.796 (0.237%), neg=0, invalid=766 0021: dt=32.368000, rms=0.794 (0.254%), neg=0, invalid=766 0022: dt=32.368000, rms=0.791 (0.287%), neg=0, invalid=766 0023: dt=32.368000, rms=0.789 (0.324%), neg=0, invalid=766 0024: dt=32.368000, rms=0.786 (0.313%), neg=0, invalid=766 0025: dt=32.368000, rms=0.784 (0.290%), neg=0, invalid=766 0026: dt=32.368000, rms=0.782 (0.245%), neg=0, invalid=766 0027: dt=32.368000, rms=0.780 (0.198%), neg=0, invalid=766 0028: dt=32.368000, rms=0.779 (0.190%), neg=0, invalid=766 0029: dt=32.368000, rms=0.777 (0.192%), neg=0, invalid=766 0030: dt=32.368000, rms=0.776 (0.208%), neg=0, invalid=766 0031: dt=32.368000, rms=0.774 (0.225%), neg=0, invalid=766 0032: dt=32.368000, rms=0.772 (0.240%), neg=0, invalid=766 0033: dt=32.368000, rms=0.770 (0.241%), neg=0, invalid=766 0034: dt=32.368000, rms=0.769 (0.208%), neg=0, invalid=766 0035: dt=32.368000, rms=0.767 (0.174%), neg=0, invalid=766 0036: dt=32.368000, rms=0.766 (0.138%), neg=0, invalid=766 0037: dt=32.368000, rms=0.766 (0.114%), neg=0, invalid=766 0038: dt=32.368000, rms=0.765 (0.126%), neg=0, invalid=766 0039: dt=32.368000, rms=0.763 (0.148%), neg=0, invalid=766 0040: dt=32.368000, rms=0.762 (0.168%), neg=0, invalid=766 0041: dt=32.368000, rms=0.761 (0.166%), neg=0, invalid=766 0042: dt=32.368000, rms=0.760 (0.140%), neg=0, invalid=766 0043: dt=32.368000, rms=0.759 (0.120%), neg=0, invalid=766 0044: dt=32.368000, rms=0.758 (0.099%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41883.633 ms 0045: dt=110.976000, rms=0.758 (0.004%), neg=0, invalid=766 0046: dt=110.976000, rms=0.757 (0.089%), neg=0, invalid=766 0047: dt=110.976000, rms=0.757 (0.094%), neg=0, invalid=766 0048: dt=110.976000, rms=0.756 (0.054%), neg=0, invalid=766 0049: dt=110.976000, rms=0.755 (0.120%), neg=0, invalid=766 0050: dt=110.976000, rms=0.754 (0.172%), neg=0, invalid=766 0051: dt=110.976000, rms=0.753 (0.179%), neg=0, invalid=766 0052: dt=110.976000, rms=0.752 (0.132%), neg=0, invalid=766 0053: dt=110.976000, rms=0.751 (0.125%), neg=0, invalid=766 0054: dt=110.976000, rms=0.749 (0.185%), neg=0, invalid=766 0055: dt=110.976000, rms=0.748 (0.206%), neg=0, invalid=766 0056: dt=110.976000, rms=0.747 (0.162%), neg=0, invalid=766 0057: dt=110.976000, rms=0.746 (0.113%), neg=0, invalid=766 0058: dt=110.976000, rms=0.745 (0.165%), neg=0, invalid=766 0059: dt=110.976000, rms=0.743 (0.174%), neg=0, invalid=766 0060: dt=110.976000, rms=0.742 (0.152%), neg=0, invalid=766 0061: dt=110.976000, rms=0.741 (0.141%), neg=0, invalid=766 0062: dt=110.976000, rms=0.740 (0.128%), neg=0, invalid=766 0063: dt=110.976000, rms=0.739 (0.180%), neg=0, invalid=766 0064: dt=110.976000, rms=0.738 (0.149%), neg=0, invalid=766 0065: dt=110.976000, rms=0.737 (0.128%), neg=0, invalid=766 0066: dt=110.976000, rms=0.736 (0.109%), neg=0, invalid=766 0067: dt=110.976000, rms=0.735 (0.176%), neg=0, invalid=766 0068: dt=110.976000, rms=0.733 (0.180%), neg=0, invalid=766 0069: dt=110.976000, rms=0.733 (0.110%), neg=0, invalid=766 0070: dt=110.976000, rms=0.732 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41952.984 ms 0071: dt=369.920000, rms=0.731 (0.145%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39600.602 ms 0072: dt=1.734000, rms=0.731 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.731, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39388.504 ms 0073: dt=18.496000, rms=0.731 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39522.551 ms 0074: dt=8.092000, rms=0.731 (0.004%), neg=0, invalid=766 0075: dt=8.092000, rms=0.731 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.741, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39382.695 ms 0076: dt=145.152000, rms=0.734 (0.909%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36941.910 ms 0077: dt=36.288000, rms=0.724 (1.329%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36930.234 ms 0078: dt=20.736000, rms=0.723 (0.114%), neg=0, invalid=766 0079: dt=20.736000, rms=0.722 (0.214%), neg=0, invalid=766 0080: dt=20.736000, rms=0.719 (0.359%), neg=0, invalid=766 0081: dt=20.736000, rms=0.716 (0.469%), neg=0, invalid=766 0082: dt=20.736000, rms=0.712 (0.554%), neg=0, invalid=766 0083: dt=20.736000, rms=0.708 (0.589%), neg=0, invalid=766 0084: dt=20.736000, rms=0.703 (0.609%), neg=0, invalid=766 0085: dt=20.736000, rms=0.699 (0.592%), neg=0, invalid=766 0086: dt=20.736000, rms=0.695 (0.556%), neg=0, invalid=766 0087: dt=20.736000, rms=0.692 (0.502%), neg=0, invalid=766 0088: dt=20.736000, rms=0.689 (0.448%), neg=0, invalid=766 0089: dt=20.736000, rms=0.686 (0.421%), neg=0, invalid=766 0090: dt=20.736000, rms=0.683 (0.380%), neg=0, invalid=766 0091: dt=20.736000, rms=0.681 (0.341%), neg=0, invalid=766 0092: dt=20.736000, rms=0.679 (0.300%), neg=0, invalid=766 0093: dt=20.736000, rms=0.677 (0.274%), neg=0, invalid=766 0094: dt=20.736000, rms=0.675 (0.245%), neg=0, invalid=766 0095: dt=20.736000, rms=0.674 (0.215%), neg=0, invalid=766 0096: dt=20.736000, rms=0.673 (0.182%), neg=0, invalid=766 0097: dt=20.736000, rms=0.672 (0.163%), neg=0, invalid=766 0098: dt=20.736000, rms=0.670 (0.164%), neg=0, invalid=766 0099: dt=20.736000, rms=0.669 (0.162%), neg=0, invalid=766 0100: dt=20.736000, rms=0.668 (0.170%), neg=0, invalid=766 0101: dt=20.736000, rms=0.667 (0.170%), neg=0, invalid=766 0102: dt=20.736000, rms=0.666 (0.151%), neg=0, invalid=766 0103: dt=20.736000, rms=0.665 (0.129%), neg=0, invalid=766 0104: dt=20.736000, rms=0.665 (0.109%), neg=0, invalid=766 0105: dt=20.736000, rms=0.664 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41817.109 ms 0106: dt=145.152000, rms=0.663 (0.107%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36930.465 ms 0107: dt=9.072000, rms=0.663 (0.014%), neg=0, invalid=766 0108: dt=9.072000, rms=0.663 (0.009%), neg=0, invalid=766 0109: dt=9.072000, rms=0.663 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39446.145 ms 0110: dt=15.552000, rms=0.663 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41828.637 ms 0111: dt=25.920000, rms=0.663 (0.019%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41820.715 ms 0112: dt=25.920000, rms=0.663 (0.008%), neg=0, invalid=766 0113: dt=25.920000, rms=0.663 (-0.006%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.694, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42086.152 ms 0114: dt=2.400000, rms=0.694 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39512.402 ms 0115: dt=0.300000, rms=0.694 (0.000%), neg=0, invalid=766 0116: dt=0.300000, rms=0.694 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39371.195 ms 0117: dt=0.000000, rms=0.694 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.784, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39380.270 ms 0118: dt=4.656842, rms=0.764 (2.499%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39379.922 ms 0119: dt=2.094340, rms=0.764 (0.103%), neg=0, invalid=766 0120: dt=2.094340, rms=0.764 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.764, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37063.387 ms 0121: dt=0.000000, rms=0.764 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.865, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39552.559 ms 0122: dt=1.373585, rms=0.858 (0.887%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36940.449 ms 0123: dt=2.018265, rms=0.851 (0.800%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36963.516 ms 0124: dt=0.448000, rms=0.850 (0.082%), neg=0, invalid=766 0125: dt=0.448000, rms=0.850 (0.020%), neg=0, invalid=766 0126: dt=0.448000, rms=0.850 (0.003%), neg=0, invalid=766 0127: dt=0.448000, rms=0.850 (-0.020%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.850, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36930.172 ms 0128: dt=1.536000, rms=0.848 (0.236%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34754.258 ms 0129: dt=0.000000, rms=0.848 (0.001%), neg=0, invalid=766 0130: dt=0.100000, rms=0.848 (-0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.766, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36826.598 ms 0131: dt=0.384000, rms=0.742 (3.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29552.580 ms 0132: dt=0.000000, rms=0.742 (0.005%), neg=0, invalid=766 0133: dt=0.050000, rms=0.742 (-0.566%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.742, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29561.621 ms 0134: dt=0.000000, rms=0.742 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11410 (14) Left_Lateral_Ventricle (4): linear fit = 0.45 x + 0.0 (2791 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.45 x + 0.0 (2791 voxels, peak = 11), gca=10.8 gca peak = 0.14022 (22) mri peak = 0.10467 (13) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (1749 voxels, overlap=0.084) Right_Lateral_Ventricle (43): linear fit = 0.50 x + 0.0 (1749 voxels, peak = 11), gca=11.0 gca peak = 0.24234 (100) mri peak = 0.11000 (98) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (315 voxels, overlap=0.994) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (315 voxels, peak = 95), gca=95.0 gca peak = 0.19192 (97) mri peak = 0.07287 (98) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (396 voxels, overlap=0.976) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (396 voxels, peak = 99), gca=99.4 gca peak = 0.24007 (63) mri peak = 0.07836 (60) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (539 voxels, overlap=0.961) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (539 voxels, peak = 60), gca=59.8 gca peak = 0.29892 (64) mri peak = 0.08343 (60) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (336 voxels, overlap=0.741) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (336 voxels, peak = 59), gca=59.2 gca peak = 0.12541 (104) mri peak = 0.07085 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (65426 voxels, overlap=0.859) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (65426 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.06606 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61320 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61320 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.02455 (67) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11301 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (11301 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.02761 (71) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (14353 voxels, overlap=0.013) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (14353 voxels, peak = 76), gca=75.6 gca peak = 0.15182 (70) mri peak = 0.06261 (66) Right_Caudate (50): linear fit = 0.90 x + 0.0 (359 voxels, overlap=0.681) Right_Caudate (50): linear fit = 0.90 x + 0.0 (359 voxels, peak = 63), gca=63.0 gca peak = 0.14251 (76) mri peak = 0.10001 (71) Left_Caudate (11): linear fit = 0.90 x + 0.0 (601 voxels, overlap=0.512) Left_Caudate (11): linear fit = 0.90 x + 0.0 (601 voxels, peak = 68), gca=68.4 gca peak = 0.12116 (60) mri peak = 0.03746 ( 7) Left_Cerebellum_Cortex (8): linear fit = 0.10 x + 0.0 (7044 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 0.10 x + 0.0 (7044 voxels, peak = 6), gca=6.0 gca peak = 0.12723 (61) mri peak = 0.02902 (50) Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (9294 voxels, overlap=0.235) Right_Cerebellum_Cortex (47): linear fit = 0.90 x + 0.0 (9294 voxels, peak = 55), gca=54.9 gca peak = 0.22684 (88) mri peak = 0.05715 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5304 voxels, overlap=0.769) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5304 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.08416 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6397 voxels, overlap=0.506) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6397 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.08293 (65) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (195 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (195 voxels, peak = 64), gca=63.5 gca peak = 0.39668 (62) mri peak = 0.08149 (60) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (296 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (296 voxels, peak = 59), gca=58.9 gca peak = 0.10129 (93) mri peak = 0.06032 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4341 voxels, overlap=0.980) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4341 voxels, peak = 93), gca=93.0 gca peak = 0.12071 (89) mri peak = 0.05326 (95) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3884 voxels, overlap=0.804) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3884 voxels, peak = 93), gca=93.4 gca peak = 0.13716 (82) mri peak = 0.05939 (87) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1923 voxels, overlap=0.903) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1923 voxels, peak = 84), gca=84.0 gca peak = 0.15214 (84) mri peak = 0.05368 (79) Right_Putamen (51): linear fit = 0.95 x + 0.0 (1731 voxels, overlap=0.918) Right_Putamen (51): linear fit = 0.95 x + 0.0 (1731 voxels, peak = 80), gca=79.8 gca peak = 0.08983 (85) mri peak = 0.06106 (95) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8492 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.10 x + 0.0 (8492 voxels, peak = 94), gca=93.5 gca peak = 0.11809 (92) mri peak = 0.07581 (100) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (738 voxels, overlap=0.635) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (738 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.07816 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (917 voxels, overlap=0.676) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (917 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.23156 (17) Third_Ventricle (14): linear fit = 0.45 x + 0.0 (79 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.45 x + 0.0 (79 voxels, peak = 16), gca=16.2 gca peak = 0.13542 (27) mri peak = 0.14024 (15) Fourth_Ventricle (15): linear fit = 0.45 x + 0.0 (467 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.45 x + 0.0 (467 voxels, peak = 12), gca=12.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Cerebellum_Cortex = 0.12116 (60) 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) not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 0.90 x + 0: 55 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.47 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.765, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34455.070 ms 0135: dt=73.984000, rms=0.759 (0.787%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34625.707 ms 0136: dt=73.984000, rms=0.758 (0.104%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34592.523 ms 0137: dt=92.480000, rms=0.757 (0.181%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29783.451 ms 0138: dt=2.023000, rms=0.757 (0.003%), neg=0, invalid=766 0139: dt=2.023000, rms=0.756 (0.004%), neg=0, invalid=766 0140: dt=1.011500, rms=0.756 (0.002%), neg=0, invalid=766 0141: dt=0.252875, rms=0.756 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22320.959 ms 0142: dt=0.031609, rms=0.756 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.756, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22265.580 ms 0143: dt=0.031609, rms=0.756 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32450.307 ms 0144: dt=0.007902, rms=0.756 (0.000%), neg=0, invalid=766 0145: dt=0.001976, rms=0.756 (0.000%), neg=0, invalid=766 0146: dt=0.000988, rms=0.756 (0.000%), neg=0, invalid=766 0147: dt=0.000062, rms=0.756 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.756, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17384.652 ms 0148: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.756, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17423.260 ms 0149: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.757, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17396.828 ms 0150: dt=0.000000, rms=0.757 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.757, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17394.010 ms 0151: dt=0.000000, rms=0.757 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.757, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17387.029 ms 0152: dt=0.000000, rms=0.757 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.757, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17486.121 ms 0153: dt=0.000000, rms=0.757 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.758, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34479.797 ms 0154: dt=0.448000, rms=0.746 (1.518%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34534.750 ms 0155: dt=0.448000, rms=0.736 (1.335%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34475.809 ms 0156: dt=0.448000, rms=0.728 (1.170%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34875.961 ms 0157: dt=0.448000, rms=0.720 (1.033%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36949.656 ms 0158: dt=1.792000, rms=0.694 (3.595%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37043.562 ms 0159: dt=1.792000, rms=0.681 (1.916%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36903.281 ms 0160: dt=1.280000, rms=0.675 (0.825%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37119.363 ms 0161: dt=1.280000, rms=0.671 (0.630%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37050.082 ms 0162: dt=1.536000, rms=0.667 (0.600%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36910.469 ms 0163: dt=1.792000, rms=0.663 (0.541%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36992.918 ms 0164: dt=1.792000, rms=0.661 (0.418%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36911.391 ms 0165: dt=1.792000, rms=0.658 (0.341%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36912.445 ms 0166: dt=1.792000, rms=0.656 (0.277%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34467.172 ms 0167: dt=1.792000, rms=0.655 (0.241%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36904.648 ms 0168: dt=1.280000, rms=0.654 (0.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37353.211 ms 0169: dt=1.792000, rms=0.653 (0.190%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37238.656 ms 0170: dt=1.792000, rms=0.652 (0.163%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36915.113 ms 0171: dt=1.792000, rms=0.651 (0.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36911.281 ms 0172: dt=5.120000, rms=0.648 (0.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34470.613 ms 0173: dt=0.448000, rms=0.648 (0.022%), neg=0, invalid=766 0174: dt=0.448000, rms=0.648 (0.021%), neg=0, invalid=766 0175: dt=0.448000, rms=0.648 (0.040%), neg=0, invalid=766 0176: dt=0.448000, rms=0.647 (0.057%), neg=0, invalid=766 0177: dt=0.448000, rms=0.647 (0.069%), neg=0, invalid=766 0178: dt=0.448000, rms=0.646 (0.080%), neg=0, invalid=766 0179: dt=0.448000, rms=0.646 (0.088%), neg=0, invalid=766 0180: dt=0.448000, rms=0.645 (0.094%), neg=0, invalid=766 0181: dt=0.448000, rms=0.645 (0.099%), neg=0, invalid=766 0182: dt=0.448000, rms=0.644 (0.098%), neg=0, invalid=766 0183: dt=0.448000, rms=0.643 (0.099%), neg=0, invalid=766 0184: dt=0.448000, rms=0.643 (0.096%), neg=0, invalid=766 0185: dt=0.448000, rms=0.642 (0.087%), neg=0, invalid=766 0186: dt=0.448000, rms=0.642 (0.087%), neg=0, invalid=766 0187: dt=0.448000, rms=0.641 (0.076%), neg=0, invalid=766 0188: dt=0.448000, rms=0.641 (0.072%), neg=0, invalid=766 0189: dt=0.448000, rms=0.640 (0.061%), neg=0, invalid=766 0190: dt=0.448000, rms=0.640 (0.054%), neg=0, invalid=766 0191: dt=0.448000, rms=0.640 (0.045%), neg=0, invalid=766 0192: dt=0.448000, rms=0.639 (0.037%), neg=0, invalid=766 0193: dt=0.448000, rms=0.639 (0.029%), neg=0, invalid=766 0194: dt=0.448000, rms=0.639 (0.029%), neg=0, invalid=766 0195: dt=0.448000, rms=0.639 (0.021%), neg=0, invalid=766 0196: dt=0.448000, rms=0.639 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34465.707 ms 0197: dt=0.000000, rms=0.639 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36908.348 ms 0198: dt=1.792000, rms=0.637 (0.217%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39345.348 ms 0199: dt=6.144000, rms=0.635 (0.338%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34464.707 ms 0200: dt=0.448000, rms=0.635 (0.015%), neg=0, invalid=766 0201: dt=0.448000, rms=0.635 (0.010%), neg=0, invalid=766 0202: dt=0.448000, rms=0.635 (0.018%), neg=0, invalid=766 0203: dt=0.448000, rms=0.635 (0.020%), neg=0, invalid=766 0204: dt=0.448000, rms=0.635 (0.019%), neg=0, invalid=766 0205: dt=0.448000, rms=0.635 (0.023%), neg=0, invalid=766 0206: dt=0.448000, rms=0.634 (0.038%), neg=0, invalid=766 0207: dt=0.448000, rms=0.634 (0.016%), neg=0, invalid=766 0208: dt=0.448000, rms=0.634 (0.024%), neg=0, invalid=766 0209: dt=0.448000, rms=0.634 (0.033%), neg=0, invalid=766 0210: dt=0.448000, rms=0.634 (0.033%), neg=0, invalid=766 0211: dt=0.448000, rms=0.633 (0.035%), neg=0, invalid=766 0212: dt=0.448000, rms=0.633 (0.035%), neg=0, invalid=766 0213: dt=0.448000, rms=0.633 (0.036%), neg=0, invalid=766 0214: dt=0.448000, rms=0.633 (0.035%), neg=0, invalid=766 0215: dt=0.448000, rms=0.633 (0.034%), neg=0, invalid=766 0216: dt=0.448000, rms=0.632 (0.032%), neg=0, invalid=766 0217: dt=0.448000, rms=0.632 (0.030%), neg=0, invalid=766 0218: dt=0.448000, rms=0.632 (0.028%), neg=0, invalid=766 0219: dt=0.448000, rms=0.632 (0.028%), neg=0, invalid=766 0220: dt=0.448000, rms=0.632 (0.028%), neg=0, invalid=766 0221: dt=0.448000, rms=0.631 (0.026%), neg=0, invalid=766 0222: dt=0.448000, rms=0.631 (0.030%), neg=0, invalid=766 0223: dt=0.448000, rms=0.631 (0.028%), neg=0, invalid=766 0224: dt=0.448000, rms=0.631 (0.028%), neg=0, invalid=766 0225: dt=0.448000, rms=0.631 (0.025%), neg=0, invalid=766 0226: dt=0.448000, rms=0.631 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39509.301 ms 0227: dt=0.768000, rms=0.631 (0.002%), neg=0, invalid=766 0228: dt=0.768000, rms=0.631 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34402.844 ms 0229: dt=0.112000, rms=0.615 (1.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34431.863 ms 0230: dt=0.112000, rms=0.609 (0.963%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34417.645 ms 0231: dt=0.157609, rms=0.602 (1.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34419.695 ms 0232: dt=0.136861, rms=0.598 (0.697%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34427.984 ms 0233: dt=0.125463, rms=0.595 (0.500%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31980.869 ms 0234: dt=0.028000, rms=0.595 (0.093%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34436.879 ms 0235: dt=0.114130, rms=0.592 (0.358%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36862.309 ms 0236: dt=0.320000, rms=0.587 (0.840%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32000.154 ms 0237: dt=0.028000, rms=0.587 (0.043%), neg=0, invalid=766 0238: dt=0.028000, rms=0.587 (0.042%), neg=0, invalid=766 0239: dt=0.028000, rms=0.587 (0.079%), neg=0, invalid=766 0240: dt=0.028000, rms=0.586 (0.110%), neg=0, invalid=766 0241: dt=0.028000, rms=0.585 (0.136%), neg=0, invalid=766 0242: dt=0.028000, rms=0.584 (0.153%), neg=0, invalid=766 0243: dt=0.028000, rms=0.583 (0.165%), neg=0, invalid=766 0244: dt=0.028000, rms=0.582 (0.172%), neg=0, invalid=766 0245: dt=0.028000, rms=0.581 (0.176%), neg=0, invalid=766 0246: dt=0.028000, rms=0.580 (0.174%), neg=0, invalid=766 0247: dt=0.028000, rms=0.579 (0.165%), neg=0, invalid=766 0248: dt=0.028000, rms=0.578 (0.157%), neg=0, invalid=766 0249: dt=0.028000, rms=0.577 (0.147%), neg=0, invalid=766 0250: dt=0.028000, rms=0.577 (0.004%), neg=0, invalid=766 0251: dt=0.028000, rms=0.577 (0.007%), neg=0, invalid=766 0252: dt=0.028000, rms=0.577 (0.011%), neg=0, invalid=766 0253: dt=0.028000, rms=0.577 (0.018%), neg=0, invalid=766 0254: dt=0.028000, rms=0.577 (0.019%), neg=0, invalid=766 0255: dt=0.028000, rms=0.577 (0.025%), neg=0, invalid=766 0256: dt=0.028000, rms=0.577 (0.029%), neg=0, invalid=766 0257: dt=0.028000, rms=0.577 (0.034%), neg=0, invalid=766 0258: dt=0.028000, rms=0.576 (0.037%), neg=0, invalid=766 0259: dt=0.028000, rms=0.576 (0.043%), neg=0, invalid=766 0260: dt=0.028000, rms=0.576 (0.045%), neg=0, invalid=766 0261: dt=0.028000, rms=0.576 (0.052%), neg=0, invalid=766 0262: dt=0.028000, rms=0.576 (0.007%), neg=0, invalid=766 0263: dt=0.028000, rms=0.575 (0.015%), neg=0, invalid=766 0264: dt=0.028000, rms=0.575 (0.023%), neg=0, invalid=766 0265: dt=0.028000, rms=0.575 (0.027%), neg=0, invalid=766 0266: dt=0.028000, rms=0.575 (0.032%), neg=0, invalid=766 0267: dt=0.028000, rms=0.575 (0.032%), neg=0, invalid=766 0268: dt=0.028000, rms=0.575 (0.039%), neg=0, invalid=766 0269: dt=0.028000, rms=0.574 (0.037%), neg=0, invalid=766 0270: dt=0.028000, rms=0.574 (0.037%), neg=0, invalid=766 0271: dt=0.028000, rms=0.574 (0.041%), neg=0, invalid=766 0272: dt=0.028000, rms=0.574 (0.038%), neg=0, invalid=766 0273: dt=0.028000, rms=0.573 (0.035%), neg=0, invalid=766 0274: dt=0.028000, rms=0.573 (0.034%), neg=0, invalid=766 0275: dt=0.028000, rms=0.573 (0.034%), neg=0, invalid=766 0276: dt=0.028000, rms=0.573 (0.030%), neg=0, invalid=766 0277: dt=0.028000, rms=0.573 (0.002%), neg=0, invalid=766 0278: dt=0.028000, rms=0.573 (0.005%), neg=0, invalid=766 0279: dt=0.028000, rms=0.573 (0.007%), neg=0, invalid=766 0280: dt=0.028000, rms=0.573 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36866.227 ms 0281: dt=0.448000, rms=0.573 (0.036%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32145.352 ms 0282: dt=0.028000, rms=0.573 (0.003%), neg=0, invalid=766 0283: dt=0.028000, rms=0.573 (0.002%), neg=0, invalid=766 0284: dt=0.028000, rms=0.573 (0.006%), neg=0, invalid=766 0285: dt=0.028000, rms=0.573 (0.007%), neg=0, invalid=766 0286: dt=0.028000, rms=0.572 (0.010%), neg=0, invalid=766 0287: dt=0.028000, rms=0.572 (0.011%), neg=0, invalid=766 0288: dt=0.028000, rms=0.572 (0.010%), neg=0, invalid=766 0289: dt=0.028000, rms=0.572 (0.012%), neg=0, invalid=766 0290: dt=0.028000, rms=0.572 (0.012%), neg=0, invalid=766 0291: dt=0.028000, rms=0.572 (0.015%), neg=0, invalid=766 0292: dt=0.028000, rms=0.572 (0.016%), neg=0, invalid=766 0293: dt=0.028000, rms=0.572 (0.015%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37045.828 ms 0294: dt=0.320000, rms=0.565 (1.234%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31985.273 ms 0295: dt=0.028000, rms=0.565 (0.024%), neg=0, invalid=766 0296: dt=0.028000, rms=0.565 (0.024%), neg=0, invalid=766 0297: dt=0.028000, rms=0.564 (0.046%), neg=0, invalid=766 0298: dt=0.028000, rms=0.564 (0.060%), neg=0, invalid=766 0299: dt=0.028000, rms=0.564 (0.071%), neg=0, invalid=766 0300: dt=0.028000, rms=0.563 (0.072%), neg=0, invalid=766 0301: dt=0.028000, rms=0.563 (0.069%), neg=0, invalid=766 0302: dt=0.028000, rms=0.562 (0.061%), neg=0, invalid=766 0303: dt=0.028000, rms=0.562 (0.049%), neg=0, invalid=766 0304: dt=0.028000, rms=0.562 (0.034%), neg=0, invalid=766 0305: dt=0.028000, rms=0.562 (0.018%), neg=0, invalid=766 0306: dt=0.028000, rms=0.562 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34432.219 ms 0307: dt=0.000000, rms=0.562 (0.001%), neg=0, invalid=766 0308: dt=0.050000, rms=0.562 (-0.027%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.559, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42106.746 ms iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0309: dt=32.000000, rms=0.546 (2.300%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41745.375 ms iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0310: dt=44.800000, rms=0.542 (0.712%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41763.270 ms 0311: dt=11.200000, rms=0.541 (0.199%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0312: dt=11.200000, rms=0.541 (0.082%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0313: dt=11.200000, rms=0.540 (0.180%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 15 iterations, nbhd size=2, neg = 0 0314: dt=11.200000, rms=0.538 (0.222%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 22 iterations, nbhd size=3, neg = 0 0315: dt=11.200000, rms=0.537 (0.194%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0316: dt=11.200000, rms=0.536 (0.196%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=2, neg = 0 0317: dt=11.200000, rms=0.536 (0.150%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0318: dt=11.200000, rms=0.535 (0.187%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0319: dt=11.200000, rms=0.534 (0.163%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0320: dt=11.200000, rms=0.533 (0.152%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=11.200000, rms=0.532 (0.166%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 22 iterations, nbhd size=3, neg = 0 0322: dt=11.200000, rms=0.531 (0.172%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 26 iterations, nbhd size=4, neg = 0 0323: dt=11.200000, rms=0.530 (0.130%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0324: dt=11.200000, rms=0.530 (0.156%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0325: dt=11.200000, rms=0.529 (0.145%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0326: dt=11.200000, rms=0.528 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0327: dt=11.200000, rms=0.528 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41885.461 ms iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0328: dt=25.600000, rms=0.527 (0.135%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41780.102 ms 0329: dt=2.800000, rms=0.527 (0.016%), neg=0, invalid=766 0330: dt=2.800000, rms=0.527 (0.018%), neg=0, invalid=766 0331: dt=2.800000, rms=0.527 (0.009%), neg=0, invalid=766 0332: dt=2.800000, rms=0.527 (0.016%), neg=0, invalid=766 0333: dt=2.800000, rms=0.527 (0.020%), neg=0, invalid=766 0334: dt=2.800000, rms=0.527 (0.028%), neg=0, invalid=766 0335: dt=2.800000, rms=0.526 (0.029%), neg=0, invalid=766 0336: dt=2.800000, rms=0.526 (0.024%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41804.805 ms iter 0, gcam->neg = 2 after 24 iterations, nbhd size=3, neg = 0 0337: dt=44.800000, rms=0.521 (0.952%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41772.141 ms 0338: dt=19.200000, rms=0.519 (0.369%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41806.176 ms 0339: dt=8.000000, rms=0.519 (0.086%), neg=0, invalid=766 0340: dt=8.000000, rms=0.518 (0.113%), neg=0, invalid=766 0341: dt=8.000000, rms=0.518 (0.136%), neg=0, invalid=766 0342: dt=8.000000, rms=0.517 (0.152%), neg=0, invalid=766 0343: dt=8.000000, rms=0.516 (0.145%), neg=0, invalid=766 0344: dt=8.000000, rms=0.515 (0.154%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0345: dt=8.000000, rms=0.515 (0.150%), neg=0, invalid=766 0346: dt=8.000000, rms=0.514 (0.085%), neg=0, invalid=766 0347: dt=8.000000, rms=0.514 (0.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41772.172 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0348: dt=38.400000, rms=0.513 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41776.594 ms 0349: dt=11.200000, rms=0.513 (0.071%), neg=0, invalid=766 0350: dt=11.200000, rms=0.513 (0.020%), neg=0, invalid=766 0351: dt=11.200000, rms=0.513 (0.037%), neg=0, invalid=766 0352: dt=11.200000, rms=0.512 (0.071%), neg=0, invalid=766 0353: dt=11.200000, rms=0.512 (0.059%), neg=0, invalid=766 0354: dt=11.200000, rms=0.512 (0.039%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.521, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44227.617 ms 0355: dt=3.456000, rms=0.520 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41782.469 ms 0356: dt=1.008000, rms=0.520 (0.007%), neg=0, invalid=766 0357: dt=1.008000, rms=0.520 (0.007%), neg=0, invalid=766 0358: dt=1.008000, rms=0.520 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44229.246 ms 0359: dt=4.032000, rms=0.520 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44435.078 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0360: dt=4.032000, rms=0.519 (0.052%), neg=0, invalid=766 0361: dt=4.032000, rms=0.519 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0362: dt=4.032000, rms=0.519 (0.008%), neg=0, invalid=766 0363: dt=4.032000, rms=0.519 (-0.092%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41797.672 ms 0364: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41785.059 ms 0365: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44141.902 ms iter 0, gcam->neg = 1319 after 15 iterations, nbhd size=1, neg = 0 0366: dt=1.890293, rms=0.458 (10.680%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44172.371 ms 0367: dt=0.000094, rms=0.458 (0.001%), neg=0, invalid=766 0368: dt=0.000094, rms=0.458 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.458, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44168.590 ms 0369: dt=0.000375, rms=0.458 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41884.402 ms 0370: dt=0.000000, rms=0.458 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44242.340 ms iter 0, gcam->neg = 507 after 19 iterations, nbhd size=2, neg = 0 0371: dt=0.484043, rms=0.428 (2.519%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44180.762 ms 0372: dt=0.000750, rms=0.428 (0.002%), neg=0, invalid=766 0373: dt=0.000750, rms=0.428 (0.000%), neg=0, invalid=766 0374: dt=0.000750, rms=0.428 (0.000%), neg=0, invalid=766 0375: dt=0.000750, rms=0.428 (0.001%), neg=0, invalid=766 0376: dt=0.000750, rms=0.428 (0.001%), neg=0, invalid=766 0377: dt=0.000750, rms=0.428 (0.002%), neg=0, invalid=766 0378: dt=0.000750, rms=0.428 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44168.547 ms iter 0, gcam->neg = 25 after 15 iterations, nbhd size=2, neg = 0 0379: dt=0.080000, rms=0.428 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44170.234 ms 0380: dt=0.001000, rms=0.428 (0.008%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.428, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44178.684 ms iter 0, gcam->neg = 81 after 16 iterations, nbhd size=2, neg = 0 0381: dt=0.112000, rms=0.426 (0.390%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44262.062 ms iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0382: dt=0.007000, rms=0.426 (0.012%), neg=0, invalid=766 0383: dt=0.007000, rms=0.426 (0.022%), neg=0, invalid=766 0384: dt=0.007000, rms=0.426 (0.040%), neg=0, invalid=766 0385: dt=0.007000, rms=0.426 (0.056%), neg=0, invalid=766 0386: dt=0.007000, rms=0.426 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0387: dt=0.007000, rms=0.425 (0.086%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0388: dt=0.007000, rms=0.425 (0.090%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0389: dt=0.007000, rms=0.425 (0.092%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0390: dt=0.007000, rms=0.424 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0391: dt=0.007000, rms=0.424 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0392: dt=0.007000, rms=0.423 (0.095%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0393: dt=0.007000, rms=0.423 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 16 iterations, nbhd size=2, neg = 0 0394: dt=0.007000, rms=0.423 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44163.629 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0395: dt=0.005000, rms=0.423 (0.003%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44132.367 ms iter 0, gcam->neg = 78 after 7 iterations, nbhd size=1, neg = 0 0396: dt=0.115706, rms=0.419 (0.659%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44200.539 ms iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0397: dt=0.007000, rms=0.419 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=0.007000, rms=0.419 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=0.007000, rms=0.418 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0400: dt=0.007000, rms=0.418 (0.079%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0401: dt=0.007000, rms=0.418 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0402: dt=0.007000, rms=0.417 (0.117%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0403: dt=0.007000, rms=0.417 (0.126%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0404: dt=0.007000, rms=0.416 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0405: dt=0.007000, rms=0.416 (0.135%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0406: dt=0.007000, rms=0.415 (0.136%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=2, neg = 0 0407: dt=0.007000, rms=0.414 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0408: dt=0.007000, rms=0.414 (0.136%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0409: dt=0.007000, rms=0.413 (0.134%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 6 iterations, nbhd size=1, neg = 0 0410: dt=0.007000, rms=0.413 (0.125%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0411: dt=0.007000, rms=0.412 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0412: dt=0.007000, rms=0.412 (0.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44764.855 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0413: dt=0.028000, rms=0.412 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0414: dt=0.028000, rms=0.412 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 26 iterations, nbhd size=3, neg = 0 0415: dt=0.028000, rms=0.412 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 55 after 15 iterations, nbhd size=2, neg = 0 0416: dt=0.028000, rms=0.412 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 91 after 12 iterations, nbhd size=1, neg = 0 0417: dt=0.028000, rms=0.411 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 120 after 19 iterations, nbhd size=2, neg = 0 0418: dt=0.028000, rms=0.411 (0.006%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77362.070 ms iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0419: dt=0.007000, rms=0.411 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76340.305 ms iter 0, gcam->neg = 70 after 23 iterations, nbhd size=3, neg = 0 0420: dt=0.112000, rms=0.410 (0.364%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75919.711 ms 0421: dt=0.001750, rms=0.410 (-0.002%), neg=0, invalid=766 0422: dt=0.001750, rms=0.410 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0423: dt=0.001750, rms=0.410 (0.008%), neg=0, invalid=766 0424: dt=0.001750, rms=0.410 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=0.001750, rms=0.410 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=0.001750, rms=0.410 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0427: dt=0.001750, rms=0.410 (0.020%), neg=0, invalid=766 0428: dt=0.001750, rms=0.409 (0.028%), neg=0, invalid=766 0429: dt=0.001750, rms=0.409 (0.029%), neg=0, invalid=766 0430: dt=0.001750, rms=0.409 (0.030%), neg=0, invalid=766 0431: dt=0.001750, rms=0.409 (0.030%), neg=0, invalid=766 0432: dt=0.001750, rms=0.409 (0.033%), neg=0, invalid=766 0433: dt=0.001750, rms=0.409 (0.035%), neg=0, invalid=766 0434: dt=0.001750, rms=0.409 (0.036%), neg=0, invalid=766 0435: dt=0.001750, rms=0.408 (0.034%), neg=0, invalid=766 0436: dt=0.001750, rms=0.408 (0.036%), neg=0, invalid=766 0437: dt=0.001750, rms=0.408 (0.034%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78680.203 ms iter 0, gcam->neg = 10 after 45 iterations, nbhd size=4, neg = 0 0438: dt=6.418605, rms=0.408 (-0.164%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85673.141 ms iter 0, gcam->neg = 54 after 49 iterations, nbhd size=4, neg = 0 0439: dt=19.200000, rms=0.408 (0.158%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85235.383 ms iter 0, gcam->neg = 34 after 37 iterations, nbhd size=4, neg = 0 0440: dt=6.400000, rms=0.408 (-0.019%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84661.422 ms iter 0, gcam->neg = 59 after 49 iterations, nbhd size=4, neg = 0 0441: dt=1.008000, rms=0.408 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82914.391 ms iter 0, gcam->neg = 82 after 53 iterations, nbhd size=4, neg = 0 0442: dt=2.107143, rms=0.407 (0.141%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 84562.539 ms iter 0, gcam->neg = 77 after 54 iterations, nbhd size=4, neg = 0 0443: dt=1.728000, rms=0.407 (0.135%), neg=0, invalid=766 iter 0, gcam->neg = 63 after 51 iterations, nbhd size=4, neg = 0 0444: dt=1.728000, rms=0.406 (0.118%), neg=0, invalid=766 iter 0, gcam->neg = 138 after 67 iterations, nbhd size=4, neg = 0 0445: dt=1.728000, rms=0.406 (0.132%), neg=0, invalid=766 iter 0, gcam->neg = 205 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 42282.742 ms iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.002 (44.947%) gcamFindOptimalTimeStep: Complete in 44194.184 ms iter 2, dt=0.000328: new neg 1, old_neg 1, delta 0, rms=0.001 (50.926%) gcamFindOptimalTimeStep: Complete in 39224.355 ms iter 3, dt=0.000009: new neg 1, old_neg 1, delta 0, rms=0.001 (0.244%) gcamFindOptimalTimeStep: Complete in 44002.996 ms iter 4, dt=0.000006: new neg 1, old_neg 1, delta 0, rms=0.001 (0.163%) gcamFindOptimalTimeStep: Complete in 42195.137 ms iter 5, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.003%) ---------- unfolding failed - restoring original position -------------------- 0446: dt=1.728000, rms=0.406 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80888.961 ms iter 0, gcam->neg = 45 after 46 iterations, nbhd size=1, neg = 0 0447: dt=0.864000, rms=0.405 (0.036%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72791.984 ms iter 0, gcam->neg = 47 after 56 iterations, nbhd size=2, neg = 0 0448: dt=1.187500, rms=0.405 (0.031%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68522.047 ms iter 0, gcam->neg = 28 after 26 iterations, nbhd size=3, neg = 0 0449: dt=0.272727, rms=0.405 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59411.363 ms iter 0, gcam->neg = 23 after 26 iterations, nbhd size=3, neg = 0 0450: dt=0.208955, rms=0.405 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 51 iterations, nbhd size=2, neg = 0 0451: dt=0.208955, rms=0.405 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 57 after 31 iterations, nbhd size=3, neg = 0 0452: dt=0.208955, rms=0.405 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 90 after 67 iterations, nbhd size=2, neg = 0 0453: dt=0.208955, rms=0.405 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 99 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 33674.109 ms iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.001 (53.993%) 0454: dt=0.208955, rms=0.405 (-0.157%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52993.676 ms iter 0, gcam->neg = 40 after 43 iterations, nbhd size=4, neg = 0 0455: dt=0.290000, rms=0.404 (0.105%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55407.102 ms iter 0, gcam->neg = 61 after 42 iterations, nbhd size=4, neg = 0 0456: dt=0.448000, rms=0.404 (0.088%), neg=0, invalid=766 iter 0, gcam->neg = 71 after 46 iterations, nbhd size=4, neg = 0 0457: dt=0.448000, rms=0.403 (0.162%), neg=0, invalid=766 iter 0, gcam->neg = 144 after 38 iterations, nbhd size=3, neg = 0 0458: dt=0.448000, rms=0.403 (0.219%), neg=0, invalid=766 iter 0, gcam->neg = 215 after 43 iterations, nbhd size=3, neg = 0 0459: dt=0.448000, rms=0.402 (0.240%), neg=0, invalid=766 iter 0, gcam->neg = 261 after 43 iterations, nbhd size=3, neg = 0 0460: dt=0.448000, rms=0.400 (0.324%), neg=0, invalid=766 iter 0, gcam->neg = 288 after 57 iterations, nbhd size=4, neg = 0 0461: dt=0.448000, rms=0.399 (0.216%), neg=0, invalid=766 iter 0, gcam->neg = 317 after 54 iterations, nbhd size=2, neg = 0 0462: dt=0.448000, rms=0.399 (0.202%), neg=0, invalid=766 iter 0, gcam->neg = 361 after 50 iterations, nbhd size=3, neg = 0 0463: dt=0.448000, rms=0.398 (0.157%), neg=0, invalid=766 iter 0, gcam->neg = 387 after 75 iterations, nbhd size=3, neg = 0 0464: dt=0.448000, rms=0.397 (0.121%), neg=0, invalid=766 iter 0, gcam->neg = 393 after 47 iterations, nbhd size=3, neg = 0 0465: dt=0.448000, rms=0.397 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78518.375 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0466: dt=0.016000, rms=0.397 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0467: dt=0.016000, rms=0.397 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0468: dt=0.016000, rms=0.397 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0469: dt=0.016000, rms=0.397 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0470: dt=0.016000, rms=0.397 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0471: dt=0.016000, rms=0.397 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0472: dt=0.016000, rms=0.397 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0473: dt=0.016000, rms=0.397 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 16 iterations, nbhd size=2, neg = 0 0474: dt=0.016000, rms=0.397 (0.016%), neg=0, invalid=766 0475: dt=0.016000, rms=0.397 (0.022%), neg=0, invalid=766 0476: dt=0.016000, rms=0.397 (0.022%), neg=0, invalid=766 0477: dt=0.016000, rms=0.396 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0478: dt=0.016000, rms=0.396 (0.020%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82925.781 ms iter 0, gcam->neg = 98 after 15 iterations, nbhd size=2, neg = 0 0479: dt=0.080000, rms=0.393 (0.412%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81231.141 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0480: dt=0.007000, rms=0.393 (0.027%), neg=0, invalid=766 0481: dt=0.007000, rms=0.393 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0482: dt=0.007000, rms=0.392 (0.057%), neg=0, invalid=766 0483: dt=0.007000, rms=0.392 (0.079%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0484: dt=0.007000, rms=0.392 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0485: dt=0.007000, rms=0.391 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0486: dt=0.007000, rms=0.391 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0487: dt=0.007000, rms=0.390 (0.131%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 24 iterations, nbhd size=3, neg = 0 0488: dt=0.007000, rms=0.390 (0.125%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 17 iterations, nbhd size=2, neg = 0 0489: dt=0.007000, rms=0.389 (0.128%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 14 iterations, nbhd size=2, neg = 0 0490: dt=0.007000, rms=0.389 (0.132%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 8 iterations, nbhd size=1, neg = 0 0491: dt=0.007000, rms=0.388 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 14 iterations, nbhd size=2, neg = 0 0492: dt=0.007000, rms=0.388 (0.125%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 17 iterations, nbhd size=2, neg = 0 0493: dt=0.007000, rms=0.387 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68518.758 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0494: dt=0.003000, rms=0.387 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0495: dt=0.003000, rms=0.387 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0496: dt=0.003000, rms=0.387 (0.007%), neg=0, invalid=766 0497: dt=0.003000, rms=0.387 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0498: dt=0.003000, rms=0.387 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0499: dt=0.003000, rms=0.387 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 13 iterations, nbhd size=2, neg = 0 0500: dt=0.003000, rms=0.387 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0501: dt=0.003000, rms=0.387 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0502: dt=0.003000, rms=0.387 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 17 iterations, nbhd size=2, neg = 0 0503: dt=0.003000, rms=0.387 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 85332.789 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0504: dt=0.007000, rms=0.387 (0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82459.680 ms iter 0, gcam->neg = 11 after 19 iterations, nbhd size=2, neg = 0 0505: dt=0.028000, rms=0.387 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 78834.781 ms iter 0, gcam->neg = 6 after 17 iterations, nbhd size=2, neg = 0 0506: dt=0.016000, rms=0.386 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 16 iterations, nbhd size=2, neg = 0 0507: dt=0.016000, rms=0.386 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 8 iterations, nbhd size=1, neg = 0 0508: dt=0.016000, rms=0.386 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 8 iterations, nbhd size=1, neg = 0 0509: dt=0.016000, rms=0.385 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 9 iterations, nbhd size=1, neg = 0 0510: dt=0.016000, rms=0.385 (0.147%), neg=0, invalid=766 iter 0, gcam->neg = 49 after 19 iterations, nbhd size=2, neg = 0 0511: dt=0.016000, rms=0.384 (0.118%), neg=0, invalid=766 iter 0, gcam->neg = 49 after 20 iterations, nbhd size=2, neg = 0 0512: dt=0.016000, rms=0.384 (0.157%), neg=0, invalid=766 iter 0, gcam->neg = 60 after 10 iterations, nbhd size=1, neg = 0 0513: dt=0.016000, rms=0.383 (0.175%), neg=0, invalid=766 iter 0, gcam->neg = 66 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28591.492 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0514: dt=0.016000, rms=0.383 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50937.066 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0515: dt=0.001500, rms=0.383 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53053.855 ms 0516: dt=0.007000, rms=0.383 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51667.371 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0517: dt=0.001750, rms=0.383 (0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51115.688 ms iter 0, gcam->neg = 14 after 15 iterations, nbhd size=2, neg = 0 0518: dt=0.028000, rms=0.382 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50973.324 ms iter 0, gcam->neg = 22 after 14 iterations, nbhd size=2, neg = 0 0519: dt=0.028000, rms=0.382 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 16 iterations, nbhd size=2, neg = 0 0520: dt=0.028000, rms=0.381 (0.092%), neg=0, invalid=766 iter 0, gcam->neg = 61 after 15 iterations, nbhd size=2, neg = 0 0521: dt=0.028000, rms=0.381 (0.174%), neg=0, invalid=766 iter 0, gcam->neg = 116 after 18 iterations, nbhd size=2, neg = 0 0522: dt=0.028000, rms=0.380 (0.198%), neg=0, invalid=766 iter 0, gcam->neg = 158 after 20 iterations, nbhd size=2, neg = 0 0523: dt=0.028000, rms=0.379 (0.215%), neg=0, invalid=766 iter 0, gcam->neg = 172 after 19 iterations, nbhd size=2, neg = 0 0524: dt=0.028000, rms=0.378 (0.219%), neg=0, invalid=766 iter 0, gcam->neg = 218 after 27 iterations, nbhd size=3, neg = 0 0525: dt=0.028000, rms=0.377 (0.207%), neg=0, invalid=766 iter 0, gcam->neg = 254 after 20 iterations, nbhd size=2, neg = 0 0526: dt=0.028000, rms=0.377 (0.182%), neg=0, invalid=766 iter 0, gcam->neg = 331 after 30 iterations, nbhd size=3, neg = 0 0527: dt=0.028000, rms=0.376 (0.147%), neg=0, invalid=766 iter 0, gcam->neg = 387 after 20 iterations, nbhd size=2, neg = 0 0528: dt=0.028000, rms=0.376 (0.112%), neg=0, invalid=766 iter 0, gcam->neg = 476 after 20 iterations, nbhd size=2, neg = 0 0529: dt=0.028000, rms=0.375 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51453.496 ms 0530: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0531: dt=0.000438, rms=0.375 (0.001%), neg=0, invalid=766 0532: dt=0.000438, rms=0.375 (0.001%), neg=0, invalid=766 0533: dt=0.000438, rms=0.375 (0.001%), neg=0, invalid=766 0534: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0535: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0536: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0537: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0538: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 0539: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 0540: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 0541: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 0542: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0543: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 0544: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 0545: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0546: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0547: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53618.344 ms iter 0, gcam->neg = 19 after 16 iterations, nbhd size=2, neg = 0 0548: dt=0.028000, rms=0.375 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54872.656 ms 0549: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0550: dt=0.000438, rms=0.375 (0.001%), neg=0, invalid=766 0551: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 0552: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 0553: dt=0.000438, rms=0.375 (0.005%), neg=0, invalid=766 0554: dt=0.000438, rms=0.375 (0.006%), neg=0, invalid=766 0555: dt=0.000438, rms=0.375 (0.007%), neg=0, invalid=766 0556: dt=0.000438, rms=0.375 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0557: dt=0.000438, rms=0.375 (0.008%), neg=0, invalid=766 0558: dt=0.000438, rms=0.375 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0559: dt=0.000438, rms=0.375 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0560: dt=0.000438, rms=0.375 (0.010%), neg=0, invalid=766 0561: dt=0.000438, rms=0.375 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0562: dt=0.000438, rms=0.375 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0563: dt=0.000438, rms=0.375 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0564: dt=0.000438, rms=0.374 (0.011%), neg=0, invalid=766 0565: dt=0.000438, rms=0.374 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0566: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0567: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0568: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0569: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0570: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0571: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0572: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0573: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50003.848 ms iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0574: dt=0.016000, rms=0.373 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50280.809 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0575: dt=0.005000, rms=0.373 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0576: dt=0.005000, rms=0.373 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0577: dt=0.005000, rms=0.372 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0578: dt=0.005000, rms=0.372 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=1, neg = 0 0579: dt=0.005000, rms=0.372 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0580: dt=0.005000, rms=0.372 (0.078%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 17 iterations, nbhd size=2, neg = 0 0581: dt=0.005000, rms=0.371 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=1, neg = 0 0582: dt=0.005000, rms=0.371 (0.091%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 9 iterations, nbhd size=1, neg = 0 0583: dt=0.005000, rms=0.371 (0.097%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 17 iterations, nbhd size=2, neg = 0 0584: dt=0.005000, rms=0.370 (0.093%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.370, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49370.488 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0585: dt=0.007000, rms=0.370 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50880.367 ms iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0586: dt=0.007000, rms=0.370 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52717.738 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0587: dt=0.007000, rms=0.370 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0588: dt=0.007000, rms=0.370 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0589: dt=0.007000, rms=0.370 (0.052%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 11 iterations, nbhd size=1, neg = 0 0590: dt=0.007000, rms=0.369 (0.086%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 22 iterations, nbhd size=2, neg = 0 0591: dt=0.007000, rms=0.369 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 34 after 10 iterations, nbhd size=1, neg = 0 0592: dt=0.007000, rms=0.369 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 39 after 16 iterations, nbhd size=2, neg = 0 0593: dt=0.007000, rms=0.368 (0.127%), neg=0, invalid=766 iter 0, gcam->neg = 44 after 21 iterations, nbhd size=2, neg = 0 0594: dt=0.007000, rms=0.368 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 55 after 21 iterations, nbhd size=2, neg = 0 0595: dt=0.007000, rms=0.367 (0.142%), neg=0, invalid=766 iter 0, gcam->neg = 56 after 16 iterations, nbhd size=2, neg = 0 0596: dt=0.007000, rms=0.367 (0.147%), neg=0, invalid=766 iter 0, gcam->neg = 53 after 21 iterations, nbhd size=2, neg = 0 0597: dt=0.007000, rms=0.366 (0.148%), neg=0, invalid=766 iter 0, gcam->neg = 45 after 23 iterations, nbhd size=2, neg = 0 0598: dt=0.007000, rms=0.366 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 56 after 20 iterations, nbhd size=2, neg = 0 0599: dt=0.007000, rms=0.365 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 48 after 22 iterations, nbhd size=2, neg = 0 0600: dt=0.007000, rms=0.365 (0.095%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 19 iterations, nbhd size=2, neg = 0 0601: dt=0.007000, rms=0.364 (0.118%), neg=0, invalid=766 iter 0, gcam->neg = 50 after 17 iterations, nbhd size=2, neg = 0 0602: dt=0.007000, rms=0.364 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50831.668 ms 0603: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=766 0604: dt=0.001750, rms=0.364 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0605: dt=0.001750, rms=0.364 (0.004%), neg=0, invalid=766 0606: dt=0.001750, rms=0.364 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0607: dt=0.001750, rms=0.364 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0608: dt=0.001750, rms=0.364 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0609: dt=0.001750, rms=0.364 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0610: dt=0.001750, rms=0.364 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0611: dt=0.001750, rms=0.364 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0612: dt=0.001750, rms=0.364 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0613: dt=0.001750, rms=0.364 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 19 iterations, nbhd size=2, neg = 0 0614: dt=0.001750, rms=0.364 (0.006%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 5 hours, 49 minutes and 51 seconds. #-------------------------------------- #@# CA Reg Inv Wed Jul 6 19:59:33 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Jul 6 20:00:30 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11364286 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 2 seconds. #-------------------------------------- #@# SkullLTA Wed Jul 6 20:01:32 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (42, 46, 26) --> (208, 226, 230) using (97, 106, 128) as brain centroid... mean wm in atlas = 126, using box (77,84,103) --> (117, 128,153) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10315.0, old_max_log_p =-10371.2 (thresh=-10360.8) 1.008 0.012 -0.013 -1.938; -0.003 1.162 0.207 -54.044; 0.017 -0.181 1.111 -4.375; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10315.0, old_max_log_p =-10315.0 (thresh=-10304.7) 1.008 0.012 -0.013 -1.938; -0.003 1.162 0.207 -54.044; 0.017 -0.181 1.111 -4.375; 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=-10300.0, old_max_log_p =-10315.0 (thresh=-10304.7) 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.074 1.541; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10300.0, old_max_log_p =-10300.0 (thresh=-10289.7) 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.074 1.541; 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=-10299.8, old_max_log_p =-10300.0 (thresh=-10289.7) 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.075 1.418; 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 1.04515 0.00376 0.05680 -15.61169; -0.00389 1.16772 0.16952 -50.18874; -0.05204 -0.13939 1.07498 1.41842; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04515 0.00376 0.05680 -15.61169; -0.00389 1.16772 0.16952 -50.18874; -0.05204 -0.13939 1.07498 1.41842; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10299.8 tol 0.000010 Resulting transform: 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.075 1.418; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10299.8 (old=-10371.2) transform before final EM align: 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.075 1.418; 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 1.04515 0.00376 0.05680 -15.61169; -0.00389 1.16772 0.16952 -50.18874; -0.05204 -0.13939 1.07498 1.41842; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04515 0.00376 0.05680 -15.61169; -0.00389 1.16772 0.16952 -50.18874; -0.05204 -0.13939 1.07498 1.41842; 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) = 1145003.2 tol 0.000000 final transform: 1.045 0.004 0.057 -15.612; -0.004 1.168 0.170 -50.189; -0.052 -0.139 1.075 1.418; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 20 minutes and 29 seconds. #-------------------------------------- #@# SubCort Seg Wed Jul 6 20:22:02 EDT 2016 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute-0-38 machine x86_64 user fdu0 Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations A difference found, saving. mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10552 (13) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (5660 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (5660 voxels, peak = 13), gca=12.8 gca peak = 0.14982 (20) mri peak = 0.09917 (15) Right_Lateral_Ventricle (43): linear fit = 0.55 x + 0.0 (5023 voxels, overlap=0.278) Right_Lateral_Ventricle (43): linear fit = 0.55 x + 0.0 (5023 voxels, peak = 11), gca=11.0 gca peak = 0.28003 (97) mri peak = 0.09589 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (362 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (362 voxels, peak = 97), gca=97.0 gca peak = 0.18160 (96) mri peak = 0.08970 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (440 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (440 voxels, peak = 96), gca=96.0 gca peak = 0.27536 (62) mri peak = 0.07932 (63) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (632 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (632 voxels, peak = 59), gca=58.9 gca peak = 0.32745 (63) mri peak = 0.08381 (62) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (436 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (436 voxels, peak = 58), gca=58.3 gca peak = 0.08597 (105) mri peak = 0.07396 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39763 voxels, overlap=0.785) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39763 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.06876 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39938 voxels, overlap=0.785) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (39938 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.03347 (73) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (9496 voxels, overlap=0.315) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (9496 voxels, peak = 72), gca=72.4 gca peak = 0.08598 (64) mri peak = 0.03005 (77) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (12572 voxels, overlap=0.097) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (12572 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.08701 (72) Right_Caudate (50): linear fit = 1.00 x + 0.0 (764 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (764 voxels, peak = 71), gca=71.0 gca peak = 0.18227 (75) mri peak = 0.07880 (74) Left_Caudate (11): linear fit = 0.95 x + 0.0 (695 voxels, overlap=0.686) Left_Caudate (11): linear fit = 0.95 x + 0.0 (695 voxels, peak = 71), gca=71.2 gca peak = 0.10629 (62) mri peak = 0.04109 (51) Left_Cerebellum_Cortex (8): linear fit = 0.90 x + 0.0 (5684 voxels, overlap=0.558) Left_Cerebellum_Cortex (8): linear fit = 0.90 x + 0.0 (5684 voxels, peak = 56), gca=55.8 gca peak = 0.11668 (59) mri peak = 0.04205 (55) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (6274 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (6274 voxels, peak = 56), gca=56.0 gca peak = 0.17849 (88) mri peak = 0.07149 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5098 voxels, overlap=0.873) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5098 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.09344 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6144 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6144 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.09844 (65) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (214 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (214 voxels, peak = 66), gca=65.6 gca peak = 0.42394 (62) mri peak = 0.07087 (67) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (253 voxels, overlap=0.994) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (253 voxels, peak = 67), gca=66.7 gca peak = 0.10041 (96) mri peak = 0.06577 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3570 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3570 voxels, peak = 96), gca=96.0 gca peak = 0.13978 (88) mri peak = 0.06068 (92) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3989 voxels, overlap=0.872) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3989 voxels, peak = 92), gca=92.4 gca peak = 0.08514 (81) mri peak = 0.07195 (84) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1515 voxels, overlap=0.932) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1515 voxels, peak = 83), gca=83.0 gca peak = 0.09624 (82) mri peak = 0.05429 (78) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1360 voxels, overlap=0.922) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1360 voxels, peak = 80), gca=80.0 gca peak = 0.07543 (88) mri peak = 0.06178 (93) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9477 voxels, overlap=0.657) Brain_Stem (16): linear fit = 1.08 x + 0.0 (9477 voxels, peak = 95), gca=94.6 gca peak = 0.12757 (95) mri peak = 0.07821 (100) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (938 voxels, overlap=0.767) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (938 voxels, peak = 100), gca=99.7 gca peak = 0.17004 (92) mri peak = 0.07545 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1027 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1027 voxels, peak = 97), gca=96.6 gca peak = 0.21361 (36) mri peak = 0.18132 (17) Third_Ventricle (14): linear fit = 0.45 x + 0.0 (177 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.45 x + 0.0 (177 voxels, peak = 16), gca=16.2 gca peak = 0.26069 (23) mri peak = 0.13066 (15) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (574 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (574 voxels, peak = 14), gca=13.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) 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 1.06 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.51 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.25616 (13) mri peak = 0.10552 (13) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (5660 voxels, overlap=0.997) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (5660 voxels, peak = 13), gca=13.3 gca peak = 0.22431 (11) mri peak = 0.09917 (15) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (5023 voxels, overlap=0.998) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (5023 voxels, peak = 12), gca=12.4 gca peak = 0.28002 (97) mri peak = 0.09589 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (362 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (362 voxels, peak = 97), gca=97.0 gca peak = 0.15660 (98) mri peak = 0.08970 (102) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (440 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (440 voxels, peak = 100), gca=100.4 gca peak = 0.26332 (59) mri peak = 0.07932 (63) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (632 voxels, overlap=0.987) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (632 voxels, peak = 60), gca=60.5 gca peak = 0.28887 (58) mri peak = 0.08381 (62) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (436 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (436 voxels, peak = 58), gca=58.0 gca peak = 0.08345 (108) mri peak = 0.07396 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39763 voxels, overlap=0.819) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39763 voxels, peak = 108), gca=108.0 gca peak = 0.08551 (108) mri peak = 0.06876 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39938 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39938 voxels, peak = 108), gca=108.0 gca peak = 0.06961 (72) mri peak = 0.03347 (73) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (9496 voxels, overlap=0.558) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (9496 voxels, peak = 70), gca=70.2 gca peak = 0.07104 (77) mri peak = 0.03005 (77) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (12572 voxels, overlap=0.635) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (12572 voxels, peak = 77), gca=77.0 gca peak = 0.24426 (71) mri peak = 0.08701 (72) Right_Caudate (50): linear fit = 1.00 x + 0.0 (764 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (764 voxels, peak = 71), gca=71.0 gca peak = 0.17712 (71) mri peak = 0.07880 (74) Left_Caudate (11): linear fit = 0.98 x + 0.0 (695 voxels, overlap=0.939) Left_Caudate (11): linear fit = 0.98 x + 0.0 (695 voxels, peak = 69), gca=69.2 gca peak = 0.11935 (56) mri peak = 0.04109 (51) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (5684 voxels, overlap=0.983) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (5684 voxels, peak = 55), gca=54.6 gca peak = 0.12447 (57) mri peak = 0.04205 (55) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (6274 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (6274 voxels, peak = 58), gca=58.4 gca peak = 0.16943 (92) mri peak = 0.07149 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5098 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5098 voxels, peak = 92), gca=92.0 gca peak = 0.15715 (93) mri peak = 0.09344 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6144 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6144 voxels, peak = 93), gca=93.0 gca peak = 0.34509 (65) mri peak = 0.09844 (65) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (214 voxels, overlap=0.996) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (214 voxels, peak = 65), gca=65.0 gca peak = 0.33110 (67) mri peak = 0.07087 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (253 voxels, overlap=0.978) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (253 voxels, peak = 67), gca=67.0 gca peak = 0.10723 (96) mri peak = 0.06577 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3570 voxels, overlap=0.994) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3570 voxels, peak = 96), gca=96.0 gca peak = 0.11283 (92) mri peak = 0.06068 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3989 voxels, overlap=0.967) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3989 voxels, peak = 92), gca=92.0 gca peak = 0.08397 (83) mri peak = 0.07195 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1515 voxels, overlap=0.990) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1515 voxels, peak = 83), gca=83.0 gca peak = 0.11177 (74) mri peak = 0.05429 (78) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1360 voxels, overlap=0.997) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1360 voxels, peak = 74), gca=74.0 gca peak = 0.07200 (92) mri peak = 0.06178 (93) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9477 voxels, overlap=0.836) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9477 voxels, peak = 92), gca=92.0 gca peak = 0.10813 (99) mri peak = 0.07821 (100) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (938 voxels, overlap=0.835) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (938 voxels, peak = 99), gca=99.0 gca peak = 0.14351 (97) mri peak = 0.07545 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1027 voxels, overlap=0.900) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1027 voxels, peak = 97), gca=97.0 gca peak = 0.29956 (19) mri peak = 0.18132 (17) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (177 voxels, overlap=0.893) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (177 voxels, peak = 16), gca=15.7 gca peak = 0.36617 (12) mri peak = 0.13066 (15) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (574 voxels, overlap=0.965) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (574 voxels, peak = 14), gca=13.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24950 (33) gca peak CSF = 0.26689 (21) gca peak Left_Accumbens_area = 0.36291 (67) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.64071 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31138 (30) gca peak Right_Accumbens_area = 0.37937 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (23) gca peak WM_hypointensities = 0.14652 (84) gca peak non_WM_hypointensities = 0.11940 (54) gca peak Optic_Chiasm = 0.34490 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.03 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 24212 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 378 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 95637 changed. image ll: -2.239, PF=1.000 pass 2: 15182 changed. image ll: -2.237, PF=1.000 pass 3: 4731 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 51 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/cc_up.lta AD08 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/norm.mgz 12828 voxels in left wm, 28203 in right wm, xrange [122, 130] searching rotation angles z=[-9 5], y=[-9 5] searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 global minimum found at slice 126.0, rotations (-1.91, -2.55) final transformation (x=126.0, yr=-1.915, zr=-2.551): 0.998 0.045 -0.033 0.259; -0.044 0.999 0.001 16.575; 0.033 0.000 0.999 25.844; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 142 188 eigenvectors: -0.000 -0.000 1.000; 0.038 -0.999 -0.000; 0.999 0.038 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Wed Jul 6 20:42:44 EDT 2016 mri_seg_diff --seg aseg.auto.mgz --diff-in aseg.manedit.mgz --merged aseg.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_seg_diff --seg aseg.auto.mgz --diff-in aseg.manedit.mgz --merged aseg.mgz sysname Linux hostname compute-0-38 machine x86_64 user fdu0 Seg1 aseg.auto.mgz Seg2 (null) Diff (null) InDiff aseg.manedit.mgz Merged aseg.mgz ForceDiff 0 Merging difference segmentation #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 6 20:42:51 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_normalize -f /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 0 control points... MRI3dGentleNormalize: mean = 0.0, nctrl = 0, norm failed using MR volume brainmask.mgz to mask input volume... removing outliers in the aseg WM... 3590 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 50 seconds. white matter peak found at 111 white matter peak found at 108 gm peak at 70 (70), valley at 32 (32) csf peak at 12, setting threshold to 50 white matter peak found at 111 white matter peak found at 110 gm peak at 69 (69), valley at 58 (58) csf peak at 12, setting threshold to 50 #-------------------------------------------- #@# Mask BFS Wed Jul 6 20:47:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1533388 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jul 6 20:47:47 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-38 machine x86_64 user fdu0 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-38 machine x86_64 user fdu0 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.6 +- 5.6 [80.0 --> 125.0] GM (69.0) : 67.0 +- 11.6 [30.0 --> 96.0] setting bottom of white matter range to 78.5 setting top of gray matter range to 90.1 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... 11575 sparsely connected voxels removed... thickening thin strands.... 20 segments, 7479 filled 1919 bright non-wm voxels segmented. 5802 diagonally connected voxels added... white matter segmentation took 1.9 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.64 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 1686 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52650 voxels turned on, 64258 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+): 456 found - 456 modified | TOTAL: 456 pass 2 (xy+): 0 found - 456 modified | TOTAL: 456 pass 1 (xy-): 406 found - 406 modified | TOTAL: 862 pass 2 (xy-): 0 found - 406 modified | TOTAL: 862 pass 1 (yz+): 338 found - 338 modified | TOTAL: 1200 pass 2 (yz+): 0 found - 338 modified | TOTAL: 1200 pass 1 (yz-): 302 found - 302 modified | TOTAL: 1502 pass 2 (yz-): 0 found - 302 modified | TOTAL: 1502 pass 1 (xz+): 284 found - 284 modified | TOTAL: 1786 pass 2 (xz+): 0 found - 284 modified | TOTAL: 1786 pass 1 (xz-): 268 found - 268 modified | TOTAL: 2054 pass 2 (xz-): 0 found - 268 modified | TOTAL: 2054 Iteration Number : 1 pass 1 (+++): 75 found - 75 modified | TOTAL: 75 pass 2 (+++): 0 found - 75 modified | TOTAL: 75 pass 1 (+++): 71 found - 71 modified | TOTAL: 146 pass 2 (+++): 0 found - 71 modified | TOTAL: 146 pass 1 (+++): 69 found - 69 modified | TOTAL: 215 pass 2 (+++): 0 found - 69 modified | TOTAL: 215 pass 1 (+++): 66 found - 66 modified | TOTAL: 281 pass 2 (+++): 0 found - 66 modified | TOTAL: 281 Iteration Number : 1 pass 1 (++): 300 found - 300 modified | TOTAL: 300 pass 2 (++): 0 found - 300 modified | TOTAL: 300 pass 1 (+-): 253 found - 253 modified | TOTAL: 553 pass 2 (+-): 1 found - 254 modified | TOTAL: 554 pass 3 (+-): 0 found - 254 modified | TOTAL: 554 pass 1 (--): 267 found - 267 modified | TOTAL: 821 pass 2 (--): 2 found - 269 modified | TOTAL: 823 pass 3 (--): 0 found - 269 modified | TOTAL: 823 pass 1 (-+): 245 found - 245 modified | TOTAL: 1068 pass 2 (-+): 0 found - 245 modified | TOTAL: 1068 Iteration Number : 2 pass 1 (xy+): 34 found - 34 modified | TOTAL: 34 pass 2 (xy+): 0 found - 34 modified | TOTAL: 34 pass 1 (xy-): 22 found - 22 modified | TOTAL: 56 pass 2 (xy-): 0 found - 22 modified | TOTAL: 56 pass 1 (yz+): 27 found - 27 modified | TOTAL: 83 pass 2 (yz+): 0 found - 27 modified | TOTAL: 83 pass 1 (yz-): 29 found - 29 modified | TOTAL: 112 pass 2 (yz-): 0 found - 29 modified | TOTAL: 112 pass 1 (xz+): 19 found - 19 modified | TOTAL: 131 pass 2 (xz+): 0 found - 19 modified | TOTAL: 131 pass 1 (xz-): 20 found - 20 modified | TOTAL: 151 pass 2 (xz-): 0 found - 20 modified | TOTAL: 151 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 pass 1 (+++): 1 found - 1 modified | TOTAL: 7 pass 2 (+++): 0 found - 1 modified | TOTAL: 7 pass 1 (+++): 3 found - 3 modified | TOTAL: 10 pass 2 (+++): 0 found - 3 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 12 found - 12 modified | TOTAL: 12 pass 2 (++): 0 found - 12 modified | TOTAL: 12 pass 1 (+-): 11 found - 11 modified | TOTAL: 23 pass 2 (+-): 0 found - 11 modified | TOTAL: 23 pass 1 (--): 13 found - 13 modified | TOTAL: 36 pass 2 (--): 1 found - 14 modified | TOTAL: 37 pass 3 (--): 0 found - 14 modified | TOTAL: 37 pass 1 (-+): 7 found - 7 modified | TOTAL: 44 pass 2 (-+): 0 found - 7 modified | TOTAL: 44 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 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 (--): 3 found - 3 modified | TOTAL: 3 pass 2 (--): 0 found - 3 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3626 (out of 556918: 0.651083) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Wed Jul 6 20:50:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.008 0.012 -0.013 -1.938; -0.006 1.176 0.061 -38.134; 0.014 -0.024 0.981 -9.032; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1319 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75) no need to search using seed (126, 104, 94), TAL = (2.0, -34.0, 24.0) talairach voxel to voxel transform 0.991 -0.010 0.014 1.658; 0.005 0.849 -0.052 31.924; -0.015 0.021 1.018 9.956; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 104, 94) --> (2.0, -34.0, 24.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, -34.00, 24.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -34.00, 24.00) SRC: (108.96, 115.91, 106.20) search lh wm seed point around talairach space (-16.00, -34.00, 24.00), SRC: (144.65, 116.11, 105.68) 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 Wed Jul 6 20:51:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 6 found - 6 modified | TOTAL: 8 pass 2 (xy-): 0 found - 6 modified | TOTAL: 8 pass 1 (yz+): 4 found - 4 modified | TOTAL: 12 pass 2 (yz+): 0 found - 4 modified | TOTAL: 12 pass 1 (yz-): 3 found - 3 modified | TOTAL: 15 pass 2 (yz-): 0 found - 3 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 2 found - 2 modified | TOTAL: 19 pass 2 (xz-): 0 found - 2 modified | TOTAL: 19 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 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 0 found - 0 modified | TOTAL: 4 pass 1 (--): 1 found - 1 modified | TOTAL: 5 pass 2 (--): 0 found - 1 modified | TOTAL: 5 pass 1 (-+): 0 found - 0 modified | TOTAL: 5 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 = 24 (out of 271450: 0.008841) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 50: 1865 vertices, 1997 faces slice 60: 7868 vertices, 8157 faces slice 70: 18219 vertices, 18592 faces slice 80: 30833 vertices, 31265 faces slice 90: 43267 vertices, 43656 faces slice 100: 54370 vertices, 54804 faces slice 110: 67216 vertices, 67660 faces slice 120: 79594 vertices, 80064 faces slice 130: 91094 vertices, 91536 faces slice 140: 102374 vertices, 102807 faces slice 150: 111961 vertices, 112356 faces slice 160: 119627 vertices, 119969 faces slice 170: 126674 vertices, 127012 faces slice 180: 133247 vertices, 133571 faces slice 190: 138309 vertices, 138600 faces slice 200: 142077 vertices, 142281 faces slice 210: 142700 vertices, 142832 faces slice 220: 142700 vertices, 142832 faces slice 230: 142700 vertices, 142832 faces slice 240: 142700 vertices, 142832 faces slice 250: 142700 vertices, 142832 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... 142700 voxel in cpt #1: X=-132 [v=142700,e=428496,f=285664] located at (-25.861780, -12.870456, 7.929713) For the whole surface: X=-132 [v=142700,e=428496,f=285664] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jul 6 20:51:37 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 Wed Jul 6 20:51:42 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts avg radius = 47.1 mm, total surface area = 72737 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.110 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.055 (target=0.015) step 020: RMS=0.049 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Jul 6 20:52:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.57 (0.00-->6.92) (max @ vno 77466 --> 77483) face area 0.03 +- 0.03 (-0.20-->0.55) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.221, avgs=0 005/300: dt: 0.9000, rms radial error=175.965, avgs=0 010/300: dt: 0.9000, rms radial error=175.412, avgs=0 015/300: dt: 0.9000, rms radial error=174.686, avgs=0 020/300: dt: 0.9000, rms radial error=173.859, avgs=0 025/300: dt: 0.9000, rms radial error=172.973, avgs=0 030/300: dt: 0.9000, rms radial error=172.056, avgs=0 035/300: dt: 0.9000, rms radial error=171.121, avgs=0 040/300: dt: 0.9000, rms radial error=170.179, avgs=0 045/300: dt: 0.9000, rms radial error=169.235, avgs=0 050/300: dt: 0.9000, rms radial error=168.292, avgs=0 055/300: dt: 0.9000, rms radial error=167.351, avgs=0 060/300: dt: 0.9000, rms radial error=166.414, avgs=0 065/300: dt: 0.9000, rms radial error=165.481, avgs=0 070/300: dt: 0.9000, rms radial error=164.553, avgs=0 075/300: dt: 0.9000, rms radial error=163.629, avgs=0 080/300: dt: 0.9000, rms radial error=162.710, avgs=0 085/300: dt: 0.9000, rms radial error=161.796, avgs=0 090/300: dt: 0.9000, rms radial error=160.886, avgs=0 095/300: dt: 0.9000, rms radial error=159.982, avgs=0 100/300: dt: 0.9000, rms radial error=159.082, avgs=0 105/300: dt: 0.9000, rms radial error=158.188, avgs=0 110/300: dt: 0.9000, rms radial error=157.298, avgs=0 115/300: dt: 0.9000, rms radial error=156.413, avgs=0 120/300: dt: 0.9000, rms radial error=155.532, avgs=0 125/300: dt: 0.9000, rms radial error=154.657, avgs=0 130/300: dt: 0.9000, rms radial error=153.786, avgs=0 135/300: dt: 0.9000, rms radial error=152.920, avgs=0 140/300: dt: 0.9000, rms radial error=152.059, avgs=0 145/300: dt: 0.9000, rms radial error=151.202, avgs=0 150/300: dt: 0.9000, rms radial error=150.350, avgs=0 155/300: dt: 0.9000, rms radial error=149.503, avgs=0 160/300: dt: 0.9000, rms radial error=148.660, avgs=0 165/300: dt: 0.9000, rms radial error=147.822, avgs=0 170/300: dt: 0.9000, rms radial error=146.989, avgs=0 175/300: dt: 0.9000, rms radial error=146.160, avgs=0 180/300: dt: 0.9000, rms radial error=145.336, avgs=0 185/300: dt: 0.9000, rms radial error=144.517, avgs=0 190/300: dt: 0.9000, rms radial error=143.702, avgs=0 195/300: dt: 0.9000, rms radial error=142.892, avgs=0 200/300: dt: 0.9000, rms radial error=142.086, avgs=0 205/300: dt: 0.9000, rms radial error=141.285, avgs=0 210/300: dt: 0.9000, rms radial error=140.488, avgs=0 215/300: dt: 0.9000, rms radial error=139.695, avgs=0 220/300: dt: 0.9000, rms radial error=138.908, avgs=0 225/300: dt: 0.9000, rms radial error=138.124, avgs=0 230/300: dt: 0.9000, rms radial error=137.345, avgs=0 235/300: dt: 0.9000, rms radial error=136.571, avgs=0 240/300: dt: 0.9000, rms radial error=135.800, avgs=0 245/300: dt: 0.9000, rms radial error=135.034, avgs=0 250/300: dt: 0.9000, rms radial error=134.272, avgs=0 255/300: dt: 0.9000, rms radial error=133.515, avgs=0 260/300: dt: 0.9000, rms radial error=132.761, avgs=0 265/300: dt: 0.9000, rms radial error=132.012, avgs=0 270/300: dt: 0.9000, rms radial error=131.267, avgs=0 275/300: dt: 0.9000, rms radial error=130.526, avgs=0 280/300: dt: 0.9000, rms radial error=129.790, avgs=0 285/300: dt: 0.9000, rms radial error=129.058, avgs=0 290/300: dt: 0.9000, rms radial error=128.330, avgs=0 295/300: dt: 0.9000, rms radial error=127.605, avgs=0 300/300: dt: 0.9000, rms radial error=126.885, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16730.28 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2816.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 307.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00869 epoch 4 (K=640.0), pass 1, starting sse = 20.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00656 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Jul 6 20:58:17 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 AD08 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-132 (nv=142700, nf=285664, ne=428496, g=67) 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... 5608 ambiguous faces found in tessellation segmenting defects... 84 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 44 into 34 83 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5625 (-4.7813) -vertex loglikelihood: -6.9072 (-3.4536) -normal dot loglikelihood: -3.6153 (-3.6153) -quad curv loglikelihood: -6.6806 (-3.3403) Total Loglikelihood : -26.7657 CORRECTING DEFECT 0 (vertices=108, convex hull=110) After retessellation of defect 0, euler #=-78 (139094,415444,276272) : difference with theory (-80) = -2 CORRECTING DEFECT 1 (vertices=19, convex hull=47) After retessellation of defect 1, euler #=-77 (139102,415483,276304) : difference with theory (-79) = -2 CORRECTING DEFECT 2 (vertices=5, convex hull=24) After retessellation of defect 2, euler #=-76 (139104,415497,276317) : difference with theory (-78) = -2 CORRECTING DEFECT 3 (vertices=27, convex hull=56) After retessellation of defect 3, euler #=-75 (139118,415563,276370) : difference with theory (-77) = -2 CORRECTING DEFECT 4 (vertices=22, convex hull=58) After retessellation of defect 4, euler #=-74 (139127,415613,276412) : difference with theory (-76) = -2 CORRECTING DEFECT 5 (vertices=17, convex hull=49) After retessellation of defect 5, euler #=-73 (139135,415656,276448) : difference with theory (-75) = -2 CORRECTING DEFECT 6 (vertices=31, convex hull=46) After retessellation of defect 6, euler #=-72 (139144,415697,276481) : difference with theory (-74) = -2 CORRECTING DEFECT 7 (vertices=27, convex hull=59) After retessellation of defect 7, euler #=-71 (139163,415777,276543) : difference with theory (-73) = -2 CORRECTING DEFECT 8 (vertices=51, convex hull=83) After retessellation of defect 8, euler #=-70 (139199,415921,276652) : difference with theory (-72) = -2 CORRECTING DEFECT 9 (vertices=43, convex hull=71) After retessellation of defect 9, euler #=-69 (139224,416025,276732) : difference with theory (-71) = -2 CORRECTING DEFECT 10 (vertices=22, convex hull=50) After retessellation of defect 10, euler #=-68 (139233,416071,276770) : difference with theory (-70) = -2 CORRECTING DEFECT 11 (vertices=25, convex hull=54) After retessellation of defect 11, euler #=-67 (139242,416116,276807) : difference with theory (-69) = -2 CORRECTING DEFECT 12 (vertices=36, convex hull=86) After retessellation of defect 12, euler #=-66 (139253,416187,276868) : difference with theory (-68) = -2 CORRECTING DEFECT 13 (vertices=5, convex hull=26) After retessellation of defect 13, euler #=-65 (139255,416200,276880) : difference with theory (-67) = -2 CORRECTING DEFECT 14 (vertices=36, convex hull=74) After retessellation of defect 14, euler #=-64 (139268,416269,276937) : difference with theory (-66) = -2 CORRECTING DEFECT 15 (vertices=10, convex hull=13) After retessellation of defect 15, euler #=-63 (139269,416274,276942) : difference with theory (-65) = -2 CORRECTING DEFECT 16 (vertices=22, convex hull=42) After retessellation of defect 16, euler #=-62 (139280,416320,276978) : difference with theory (-64) = -2 CORRECTING DEFECT 17 (vertices=47, convex hull=47) After retessellation of defect 17, euler #=-61 (139292,416374,277021) : difference with theory (-63) = -2 CORRECTING DEFECT 18 (vertices=30, convex hull=51) After retessellation of defect 18, euler #=-60 (139307,416436,277069) : difference with theory (-62) = -2 CORRECTING DEFECT 19 (vertices=36, convex hull=27) After retessellation of defect 19, euler #=-59 (139313,416460,277088) : difference with theory (-61) = -2 CORRECTING DEFECT 20 (vertices=58, convex hull=83) After retessellation of defect 20, euler #=-58 (139348,416594,277188) : difference with theory (-60) = -2 CORRECTING DEFECT 21 (vertices=21, convex hull=38) After retessellation of defect 21, euler #=-57 (139352,416621,277212) : difference with theory (-59) = -2 CORRECTING DEFECT 22 (vertices=12, convex hull=21) After retessellation of defect 22, euler #=-56 (139357,416641,277228) : difference with theory (-58) = -2 CORRECTING DEFECT 23 (vertices=274, convex hull=151) After retessellation of defect 23, euler #=-55 (139422,416903,277426) : difference with theory (-57) = -2 CORRECTING DEFECT 24 (vertices=24, convex hull=57) After retessellation of defect 24, euler #=-54 (139432,416950,277464) : difference with theory (-56) = -2 CORRECTING DEFECT 25 (vertices=56, convex hull=79) After retessellation of defect 25, euler #=-53 (139460,417070,277557) : difference with theory (-55) = -2 CORRECTING DEFECT 26 (vertices=23, convex hull=21) After retessellation of defect 26, euler #=-52 (139462,417082,277568) : difference with theory (-54) = -2 CORRECTING DEFECT 27 (vertices=9, convex hull=14) After retessellation of defect 27, euler #=-51 (139462,417085,277572) : difference with theory (-53) = -2 CORRECTING DEFECT 28 (vertices=31, convex hull=57) After retessellation of defect 28, euler #=-50 (139475,417146,277621) : difference with theory (-52) = -2 CORRECTING DEFECT 29 (vertices=15, convex hull=20) After retessellation of defect 29, euler #=-49 (139476,417156,277631) : difference with theory (-51) = -2 CORRECTING DEFECT 30 (vertices=21, convex hull=26) After retessellation of defect 30, euler #=-48 (139479,417175,277648) : difference with theory (-50) = -2 CORRECTING DEFECT 31 (vertices=71, convex hull=61) After retessellation of defect 31, euler #=-47 (139512,417297,277738) : difference with theory (-49) = -2 CORRECTING DEFECT 32 (vertices=28, convex hull=60) After retessellation of defect 32, euler #=-46 (139521,417349,277782) : difference with theory (-48) = -2 CORRECTING DEFECT 33 (vertices=64, convex hull=91) After retessellation of defect 33, euler #=-45 (139541,417447,277861) : difference with theory (-47) = -2 CORRECTING DEFECT 34 (vertices=132, convex hull=124) After retessellation of defect 34, euler #=-43 (139591,417663,278029) : difference with theory (-46) = -3 CORRECTING DEFECT 35 (vertices=70, convex hull=96) After retessellation of defect 35, euler #=-43 (139609,417758,278106) : difference with theory (-45) = -2 CORRECTING DEFECT 36 (vertices=63, convex hull=100) After retessellation of defect 36, euler #=-42 (139640,417892,278210) : difference with theory (-44) = -2 CORRECTING DEFECT 37 (vertices=21, convex hull=54) After retessellation of defect 37, euler #=-41 (139650,417943,278252) : difference with theory (-43) = -2 CORRECTING DEFECT 38 (vertices=33, convex hull=69) After retessellation of defect 38, euler #=-40 (139661,417999,278298) : difference with theory (-42) = -2 CORRECTING DEFECT 39 (vertices=9, convex hull=32) After retessellation of defect 39, euler #=-39 (139663,418016,278314) : difference with theory (-41) = -2 CORRECTING DEFECT 40 (vertices=32, convex hull=42) After retessellation of defect 40, euler #=-38 (139667,418047,278342) : difference with theory (-40) = -2 CORRECTING DEFECT 41 (vertices=11, convex hull=17) After retessellation of defect 41, euler #=-37 (139667,418051,278347) : difference with theory (-39) = -2 CORRECTING DEFECT 42 (vertices=126, convex hull=103) After retessellation of defect 42, euler #=-37 (139676,418131,278418) : difference with theory (-38) = -1 CORRECTING DEFECT 43 (vertices=31, convex hull=65) After retessellation of defect 43, euler #=-36 (139693,418206,278477) : difference with theory (-37) = -1 CORRECTING DEFECT 44 (vertices=34, convex hull=61) After retessellation of defect 44, euler #=-35 (139702,418253,278516) : difference with theory (-36) = -1 CORRECTING DEFECT 45 (vertices=509, convex hull=97) After retessellation of defect 45, euler #=-34 (139749,418436,278653) : difference with theory (-35) = -1 CORRECTING DEFECT 46 (vertices=25, convex hull=47) After retessellation of defect 46, euler #=-33 (139758,418478,278687) : difference with theory (-34) = -1 CORRECTING DEFECT 47 (vertices=88, convex hull=90) After retessellation of defect 47, euler #=-32 (139804,418649,278813) : difference with theory (-33) = -1 CORRECTING DEFECT 48 (vertices=30, convex hull=68) After retessellation of defect 48, euler #=-31 (139824,418733,278878) : difference with theory (-32) = -1 CORRECTING DEFECT 49 (vertices=31, convex hull=55) After retessellation of defect 49, euler #=-30 (139836,418793,278927) : difference with theory (-31) = -1 CORRECTING DEFECT 50 (vertices=19, convex hull=27) After retessellation of defect 50, euler #=-29 (139840,418815,278946) : difference with theory (-30) = -1 CORRECTING DEFECT 51 (vertices=36, convex hull=58) After retessellation of defect 51, euler #=-28 (139857,418887,279002) : difference with theory (-29) = -1 CORRECTING DEFECT 52 (vertices=38, convex hull=34) After retessellation of defect 52, euler #=-27 (139862,418917,279028) : difference with theory (-28) = -1 CORRECTING DEFECT 53 (vertices=17, convex hull=27) After retessellation of defect 53, euler #=-26 (139866,418934,279042) : difference with theory (-27) = -1 CORRECTING DEFECT 54 (vertices=91, convex hull=41) After retessellation of defect 54, euler #=-25 (139877,418982,279080) : difference with theory (-26) = -1 CORRECTING DEFECT 55 (vertices=44, convex hull=88) After retessellation of defect 55, euler #=-24 (139889,419059,279146) : difference with theory (-25) = -1 CORRECTING DEFECT 56 (vertices=26, convex hull=52) After retessellation of defect 56, euler #=-23 (139904,419122,279195) : difference with theory (-24) = -1 CORRECTING DEFECT 57 (vertices=82, convex hull=102) After retessellation of defect 57, euler #=-22 (139954,419318,279342) : difference with theory (-23) = -1 CORRECTING DEFECT 58 (vertices=30, convex hull=60) After retessellation of defect 58, euler #=-21 (139973,419400,279406) : difference with theory (-22) = -1 CORRECTING DEFECT 59 (vertices=23, convex hull=23) After retessellation of defect 59, euler #=-20 (139976,419417,279421) : difference with theory (-21) = -1 CORRECTING DEFECT 60 (vertices=18, convex hull=27) After retessellation of defect 60, euler #=-19 (139978,419430,279433) : difference with theory (-20) = -1 CORRECTING DEFECT 61 (vertices=10, convex hull=25) Warning - incorrect dp selected!!!!(-92.396694 >= -92.396702 ) After retessellation of defect 61, euler #=-18 (139980,419444,279446) : difference with theory (-19) = -1 CORRECTING DEFECT 62 (vertices=32, convex hull=74) After retessellation of defect 62, euler #=-17 (139989,419498,279492) : difference with theory (-18) = -1 CORRECTING DEFECT 63 (vertices=20, convex hull=25) After retessellation of defect 63, euler #=-16 (139993,419517,279508) : difference with theory (-17) = -1 CORRECTING DEFECT 64 (vertices=30, convex hull=84) After retessellation of defect 64, euler #=-15 (140011,419604,279578) : difference with theory (-16) = -1 CORRECTING DEFECT 65 (vertices=23, convex hull=63) After retessellation of defect 65, euler #=-14 (140020,419654,279620) : difference with theory (-15) = -1 CORRECTING DEFECT 66 (vertices=44, convex hull=61) After retessellation of defect 66, euler #=-13 (140037,419724,279674) : difference with theory (-14) = -1 CORRECTING DEFECT 67 (vertices=19, convex hull=54) After retessellation of defect 67, euler #=-12 (140048,419781,279721) : difference with theory (-13) = -1 CORRECTING DEFECT 68 (vertices=49, convex hull=95) After retessellation of defect 68, euler #=-11 (140074,419900,279815) : difference with theory (-12) = -1 CORRECTING DEFECT 69 (vertices=24, convex hull=57) After retessellation of defect 69, euler #=-10 (140083,419955,279862) : difference with theory (-11) = -1 CORRECTING DEFECT 70 (vertices=23, convex hull=60) After retessellation of defect 70, euler #=-9 (140097,420019,279913) : difference with theory (-10) = -1 CORRECTING DEFECT 71 (vertices=16, convex hull=51) After retessellation of defect 71, euler #=-8 (140103,420055,279944) : difference with theory (-9) = -1 CORRECTING DEFECT 72 (vertices=18, convex hull=51) After retessellation of defect 72, euler #=-7 (140113,420106,279986) : difference with theory (-8) = -1 CORRECTING DEFECT 73 (vertices=48, convex hull=76) After retessellation of defect 73, euler #=-6 (140138,420211,280067) : difference with theory (-7) = -1 CORRECTING DEFECT 74 (vertices=20, convex hull=23) After retessellation of defect 74, euler #=-5 (140140,420225,280080) : difference with theory (-6) = -1 CORRECTING DEFECT 75 (vertices=33, convex hull=68) After retessellation of defect 75, euler #=-4 (140157,420303,280142) : difference with theory (-5) = -1 CORRECTING DEFECT 76 (vertices=28, convex hull=56) After retessellation of defect 76, euler #=-3 (140166,420347,280178) : difference with theory (-4) = -1 CORRECTING DEFECT 77 (vertices=44, convex hull=79) After retessellation of defect 77, euler #=-3 (140184,420436,280249) : difference with theory (-3) = 0 CORRECTING DEFECT 78 (vertices=24, convex hull=54) After retessellation of defect 78, euler #=-2 (140192,420480,280286) : difference with theory (-2) = 0 CORRECTING DEFECT 79 (vertices=45, convex hull=77) After retessellation of defect 79, euler #=-1 (140217,420587,280369) : difference with theory (-1) = 0 CORRECTING DEFECT 80 (vertices=24, convex hull=49) After retessellation of defect 80, euler #=0 (140231,420648,280417) : difference with theory (0) = 0 CORRECTING DEFECT 81 (vertices=11, convex hull=30) After retessellation of defect 81, euler #=1 (140233,420664,280432) : difference with theory (1) = 0 CORRECTING DEFECT 82 (vertices=45, convex hull=72) After retessellation of defect 82, euler #=2 (140242,420720,280480) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.24 (0.04-->16.98) (max @ vno 101182 --> 109348) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.24 (0.04-->16.98) (max @ vno 101182 --> 109348) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 337 mutations (35.3%), 617 crossovers (64.7%), 250 vertices were eliminated building final representation... 2458 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140242, nf=280480, ne=420720, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 55.1 minutes 0 defective edges removing intersecting faces 000: 377 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 140242 - 420720 + 280480 = 2 --> 0 holes F =2V-4: 280480 = 280484-4 (0) 2E=3F: 841440 = 841440 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 63 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jul 6 21:53:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD08 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 20465 bright wm thresholded. 2114 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 94.0 +- 8.5 [70.0 --> 110.0] GM (79.0) : 76.6 +- 14.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 110.5 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 34.4 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 19.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->3.63) (max @ vno 8665 --> 139077) face area 0.27 +- 0.13 (0.00-->1.78) mean absolute distance = 0.92 +- 1.27 5285 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=64 using class modes intead of means.... mean inside = 91.2, mean outside = 69.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=78.0, 151 (151) missing vertices, mean dist 0.1 [1.1 (%38.8)->0.8 (%61.2))] %37 local maxima, %58 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.28 (0.09-->4.08) (max @ vno 139586 --> 97134) face area 0.27 +- 0.14 (0.00-->2.22) mean absolute distance = 0.50 +- 0.87 5804 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6536576.0, rms=12.08 001: dt: 0.5000, sse=7428437.5, rms=8.42 002: dt: 0.5000, sse=7923108.0, rms=6.34 003: dt: 0.5000, sse=8373418.0, rms=5.23 004: dt: 0.5000, sse=8641639.0, rms=4.65 005: dt: 0.5000, sse=8894611.0, rms=4.35 006: dt: 0.5000, sse=8957373.0, rms=4.19 007: dt: 0.5000, sse=9094307.0, rms=4.10 008: dt: 0.5000, sse=9063300.0, rms=4.04 rms = 4.01, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9124901.0, rms=4.01 010: dt: 0.2500, sse=6013530.5, rms=2.96 011: dt: 0.2500, sse=5664551.5, rms=2.60 012: dt: 0.2500, sse=5405735.0, rms=2.53 013: dt: 0.2500, sse=5321785.0, rms=2.46 rms = 2.44, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5242035.0, rms=2.44 015: dt: 0.1250, sse=5077410.5, rms=2.32 rms = 2.30, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=5037747.5, rms=2.30 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.5, 182 (40) missing vertices, mean dist -0.3 [0.7 (%59.0)->0.3 (%41.0))] %50 local maxima, %45 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 +- 0.27 (0.08-->4.13) (max @ vno 139586 --> 97134) face area 0.34 +- 0.17 (0.00-->2.97) mean absolute distance = 0.38 +- 0.54 4447 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5607579.5, rms=4.73 017: dt: 0.5000, sse=6273132.0, rms=3.52 rms = 3.76, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5723858.5, rms=2.77 019: dt: 0.2500, sse=5527801.0, rms=2.35 020: dt: 0.2500, sse=5389221.5, rms=2.15 021: dt: 0.2500, sse=5343576.0, rms=2.08 rms = 2.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5287365.5, rms=2.04 023: dt: 0.1250, sse=5175084.0, rms=1.93 rms = 1.91, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5127714.0, rms=1.91 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.4, 167 (25) missing vertices, mean dist -0.2 [0.5 (%65.7)->0.2 (%34.3))] %69 local maxima, %26 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 0.88 +- 0.27 (0.09-->4.22) (max @ vno 139586 --> 97134) face area 0.33 +- 0.17 (0.00-->3.09) mean absolute distance = 0.29 +- 0.42 4190 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5491750.0, rms=4.26 025: dt: 0.5000, sse=5963322.0, rms=3.30 rms = 3.64, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5515966.0, rms=2.40 027: dt: 0.2500, sse=5481923.5, rms=2.00 028: dt: 0.2500, sse=5423181.5, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5386807.0, rms=1.85 030: dt: 0.1250, sse=5238834.0, rms=1.71 rms = 1.69, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5192673.5, rms=1.69 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.6, 178 (21) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.2 (%42.6))] %77 local maxima, %18 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5263296.5, rms=2.45 rms = 2.57, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5413255.5, rms=1.75 033: dt: 0.2500, sse=5747103.0, rms=1.30 rms = 1.32, time step reduction 2 of 3 to 0.125... rms = 1.28, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5733288.0, rms=1.28 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group generating cortex label... 14 non-cortical segments detected only using segment with 2325 vertices erasing segment 1 (vno[0] = 70001) erasing segment 2 (vno[0] = 72331) erasing segment 3 (vno[0] = 89420) erasing segment 4 (vno[0] = 92714) erasing segment 5 (vno[0] = 94989) erasing segment 6 (vno[0] = 104874) erasing segment 7 (vno[0] = 105814) erasing segment 8 (vno[0] = 105842) erasing segment 9 (vno[0] = 105862) erasing segment 10 (vno[0] = 106713) erasing segment 11 (vno[0] = 108379) erasing segment 12 (vno[0] = 108447) erasing segment 13 (vno[0] = 110080) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/lh.cortex.label writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area vertex spacing 0.88 +- 0.27 (0.04-->4.26) (max @ vno 97134 --> 139586) face area 0.32 +- 0.17 (0.00-->3.02) refinement took 6.3 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jul 6 21:59:52 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 Wed Jul 6 21:59:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.3 mm, total surface area = 81859 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.122 (target=0.015) step 005: RMS=0.085 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.053 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.016 (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 302 vertices thresholded to be in k1 ~ [-0.29 0.53], k2 ~ [-0.09 0.07] total integrated curvature = 0.502*4pi (6.302) --> 0 handles ICI = 1.5, FI = 9.4, variation=160.717 166 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 170 vertices thresholded to be in [-0.15 0.26] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #-------------------------------------------- #@# Sphere lh Wed Jul 6 22:02:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.09 hours scaling brain by 0.295... pass 1: epoch 1 of 3 starting distance error %19.00 pass 1: epoch 2 of 3 starting distance error %18.92 unfolding complete - removing small folds... starting distance error %18.87 removing remaining folds... final distance error %18.90 #-------------------------------------------- #@# Surf Reg lh Wed Jul 6 23:07:45 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.580 curvature mean = 0.024, std = 0.938 curvature mean = 0.028, std = 0.863 curvature mean = -0.017, std = 0.959 curvature mean = 0.012, std = 0.942 curvature mean = -0.019, std = 0.971 curvature mean = 0.005, std = 0.974 curvature mean = -0.023, std = 0.973 curvature mean = 0.001, std = 0.989 curvature mean = -0.034, std = 0.331 curvature mean = 0.001, std = 0.068 curvature mean = 0.076, std = 0.297 curvature mean = 0.000, std = 0.081 curvature mean = 0.040, std = 0.471 curvature mean = 0.000, std = 0.087 curvature mean = 0.024, std = 0.604 curvature mean = 0.001, std = 0.089 curvature mean = 0.009, std = 0.718 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Jul 6 23:45:19 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 Wed Jul 6 23:45:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Jul 6 23:45:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1246 labels changed using aseg relabeling using gibbs priors... 000: 3127 changed, 140242 examined... 001: 720 changed, 13258 examined... 002: 176 changed, 4054 examined... 003: 57 changed, 1023 examined... 004: 22 changed, 339 examined... 005: 12 changed, 129 examined... 006: 4 changed, 69 examined... 007: 6 changed, 23 examined... 008: 4 changed, 27 examined... 009: 0 changed, 18 examined... 273 labels changed using aseg 000: 126 total segments, 82 labels (389 vertices) changed 001: 42 total segments, 4 labels (15 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1957 vertices marked for relabeling... 1957 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Jul 6 23:46:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 20465 bright wm thresholded. 2114 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 94.0 +- 8.5 [70.0 --> 110.0] GM (79.0) : 76.6 +- 14.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 110.5 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 34.4 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 19.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=64 using class modes intead of means.... mean inside = 91.2, mean outside = 69.9 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->3.63) (max @ vno 8665 --> 139077) face area 0.27 +- 0.13 (0.00-->1.78) mean absolute distance = 0.93 +- 1.28 5350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 3 with 442 points - only 1.36% unknown removing 4 vertex label from ripped group deleting segment 7 with 37 points - only 0.00% unknown mean border=78.0, 152 (152) missing vertices, mean dist 0.1 [1.1 (%38.8)->0.8 (%61.2))] %37 local maxima, %58 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.28 (0.09-->3.76) (max @ vno 68809 --> 65116) face area 0.27 +- 0.14 (0.00-->1.99) mean absolute distance = 0.50 +- 0.87 5842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6552842.0, rms=12.07 001: dt: 0.5000, sse=7454261.0, rms=8.41 002: dt: 0.5000, sse=7951210.5, rms=6.34 003: dt: 0.5000, sse=8404685.0, rms=5.23 004: dt: 0.5000, sse=8672549.0, rms=4.64 005: dt: 0.5000, sse=8929870.0, rms=4.34 006: dt: 0.5000, sse=8992582.0, rms=4.19 007: dt: 0.5000, sse=9132031.0, rms=4.10 008: dt: 0.5000, sse=9099035.0, rms=4.04 rms = 4.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9164616.0, rms=4.00 010: dt: 0.2500, sse=6044842.5, rms=2.96 011: dt: 0.2500, sse=5692483.5, rms=2.60 012: dt: 0.2500, sse=5434416.0, rms=2.53 013: dt: 0.2500, sse=5347533.5, rms=2.47 rms = 2.45, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5268282.0, rms=2.45 015: dt: 0.1250, sse=5100403.0, rms=2.32 rms = 2.31, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=5060169.0, rms=2.31 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 328 points - only 1.83% unknown deleting segment 9 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 59 points - only 35.59% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown mean border=80.5, 180 (36) missing vertices, mean dist -0.3 [0.7 (%59.0)->0.3 (%41.0))] %50 local maxima, %45 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 +- 0.27 (0.08-->3.62) (max @ vno 4941 --> 139077) face area 0.34 +- 0.17 (0.00-->2.39) mean absolute distance = 0.38 +- 0.54 4488 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5638249.0, rms=4.73 017: dt: 0.5000, sse=6309014.0, rms=3.52 rms = 3.76, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5758217.5, rms=2.77 019: dt: 0.2500, sse=5560744.0, rms=2.36 020: dt: 0.2500, sse=5422151.0, rms=2.16 021: dt: 0.2500, sse=5377637.0, rms=2.08 rms = 2.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5322279.5, rms=2.04 023: dt: 0.1250, sse=5207634.5, rms=1.94 rms = 1.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5159747.0, rms=1.92 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 338 points - only 1.78% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 48 points - only 33.33% unknown removing 3 vertex label from ripped group deleting segment 13 with 13 points - only 0.00% unknown deleting segment 14 with 5 points - only 40.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=83.3, 168 (23) missing vertices, mean dist -0.2 [0.5 (%65.7)->0.2 (%34.3))] %69 local maxima, %26 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 0.88 +- 0.27 (0.09-->3.70) (max @ vno 110092 --> 109304) face area 0.33 +- 0.17 (0.00-->2.57) mean absolute distance = 0.29 +- 0.42 4206 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5524511.0, rms=4.26 025: dt: 0.5000, sse=6001023.5, rms=3.30 rms = 3.64, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5551531.0, rms=2.40 027: dt: 0.2500, sse=5516627.5, rms=2.01 028: dt: 0.2500, sse=5457070.5, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5421263.0, rms=1.85 030: dt: 0.1250, sse=5273728.0, rms=1.71 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5227965.5, rms=1.70 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 401 points - only 1.50% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 8 with 27 points - only 29.63% unknown deleting segment 9 with 25 points - only 36.00% unknown deleting segment 10 with 30 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 mean border=84.6, 186 (20) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.2 (%42.6))] %77 local maxima, %18 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=5300406.0, rms=2.45 rms = 2.56, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5452801.0, rms=1.75 033: dt: 0.2500, sse=5790372.0, rms=1.30 rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.29, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5776684.0, rms=1.29 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 6 with 12 points - only 50.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 33.33% unknown smoothing surface for 5 iterations... mean border=51.8, 194 (194) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %30 local maxima, %53 large gradients and %13 min vals, 384 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=30757508.0, rms=32.32 001: dt: 0.5000, sse=23489058.0, rms=27.79 002: dt: 0.5000, sse=18131408.0, rms=23.92 003: dt: 0.5000, sse=14754232.0, rms=20.79 004: dt: 0.5000, sse=12853140.0, rms=18.22 005: dt: 0.5000, sse=11433724.0, rms=15.93 006: dt: 0.5000, sse=10400128.0, rms=13.86 007: dt: 0.5000, sse=9520772.0, rms=11.91 008: dt: 0.5000, sse=8996410.0, rms=10.15 009: dt: 0.5000, sse=8662828.0, rms=8.73 010: dt: 0.5000, sse=8726024.0, rms=7.75 011: dt: 0.5000, sse=8693177.0, rms=7.11 012: dt: 0.5000, sse=8836631.0, rms=6.74 013: dt: 0.5000, sse=8856195.0, rms=6.51 014: dt: 0.5000, sse=8937619.0, rms=6.38 015: dt: 0.5000, sse=8963670.0, rms=6.26 016: dt: 0.5000, sse=8991374.0, rms=6.21 017: dt: 0.5000, sse=9004687.0, rms=6.15 rms = 6.10, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=9004395.0, rms=6.10 019: dt: 0.2500, sse=6180831.5, rms=4.84 020: dt: 0.2500, sse=5974802.5, rms=4.47 rms = 4.46, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5785029.5, rms=4.46 022: dt: 0.1250, sse=5117638.0, rms=3.87 023: dt: 0.1250, sse=5039741.0, rms=3.77 rms = 3.76, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4995385.0, rms=3.76 positioning took 2.7 minutes mean border=48.9, 816 (39) missing vertices, mean dist 0.2 [0.1 (%44.7)->0.5 (%55.3))] %45 local maxima, %39 large gradients and %11 min vals, 150 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=5835728.5, rms=6.08 rms = 6.20, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5551875.0, rms=5.29 026: dt: 0.2500, sse=5410220.0, rms=4.77 027: dt: 0.2500, sse=5742131.0, rms=4.60 rms = 4.55, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5866132.5, rms=4.55 029: dt: 0.1250, sse=5379359.0, rms=4.06 030: dt: 0.1250, sse=5365952.0, rms=3.92 rms = 3.87, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5349754.0, rms=3.87 positioning took 0.8 minutes mean border=46.5, 908 (32) missing vertices, mean dist 0.1 [0.1 (%40.8)->0.3 (%59.2))] %59 local maxima, %26 large gradients and %11 min vals, 171 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=5666460.0, rms=5.12 rms = 6.17, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5432502.5, rms=4.37 033: dt: 0.2500, sse=5501489.0, rms=4.11 034: dt: 0.2500, sse=5780536.5, rms=4.04 rms = 4.10, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=5631257.0, rms=3.87 036: dt: 0.1250, sse=5520276.0, rms=3.61 037: dt: 0.1250, sse=5466238.0, rms=3.55 rms = 3.52, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5476543.0, rms=3.52 positioning took 0.9 minutes mean border=45.1, 1489 (31) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))] %63 local maxima, %21 large gradients and %11 min vals, 157 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5556611.0, rms=3.92 rms = 5.55, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5418418.0, rms=3.51 040: dt: 0.2500, sse=5668201.0, rms=3.44 rms = 3.50, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=5588358.0, rms=3.36 042: dt: 0.1250, sse=5531272.0, rms=3.24 043: dt: 0.1250, sse=5528230.0, rms=3.19 rms = 3.16, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5555913.0, rms=3.16 positioning took 0.8 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.03-->5.98) (max @ vno 98271 --> 97182) face area 0.39 +- 0.29 (0.00-->5.10) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed thickness calculation complete, 144:197 truncations. 69914 vertices at 0 distance 94273 vertices at 1 distance 69175 vertices at 2 distance 24600 vertices at 3 distance 6812 vertices at 4 distance 2060 vertices at 5 distance 777 vertices at 6 distance 337 vertices at 7 distance 167 vertices at 8 distance 108 vertices at 9 distance 69 vertices at 10 distance 62 vertices at 11 distance 46 vertices at 12 distance 28 vertices at 13 distance 32 vertices at 14 distance 18 vertices at 15 distance 14 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 9 vertices at 19 distance 13 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.thickness positioning took 12.1 minutes #-------------------------------------------- #@# Surf Volume lh Wed Jul 6 23:58:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Wed Jul 6 23:58:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1779 1158 2315 1.949 0.513 0.154 0.077 35 5.9 bankssts 1179 775 2203 2.547 0.750 0.185 0.093 34 4.4 caudalanteriorcingulate 2942 2008 5204 2.210 0.597 0.190 0.458 1009 23.4 caudalmiddlefrontal 2535 1550 2612 1.622 0.395 0.169 0.089 100 10.8 cuneus 663 432 1543 2.697 0.940 0.190 0.231 27 8.9 entorhinal 4145 2828 8072 2.405 0.593 0.176 0.099 353 19.7 fusiform 7388 4410 8816 1.807 0.527 0.149 0.089 187 25.9 inferiorparietal 4349 2992 7524 2.167 0.581 0.179 0.098 112 17.0 inferiortemporal 1895 1230 2235 1.741 0.653 0.182 0.194 113 13.8 isthmuscingulate 7202 4601 9697 1.920 0.499 0.170 0.086 147 25.5 lateraloccipital 4024 2652 6615 2.202 0.592 0.182 0.107 134 18.8 lateralorbitofrontal 5638 3650 7262 1.791 0.524 0.181 0.093 135 22.6 lingual 3097 1957 4260 2.009 0.770 0.182 0.220 237 26.1 medialorbitofrontal 4546 3079 8073 2.203 0.532 0.174 0.116 159 18.8 middletemporal 1058 697 2305 2.599 0.773 0.172 0.112 31 5.0 parahippocampal 2099 1250 3034 2.257 0.461 0.157 0.104 46 8.9 paracentral 2680 1901 4893 2.243 0.482 0.163 0.085 81 8.7 parsopercularis 1089 707 2079 2.251 0.461 0.216 0.133 42 5.6 parsorbitalis 1807 1215 2650 1.996 0.444 0.165 0.076 35 5.4 parstriangularis 1880 1190 1847 1.686 0.437 0.164 0.086 37 7.0 pericalcarine 7661 4625 10504 2.023 0.629 0.153 0.106 698 34.4 postcentral 1901 1277 2814 2.081 0.646 0.172 0.163 48 5.8 posteriorcingulate 7621 4806 11851 2.289 0.541 0.170 0.209 950 33.7 precentral 6672 4208 7644 1.749 0.479 0.157 0.103 278 25.0 precuneus 1368 907 2600 2.517 0.636 0.179 0.097 44 5.2 rostralanteriorcingulate 7308 5129 12270 2.011 0.571 0.197 0.127 254 36.3 rostralmiddlefrontal 10486 7229 20143 2.348 0.652 0.194 0.143 469 61.5 superiorfrontal 8720 5060 10251 1.889 0.512 0.145 0.131 457 39.7 superiorparietal 5525 3674 10173 2.372 0.555 0.143 0.097 91 14.4 superiortemporal 6454 3971 8928 2.068 0.589 0.145 0.086 321 24.3 supramarginal 345 232 628 2.141 0.427 0.222 0.155 14 2.0 frontalpole 684 455 2287 3.355 0.691 0.195 0.130 18 4.4 temporalpole 827 473 1189 2.262 0.371 0.160 0.089 18 3.1 transversetemporal 3860 2557 7204 2.667 0.698 0.171 0.115 117 15.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Jul 6 23:58:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 35 labels changed using aseg relabeling using gibbs priors... 000: 9190 changed, 140242 examined... 001: 2246 changed, 35157 examined... 002: 641 changed, 11612 examined... 003: 240 changed, 3580 examined... 004: 119 changed, 1386 examined... 005: 54 changed, 673 examined... 006: 34 changed, 341 examined... 007: 10 changed, 164 examined... 008: 9 changed, 56 examined... 009: 4 changed, 45 examined... 010: 2 changed, 26 examined... 011: 3 changed, 12 examined... 012: 4 changed, 20 examined... 013: 1 changed, 16 examined... 014: 0 changed, 7 examined... 7 labels changed using aseg 000: 292 total segments, 211 labels (2597 vertices) changed 001: 98 total segments, 18 labels (126 vertices) changed 002: 81 total segments, 1 labels (1 vertices) changed 003: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 106 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1111 vertices marked for relabeling... 1111 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jul 6 23:59:38 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1457 1006 2220 1.922 0.487 0.211 0.121 51 7.9 G_and_S_frontomargin 1543 1030 2232 1.964 0.497 0.152 0.058 21 3.7 G_and_S_occipital_inf 1650 923 2236 2.125 0.515 0.188 0.198 110 15.1 G_and_S_paracentral 1707 1121 3324 2.496 0.543 0.158 0.072 28 4.7 G_and_S_subcentral 640 435 1215 2.137 0.455 0.234 0.167 27 4.4 G_and_S_transv_frontopol 2552 1737 4262 2.182 0.628 0.167 0.080 61 8.1 G_and_S_cingul-Ant 1605 1067 2629 2.370 0.542 0.165 0.084 36 5.4 G_and_S_cingul-Mid-Ant 1528 998 2519 2.335 0.471 0.160 0.166 28 5.0 G_and_S_cingul-Mid-Post 626 429 986 1.950 0.619 0.223 0.179 25 3.1 G_cingul-Post-dorsal 372 240 506 1.852 0.644 0.202 0.151 23 1.6 G_cingul-Post-ventral 2244 1365 2403 1.584 0.388 0.182 0.108 103 11.5 G_cuneus 1795 1237 3544 2.349 0.473 0.176 0.102 71 6.7 G_front_inf-Opercular 377 242 761 2.369 0.460 0.197 0.116 12 1.8 G_front_inf-Orbital 1028 682 1917 2.197 0.429 0.187 0.101 29 3.9 G_front_inf-Triangul 3375 2339 7098 2.297 0.633 0.218 0.182 155 27.7 G_front_middle 7082 4814 15424 2.519 0.664 0.217 0.189 433 53.4 G_front_sup 793 480 1602 2.853 0.843 0.226 0.171 52 5.4 G_Ins_lg_and_S_cent_ins 693 489 1976 3.138 0.675 0.210 0.118 21 3.1 G_insular_short 2202 1373 3950 2.272 0.519 0.177 0.096 54 7.8 G_occipital_middle 1653 921 2045 1.922 0.527 0.144 0.137 218 6.7 G_occipital_sup 1654 1088 3698 2.567 0.510 0.182 0.087 40 6.0 G_oc-temp_lat-fusifor 4202 2627 5564 1.796 0.544 0.193 0.111 124 19.8 G_oc-temp_med-Lingual 1355 888 3212 2.719 0.844 0.201 0.198 60 13.6 G_oc-temp_med-Parahip 2779 1837 5213 2.166 0.634 0.215 0.148 135 17.7 G_orbital 2542 1327 2870 1.825 0.497 0.167 0.138 95 13.8 G_pariet_inf-Angular 3511 2071 5655 2.257 0.600 0.157 0.099 228 14.4 G_pariet_inf-Supramar 3661 1915 4601 1.995 0.522 0.157 0.192 184 22.5 G_parietal_sup 3014 1585 4051 2.070 0.565 0.156 0.146 136 18.0 G_postcentral 3022 1710 5448 2.520 0.542 0.185 0.357 833 18.6 G_precentral 3485 2102 4186 1.738 0.504 0.174 0.141 234 17.5 G_precuneus 1014 640 1732 2.038 0.641 0.222 0.292 117 8.4 G_rectus 654 393 786 2.035 0.891 0.196 0.407 96 14.0 G_subcallosal 649 362 1042 2.337 0.353 0.172 0.101 17 2.9 G_temp_sup-G_T_transv 2323 1527 5603 2.649 0.574 0.180 0.184 66 9.4 G_temp_sup-Lateral 563 386 1307 2.972 0.603 0.144 0.103 9 2.4 G_temp_sup-Plan_polar 1028 662 1588 2.090 0.485 0.129 0.052 17 2.2 G_temp_sup-Plan_tempo 2145 1497 4635 2.353 0.600 0.204 0.126 79 11.2 G_temporal_inf 3055 2021 5972 2.281 0.522 0.194 0.152 146 16.0 G_temporal_middle 362 244 387 1.746 0.491 0.139 0.046 3 0.7 Lat_Fis-ant-Horizont 326 224 433 1.991 0.410 0.139 0.052 3 0.7 Lat_Fis-ant-Vertical 1208 810 1453 2.065 0.465 0.136 0.046 11 2.4 Lat_Fis-post 2465 1513 3120 1.836 0.483 0.191 0.114 71 11.7 Pole_occipital 1625 1126 4415 2.786 0.835 0.198 0.115 41 7.6 Pole_temporal 2331 1517 2473 1.787 0.551 0.156 0.076 39 7.6 S_calcarine 2994 2119 3378 1.754 0.561 0.154 0.123 81 9.3 S_central 1123 776 1398 1.983 0.417 0.115 0.032 8 1.6 S_cingul-Marginalis 555 367 855 2.444 0.411 0.132 0.054 5 1.3 S_circular_insula_ant 1620 1069 2271 2.315 0.504 0.109 0.072 20 3.0 S_circular_insula_inf 1906 1267 2683 2.378 0.421 0.131 0.047 17 3.8 S_circular_insula_sup 741 531 1355 2.314 0.773 0.185 0.194 282 8.5 S_collat_transv_ant 531 349 488 1.697 0.327 0.167 0.062 7 1.4 S_collat_transv_post 1621 1137 2105 1.822 0.459 0.146 0.065 19 4.3 S_front_inf 1819 1281 2713 1.931 0.517 0.178 0.116 58 7.2 S_front_middle 2316 1622 3560 2.021 0.516 0.170 0.493 965 11.3 S_front_sup 288 189 267 1.599 0.370 0.170 0.078 5 1.0 S_interm_prim-Jensen 2580 1631 2572 1.668 0.439 0.134 0.046 31 4.9 S_intrapariet_and_P_trans 986 673 1260 1.908 0.432 0.142 0.046 10 1.8 S_oc_middle_and_Lunatus 1439 947 1611 1.829 0.337 0.122 0.037 11 2.2 S_oc_sup_and_transversal 815 551 1058 2.000 0.448 0.150 0.054 10 2.0 S_occipital_ant 753 509 978 2.116 0.400 0.140 0.052 7 1.7 S_oc-temp_lat 1957 1378 2765 2.112 0.466 0.138 0.045 18 3.7 S_oc-temp_med_and_Lingual 406 291 605 1.869 0.441 0.167 0.061 7 1.1 S_orbital_lateral 1027 663 1349 2.192 0.737 0.149 0.082 20 3.2 S_orbital_med-olfact 1525 1024 2319 2.165 0.521 0.176 0.085 34 5.3 S_orbital-H_Shaped 2309 1460 2407 1.743 0.444 0.132 0.045 27 4.4 S_parieto_occipital 1611 1000 1510 1.825 0.938 0.162 0.128 57 5.4 S_pericallosal 4059 2687 4757 1.852 0.500 0.129 0.066 548 13.5 S_postcentral 1427 993 2124 2.133 0.439 0.150 0.060 21 3.6 S_precentral-inf-part 1434 963 1845 2.068 0.460 0.148 0.061 17 4.0 S_precentral-sup-part 560 377 723 2.099 0.866 0.149 0.053 6 1.3 S_suborbital 1235 825 1449 1.733 0.387 0.173 0.165 65 10.3 S_subparietal 1644 1123 1964 1.924 0.430 0.159 0.064 28 4.4 S_temporal_inf 5920 3854 6619 1.769 0.474 0.133 0.061 96 15.0 S_temporal_sup 331 226 443 2.183 0.510 0.154 0.051 4 0.7 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Wed Jul 6 23:59:56 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 3 found - 3 modified | TOTAL: 8 pass 2 (yz-): 0 found - 3 modified | TOTAL: 8 pass 1 (xz+): 2 found - 2 modified | TOTAL: 10 pass 2 (xz+): 0 found - 2 modified | TOTAL: 10 pass 1 (xz-): 0 found - 0 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 266125: 0.003758) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 50: 1655 vertices, 1800 faces slice 60: 8679 vertices, 8984 faces slice 70: 20024 vertices, 20421 faces slice 80: 32613 vertices, 33081 faces slice 90: 44554 vertices, 44941 faces slice 100: 56741 vertices, 57214 faces slice 110: 69271 vertices, 69723 faces slice 120: 81385 vertices, 81846 faces slice 130: 93296 vertices, 93812 faces slice 140: 105142 vertices, 105651 faces slice 150: 116206 vertices, 116788 faces slice 160: 124720 vertices, 125290 faces slice 170: 132531 vertices, 133118 faces slice 180: 139370 vertices, 139928 faces slice 190: 145141 vertices, 145666 faces slice 200: 149099 vertices, 149532 faces slice 210: 149644 vertices, 149986 faces slice 220: 149644 vertices, 149986 faces slice 230: 149644 vertices, 149986 faces slice 240: 149644 vertices, 149986 faces slice 250: 149644 vertices, 149986 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... 149644 voxel in cpt #1: X=-342 [v=149644,e=449958,f=299972] located at (30.169128, -12.197162, 9.694649) For the whole surface: X=-342 [v=149644,e=449958,f=299972] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Jul 7 00:00:05 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Jul 7 00:00:10 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts avg radius = 47.2 mm, total surface area = 75803 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.091 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.063 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Jul 7 00:01:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.58 (0.00-->6.95) (max @ vno 111757 --> 112807) face area 0.02 +- 0.03 (-0.17-->0.72) scaling brain by 0.309... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.257, avgs=0 005/300: dt: 0.9000, rms radial error=175.999, avgs=0 010/300: dt: 0.9000, rms radial error=175.444, avgs=0 015/300: dt: 0.9000, rms radial error=174.717, avgs=0 020/300: dt: 0.9000, rms radial error=173.888, avgs=0 025/300: dt: 0.9000, rms radial error=173.000, avgs=0 030/300: dt: 0.9000, rms radial error=172.081, avgs=0 035/300: dt: 0.9000, rms radial error=171.145, avgs=0 040/300: dt: 0.9000, rms radial error=170.202, avgs=0 045/300: dt: 0.9000, rms radial error=169.257, avgs=0 050/300: dt: 0.9000, rms radial error=168.312, avgs=0 055/300: dt: 0.9000, rms radial error=167.369, avgs=0 060/300: dt: 0.9000, rms radial error=166.431, avgs=0 065/300: dt: 0.9000, rms radial error=165.496, avgs=0 070/300: dt: 0.9000, rms radial error=164.567, avgs=0 075/300: dt: 0.9000, rms radial error=163.642, avgs=0 080/300: dt: 0.9000, rms radial error=162.723, avgs=0 085/300: dt: 0.9000, rms radial error=161.808, avgs=0 090/300: dt: 0.9000, rms radial error=160.898, avgs=0 095/300: dt: 0.9000, rms radial error=159.993, avgs=0 100/300: dt: 0.9000, rms radial error=159.094, avgs=0 105/300: dt: 0.9000, rms radial error=158.199, avgs=0 110/300: dt: 0.9000, rms radial error=157.309, avgs=0 115/300: dt: 0.9000, rms radial error=156.424, avgs=0 120/300: dt: 0.9000, rms radial error=155.545, avgs=0 125/300: dt: 0.9000, rms radial error=154.670, avgs=0 130/300: dt: 0.9000, rms radial error=153.800, avgs=0 135/300: dt: 0.9000, rms radial error=152.934, avgs=0 140/300: dt: 0.9000, rms radial error=152.074, avgs=0 145/300: dt: 0.9000, rms radial error=151.218, avgs=0 150/300: dt: 0.9000, rms radial error=150.367, avgs=0 155/300: dt: 0.9000, rms radial error=149.521, avgs=0 160/300: dt: 0.9000, rms radial error=148.681, avgs=0 165/300: dt: 0.9000, rms radial error=147.845, avgs=0 170/300: dt: 0.9000, rms radial error=147.014, avgs=0 175/300: dt: 0.9000, rms radial error=146.188, avgs=0 180/300: dt: 0.9000, rms radial error=145.366, avgs=0 185/300: dt: 0.9000, rms radial error=144.549, avgs=0 190/300: dt: 0.9000, rms radial error=143.736, avgs=0 195/300: dt: 0.9000, rms radial error=142.928, avgs=0 200/300: dt: 0.9000, rms radial error=142.124, avgs=0 205/300: dt: 0.9000, rms radial error=141.324, avgs=0 210/300: dt: 0.9000, rms radial error=140.529, avgs=0 215/300: dt: 0.9000, rms radial error=139.739, avgs=0 220/300: dt: 0.9000, rms radial error=138.952, avgs=0 225/300: dt: 0.9000, rms radial error=138.170, avgs=0 230/300: dt: 0.9000, rms radial error=137.392, avgs=0 235/300: dt: 0.9000, rms radial error=136.619, avgs=0 240/300: dt: 0.9000, rms radial error=135.850, avgs=0 245/300: dt: 0.9000, rms radial error=135.085, avgs=0 250/300: dt: 0.9000, rms radial error=134.324, avgs=0 255/300: dt: 0.9000, rms radial error=133.568, avgs=0 260/300: dt: 0.9000, rms radial error=132.816, avgs=0 265/300: dt: 0.9000, rms radial error=132.068, avgs=0 270/300: dt: 0.9000, rms radial error=131.324, avgs=0 275/300: dt: 0.9000, rms radial error=130.585, avgs=0 280/300: dt: 0.9000, rms radial error=129.849, avgs=0 285/300: dt: 0.9000, rms radial error=129.118, avgs=0 290/300: dt: 0.9000, rms radial error=128.390, avgs=0 295/300: dt: 0.9000, rms radial error=127.667, avgs=0 300/300: dt: 0.9000, rms radial error=126.948, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17724.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3077.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 368.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00564 epoch 4 (K=640.0), pass 1, starting sse = 36.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00741 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Jul 7 00:06:43 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 AD08 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-342 (nv=149644, nf=299972, ne=449958, g=172) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 15350 ambiguous faces found in tessellation segmenting defects... 114 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 52 into 43 -merging segment 57 into 43 -merging segment 81 into 45 -merging segment 80 into 60 -merging segment 73 into 66 -merging segment 109 into 110 108 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5692 (-4.7846) -vertex loglikelihood: -6.7951 (-3.3975) -normal dot loglikelihood: -3.5521 (-3.5521) -quad curv loglikelihood: -6.4055 (-3.2028) Total Loglikelihood : -26.3219 CORRECTING DEFECT 0 (vertices=25, convex hull=81) After retessellation of defect 0, euler #=-104 (140297,416795,276394) : difference with theory (-105) = -1 CORRECTING DEFECT 1 (vertices=19, convex hull=53) After retessellation of defect 1, euler #=-103 (140309,416848,276436) : difference with theory (-104) = -1 CORRECTING DEFECT 2 (vertices=51, convex hull=97) After retessellation of defect 2, euler #=-102 (140338,416976,276536) : difference with theory (-103) = -1 CORRECTING DEFECT 3 (vertices=14, convex hull=28) After retessellation of defect 3, euler #=-101 (140341,416994,276552) : difference with theory (-102) = -1 CORRECTING DEFECT 4 (vertices=43, convex hull=80) After retessellation of defect 4, euler #=-100 (140368,417110,276642) : difference with theory (-101) = -1 CORRECTING DEFECT 5 (vertices=129, convex hull=36) After retessellation of defect 5, euler #=-99 (140373,417137,276665) : difference with theory (-100) = -1 CORRECTING DEFECT 6 (vertices=34, convex hull=77) Warning - incorrect dp selected!!!!(-81.604129 >= -81.604137 ) After retessellation of defect 6, euler #=-98 (140383,417195,276714) : difference with theory (-99) = -1 CORRECTING DEFECT 7 (vertices=19, convex hull=44) After retessellation of defect 7, euler #=-97 (140393,417239,276749) : difference with theory (-98) = -1 CORRECTING DEFECT 8 (vertices=37, convex hull=66) After retessellation of defect 8, euler #=-96 (140405,417304,276803) : difference with theory (-97) = -1 CORRECTING DEFECT 9 (vertices=43, convex hull=87) After retessellation of defect 9, euler #=-95 (140425,417396,276876) : difference with theory (-96) = -1 CORRECTING DEFECT 10 (vertices=35, convex hull=53) After retessellation of defect 10, euler #=-94 (140436,417449,276919) : difference with theory (-95) = -1 CORRECTING DEFECT 11 (vertices=76, convex hull=108) After retessellation of defect 11, euler #=-93 (140470,417598,277035) : difference with theory (-94) = -1 CORRECTING DEFECT 12 (vertices=22, convex hull=54) After retessellation of defect 12, euler #=-92 (140479,417644,277073) : difference with theory (-93) = -1 CORRECTING DEFECT 13 (vertices=7, convex hull=9) After retessellation of defect 13, euler #=-91 (140480,417649,277078) : difference with theory (-92) = -1 CORRECTING DEFECT 14 (vertices=31, convex hull=23) After retessellation of defect 14, euler #=-90 (140482,417663,277091) : difference with theory (-91) = -1 CORRECTING DEFECT 15 (vertices=79, convex hull=147) After retessellation of defect 15, euler #=-89 (140526,417856,277241) : difference with theory (-90) = -1 CORRECTING DEFECT 16 (vertices=37, convex hull=67) After retessellation of defect 16, euler #=-88 (140544,417935,277303) : difference with theory (-89) = -1 CORRECTING DEFECT 17 (vertices=45, convex hull=104) After retessellation of defect 17, euler #=-87 (140566,418044,277391) : difference with theory (-88) = -1 CORRECTING DEFECT 18 (vertices=25, convex hull=51) After retessellation of defect 18, euler #=-86 (140577,418097,277434) : difference with theory (-87) = -1 CORRECTING DEFECT 19 (vertices=10, convex hull=18) After retessellation of defect 19, euler #=-85 (140578,418106,277443) : difference with theory (-86) = -1 CORRECTING DEFECT 20 (vertices=50, convex hull=28) After retessellation of defect 20, euler #=-84 (140587,418141,277470) : difference with theory (-85) = -1 CORRECTING DEFECT 21 (vertices=51, convex hull=101) After retessellation of defect 21, euler #=-84 (140611,418264,277569) : difference with theory (-84) = 0 CORRECTING DEFECT 22 (vertices=39, convex hull=33) After retessellation of defect 22, euler #=-83 (140617,418293,277593) : difference with theory (-83) = 0 CORRECTING DEFECT 23 (vertices=29, convex hull=68) After retessellation of defect 23, euler #=-82 (140637,418381,277662) : difference with theory (-82) = 0 CORRECTING DEFECT 24 (vertices=17, convex hull=42) After retessellation of defect 24, euler #=-81 (140646,418424,277697) : difference with theory (-81) = 0 CORRECTING DEFECT 25 (vertices=23, convex hull=67) After retessellation of defect 25, euler #=-80 (140661,418494,277753) : difference with theory (-80) = 0 CORRECTING DEFECT 26 (vertices=19, convex hull=51) After retessellation of defect 26, euler #=-79 (140670,418540,277791) : difference with theory (-79) = 0 CORRECTING DEFECT 27 (vertices=47, convex hull=88) After retessellation of defect 27, euler #=-78 (140700,418670,277892) : difference with theory (-78) = 0 CORRECTING DEFECT 28 (vertices=22, convex hull=47) After retessellation of defect 28, euler #=-77 (140711,418722,277934) : difference with theory (-77) = 0 CORRECTING DEFECT 29 (vertices=210, convex hull=135) After retessellation of defect 29, euler #=-76 (140750,418901,278075) : difference with theory (-76) = 0 CORRECTING DEFECT 30 (vertices=24, convex hull=57) After retessellation of defect 30, euler #=-75 (140766,418973,278132) : difference with theory (-75) = 0 CORRECTING DEFECT 31 (vertices=129, convex hull=120) After retessellation of defect 31, euler #=-74 (140837,419241,278330) : difference with theory (-74) = 0 CORRECTING DEFECT 32 (vertices=16, convex hull=32) After retessellation of defect 32, euler #=-73 (140840,419259,278346) : difference with theory (-73) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=70) After retessellation of defect 33, euler #=-72 (140861,419351,278418) : difference with theory (-72) = 0 CORRECTING DEFECT 34 (vertices=81, convex hull=114) After retessellation of defect 34, euler #=-71 (140902,419523,278550) : difference with theory (-71) = 0 CORRECTING DEFECT 35 (vertices=47, convex hull=28) After retessellation of defect 35, euler #=-70 (140908,419550,278572) : difference with theory (-70) = 0 CORRECTING DEFECT 36 (vertices=297, convex hull=182) After retessellation of defect 36, euler #=-69 (140918,419665,278678) : difference with theory (-69) = 0 CORRECTING DEFECT 37 (vertices=39, convex hull=86) After retessellation of defect 37, euler #=-68 (140935,419753,278750) : difference with theory (-68) = 0 CORRECTING DEFECT 38 (vertices=66, convex hull=105) After retessellation of defect 38, euler #=-67 (140952,419849,278830) : difference with theory (-67) = 0 CORRECTING DEFECT 39 (vertices=5, convex hull=17) After retessellation of defect 39, euler #=-66 (140953,419855,278836) : difference with theory (-66) = 0 CORRECTING DEFECT 40 (vertices=32, convex hull=76) After retessellation of defect 40, euler #=-65 (140971,419942,278906) : difference with theory (-65) = 0 CORRECTING DEFECT 41 (vertices=25, convex hull=51) After retessellation of defect 41, euler #=-64 (140981,419987,278942) : difference with theory (-64) = 0 CORRECTING DEFECT 42 (vertices=129, convex hull=115) After retessellation of defect 42, euler #=-63 (141026,420173,279084) : difference with theory (-63) = 0 CORRECTING DEFECT 43 (vertices=912, convex hull=515) After retessellation of defect 43, euler #=-61 (141044,420516,279411) : difference with theory (-62) = -1 CORRECTING DEFECT 44 (vertices=12, convex hull=12) After retessellation of defect 44, euler #=-60 (141044,420518,279414) : difference with theory (-61) = -1 CORRECTING DEFECT 45 (vertices=1374, convex hull=507) After retessellation of defect 45, euler #=-58 (141279,421499,280162) : difference with theory (-60) = -2 CORRECTING DEFECT 46 (vertices=12, convex hull=23) After retessellation of defect 46, euler #=-57 (141282,421512,280173) : difference with theory (-59) = -2 CORRECTING DEFECT 47 (vertices=86, convex hull=95) After retessellation of defect 47, euler #=-56 (141292,421584,280236) : difference with theory (-58) = -2 CORRECTING DEFECT 48 (vertices=45, convex hull=82) After retessellation of defect 48, euler #=-55 (141319,421699,280325) : difference with theory (-57) = -2 CORRECTING DEFECT 49 (vertices=48, convex hull=84) After retessellation of defect 49, euler #=-54 (141348,421824,280422) : difference with theory (-56) = -2 CORRECTING DEFECT 50 (vertices=162, convex hull=167) After retessellation of defect 50, euler #=-53 (141387,422016,280576) : difference with theory (-55) = -2 CORRECTING DEFECT 51 (vertices=32, convex hull=78) After retessellation of defect 51, euler #=-52 (141407,422108,280649) : difference with theory (-54) = -2 CORRECTING DEFECT 52 (vertices=48, convex hull=98) After retessellation of defect 52, euler #=-51 (141441,422250,280758) : difference with theory (-53) = -2 CORRECTING DEFECT 53 (vertices=21, convex hull=53) After retessellation of defect 53, euler #=-50 (141448,422291,280793) : difference with theory (-52) = -2 CORRECTING DEFECT 54 (vertices=86, convex hull=110) After retessellation of defect 54, euler #=-49 (141493,422479,280937) : difference with theory (-51) = -2 CORRECTING DEFECT 55 (vertices=89, convex hull=155) After retessellation of defect 55, euler #=-48 (141566,422770,281156) : difference with theory (-50) = -2 CORRECTING DEFECT 56 (vertices=29, convex hull=64) After retessellation of defect 56, euler #=-47 (141584,422847,281216) : difference with theory (-49) = -2 CORRECTING DEFECT 57 (vertices=558, convex hull=314) After retessellation of defect 57, euler #=-48 (141716,423432,281668) : difference with theory (-48) = 0 CORRECTING DEFECT 58 (vertices=364, convex hull=258) After retessellation of defect 58, euler #=-46 (141850,423962,282066) : difference with theory (-47) = -1 CORRECTING DEFECT 59 (vertices=39, convex hull=98) After retessellation of defect 59, euler #=-45 (141865,424046,282136) : difference with theory (-46) = -1 CORRECTING DEFECT 60 (vertices=45, convex hull=70) After retessellation of defect 60, euler #=-44 (141896,424167,282227) : difference with theory (-45) = -1 CORRECTING DEFECT 61 (vertices=34, convex hull=74) After retessellation of defect 61, euler #=-43 (141911,424237,282283) : difference with theory (-44) = -1 CORRECTING DEFECT 62 (vertices=5, convex hull=13) After retessellation of defect 62, euler #=-42 (141911,424240,282287) : difference with theory (-43) = -1 CORRECTING DEFECT 63 (vertices=31, convex hull=61) After retessellation of defect 63, euler #=-41 (141927,424313,282345) : difference with theory (-42) = -1 CORRECTING DEFECT 64 (vertices=87, convex hull=58) After retessellation of defect 64, euler #=-39 (141936,424367,282392) : difference with theory (-41) = -2 CORRECTING DEFECT 65 (vertices=387, convex hull=298) After retessellation of defect 65, euler #=-39 (142128,425126,282959) : difference with theory (-40) = -1 CORRECTING DEFECT 66 (vertices=100, convex hull=81) After retessellation of defect 66, euler #=-38 (142144,425210,283028) : difference with theory (-39) = -1 CORRECTING DEFECT 67 (vertices=53, convex hull=32) After retessellation of defect 67, euler #=-37 (142146,425229,283046) : difference with theory (-38) = -1 CORRECTING DEFECT 68 (vertices=40, convex hull=50) After retessellation of defect 68, euler #=-36 (142158,425288,283094) : difference with theory (-37) = -1 CORRECTING DEFECT 69 (vertices=27, convex hull=72) After retessellation of defect 69, euler #=-35 (142174,425363,283154) : difference with theory (-36) = -1 CORRECTING DEFECT 70 (vertices=26, convex hull=75) After retessellation of defect 70, euler #=-34 (142187,425430,283209) : difference with theory (-35) = -1 CORRECTING DEFECT 71 (vertices=222, convex hull=172) After retessellation of defect 71, euler #=-33 (142264,425738,283441) : difference with theory (-34) = -1 CORRECTING DEFECT 72 (vertices=35, convex hull=64) After retessellation of defect 72, euler #=-32 (142286,425829,283511) : difference with theory (-33) = -1 CORRECTING DEFECT 73 (vertices=42, convex hull=77) After retessellation of defect 73, euler #=-31 (142309,425931,283591) : difference with theory (-32) = -1 CORRECTING DEFECT 74 (vertices=37, convex hull=68) After retessellation of defect 74, euler #=-31 (142334,426039,283674) : difference with theory (-31) = 0 CORRECTING DEFECT 75 (vertices=56, convex hull=80) After retessellation of defect 75, euler #=-30 (142364,426162,283768) : difference with theory (-30) = 0 CORRECTING DEFECT 76 (vertices=6, convex hull=23) After retessellation of defect 76, euler #=-29 (142365,426173,283779) : difference with theory (-29) = 0 CORRECTING DEFECT 77 (vertices=79, convex hull=83) After retessellation of defect 77, euler #=-28 (142400,426309,283881) : difference with theory (-28) = 0 CORRECTING DEFECT 78 (vertices=121, convex hull=119) After retessellation of defect 78, euler #=-27 (142430,426447,283990) : difference with theory (-27) = 0 CORRECTING DEFECT 79 (vertices=152, convex hull=124) After retessellation of defect 79, euler #=-26 (142489,426682,284167) : difference with theory (-26) = 0 CORRECTING DEFECT 80 (vertices=24, convex hull=53) After retessellation of defect 80, euler #=-25 (142501,426738,284212) : difference with theory (-25) = 0 CORRECTING DEFECT 81 (vertices=574, convex hull=184) After retessellation of defect 81, euler #=-25 (142521,426901,284355) : difference with theory (-24) = 1 CORRECTING DEFECT 82 (vertices=34, convex hull=36) After retessellation of defect 82, euler #=-24 (142527,426928,284377) : difference with theory (-23) = 1 CORRECTING DEFECT 83 (vertices=23, convex hull=61) After retessellation of defect 83, euler #=-23 (142538,426987,284426) : difference with theory (-22) = 1 CORRECTING DEFECT 84 (vertices=33, convex hull=64) After retessellation of defect 84, euler #=-22 (142549,427045,284474) : difference with theory (-21) = 1 CORRECTING DEFECT 85 (vertices=9, convex hull=14) After retessellation of defect 85, euler #=-21 (142550,427050,284479) : difference with theory (-20) = 1 CORRECTING DEFECT 86 (vertices=24, convex hull=58) After retessellation of defect 86, euler #=-20 (142561,427105,284524) : difference with theory (-19) = 1 CORRECTING DEFECT 87 (vertices=32, convex hull=62) After retessellation of defect 87, euler #=-19 (142570,427156,284567) : difference with theory (-18) = 1 CORRECTING DEFECT 88 (vertices=18, convex hull=49) After retessellation of defect 88, euler #=-18 (142581,427204,284605) : difference with theory (-17) = 1 CORRECTING DEFECT 89 (vertices=104, convex hull=124) After retessellation of defect 89, euler #=-17 (142634,427426,284775) : difference with theory (-16) = 1 CORRECTING DEFECT 90 (vertices=74, convex hull=98) After retessellation of defect 90, euler #=-16 (142665,427568,284887) : difference with theory (-15) = 1 CORRECTING DEFECT 91 (vertices=6, convex hull=14) After retessellation of defect 91, euler #=-15 (142665,427572,284892) : difference with theory (-14) = 1 CORRECTING DEFECT 92 (vertices=33, convex hull=78) After retessellation of defect 92, euler #=-14 (142675,427630,284941) : difference with theory (-13) = 1 CORRECTING DEFECT 93 (vertices=62, convex hull=79) After retessellation of defect 93, euler #=-13 (142705,427751,285033) : difference with theory (-12) = 1 CORRECTING DEFECT 94 (vertices=50, convex hull=80) After retessellation of defect 94, euler #=-12 (142730,427857,285115) : difference with theory (-11) = 1 CORRECTING DEFECT 95 (vertices=40, convex hull=80) After retessellation of defect 95, euler #=-11 (142752,427956,285193) : difference with theory (-10) = 1 CORRECTING DEFECT 96 (vertices=42, convex hull=87) After retessellation of defect 96, euler #=-10 (142768,428038,285260) : difference with theory (-9) = 1 CORRECTING DEFECT 97 (vertices=13, convex hull=15) After retessellation of defect 97, euler #=-9 (142769,428046,285268) : difference with theory (-8) = 1 CORRECTING DEFECT 98 (vertices=36, convex hull=62) After retessellation of defect 98, euler #=-8 (142779,428098,285311) : difference with theory (-7) = 1 CORRECTING DEFECT 99 (vertices=32, convex hull=66) After retessellation of defect 99, euler #=-7 (142794,428171,285370) : difference with theory (-6) = 1 CORRECTING DEFECT 100 (vertices=80, convex hull=105) After retessellation of defect 100, euler #=-6 (142822,428301,285473) : difference with theory (-5) = 1 CORRECTING DEFECT 101 (vertices=55, convex hull=51) After retessellation of defect 101, euler #=-5 (142833,428353,285515) : difference with theory (-4) = 1 CORRECTING DEFECT 102 (vertices=22, convex hull=37) After retessellation of defect 102, euler #=-4 (142837,428379,285538) : difference with theory (-3) = 1 CORRECTING DEFECT 103 (vertices=21, convex hull=43) After retessellation of defect 103, euler #=-3 (142846,428421,285572) : difference with theory (-2) = 1 CORRECTING DEFECT 104 (vertices=92, convex hull=84) After retessellation of defect 104, euler #=-1 (142863,428513,285649) : difference with theory (-1) = 0 CORRECTING DEFECT 105 (vertices=24, convex hull=62) After retessellation of defect 105, euler #=0 (142877,428577,285700) : difference with theory (0) = 0 CORRECTING DEFECT 106 (vertices=21, convex hull=56) After retessellation of defect 106, euler #=1 (142890,428635,285746) : difference with theory (1) = 0 CORRECTING DEFECT 107 (vertices=39, convex hull=78) After retessellation of defect 107, euler #=2 (142899,428691,285794) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.29 (0.05-->12.77) (max @ vno 74092 --> 86329) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.29 (0.05-->12.77) (max @ vno 74092 --> 86329) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 370 mutations (35.2%), 682 crossovers (64.8%), 1016 vertices were eliminated building final representation... 6745 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142899, nf=285794, ne=428691, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... defective orientation at vertex 130483(130484) with faces 257379 and 284321 defective orientation at vertex 130483(131101) with faces 257379 and 284317 defective orientation at vertex 130484(130483) with faces 257379 and 284321 defective orientation at vertex 130484(131101) with faces 257379 and 284320 defective orientation at vertex 131101(130484) with faces 257379 and 284320 defective orientation at vertex 131101(130483) with faces 257379 and 284317 0.004 % of the vertices (6 vertices) exhibit an orientation change topology fixing took 113.0 minutes 0 defective edges removing intersecting faces 000: 1006 intersecting 001: 49 intersecting 002: 26 intersecting 003: 16 intersecting 004: 12 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 142899 - 428691 + 285794 = 2 --> 0 holes F =2V-4: 285794 = 285798-4 (0) 2E=3F: 857382 = 857382 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 124 intersecting 001: 32 intersecting 002: 17 intersecting 003: 16 intersecting 004: 9 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Jul 7 01:59:54 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD08 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 21503 bright wm thresholded. 2109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 93.6 +- 10.1 [70.0 --> 110.0] GM (78.0) : 76.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.7 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 45.4 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->5.96) (max @ vno 74092 --> 86329) face area 0.27 +- 0.14 (0.00-->5.79) mean absolute distance = 0.92 +- 1.19 4916 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=105, GM=70 using class modes intead of means.... mean inside = 95.5, mean outside = 76.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=82.6, 188 (188) missing vertices, mean dist 0.2 [1.1 (%34.3)->0.8 (%65.7))] %33 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.29 (0.08-->7.86) (max @ vno 74092 --> 86329) face area 0.27 +- 0.15 (0.00-->4.78) mean absolute distance = 0.47 +- 0.85 5376 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6065843.5, rms=10.94 001: dt: 0.5000, sse=7100075.0, rms=7.68 002: dt: 0.5000, sse=7714815.0, rms=5.93 003: dt: 0.5000, sse=8208151.5, rms=5.00 004: dt: 0.5000, sse=8488185.0, rms=4.51 005: dt: 0.5000, sse=8680865.0, rms=4.23 006: dt: 0.5000, sse=8752968.0, rms=4.07 007: dt: 0.5000, sse=8829087.0, rms=3.95 008: dt: 0.5000, sse=8851433.0, rms=3.90 009: dt: 0.5000, sse=8848264.0, rms=3.84 rms = 3.83, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8868774.0, rms=3.83 011: dt: 0.2500, sse=5766677.0, rms=2.80 012: dt: 0.2500, sse=5405880.5, rms=2.48 013: dt: 0.2500, sse=5148283.5, rms=2.42 rms = 2.38, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5091252.5, rms=2.38 015: dt: 0.1250, sse=4925504.0, rms=2.27 rms = 2.26, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4881679.5, rms=2.26 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.0, 275 (90) missing vertices, mean dist -0.3 [0.6 (%60.4)->0.3 (%39.6))] %46 local maxima, %50 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 0.88 +- 0.28 (0.08-->7.94) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->6.51) mean absolute distance = 0.35 +- 0.53 4637 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5356882.5, rms=4.29 017: dt: 0.5000, sse=5937950.0, rms=3.25 rms = 3.48, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5460328.0, rms=2.59 019: dt: 0.2500, sse=5309976.5, rms=2.19 020: dt: 0.2500, sse=5174073.0, rms=2.02 021: dt: 0.2500, sse=5120541.0, rms=1.96 rms = 1.94, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5080278.5, rms=1.94 023: dt: 0.1250, sse=4981930.5, rms=1.86 rms = 1.85, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4944409.0, rms=1.85 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=87.5, 287 (77) missing vertices, mean dist -0.2 [0.4 (%65.4)->0.2 (%34.6))] %66 local maxima, %29 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 0.87 +- 0.28 (0.07-->7.98) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->6.44) mean absolute distance = 0.28 +- 0.42 4155 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5237303.5, rms=3.85 025: dt: 0.5000, sse=5631614.5, rms=2.97 rms = 3.34, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5248754.0, rms=2.20 027: dt: 0.2500, sse=5244473.5, rms=1.85 028: dt: 0.2500, sse=5183266.0, rms=1.77 rms = 1.76, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5157221.5, rms=1.76 030: dt: 0.1250, sse=5046006.0, rms=1.67 rms = 1.67, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5009680.5, rms=1.67 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=88.6, 294 (61) missing vertices, mean dist -0.1 [0.3 (%56.2)->0.2 (%43.8))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5053218.0, rms=2.21 rms = 2.29, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5195421.0, rms=1.61 033: dt: 0.2500, sse=5509575.0, rms=1.28 rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.27, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5500297.5, rms=1.27 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 14 non-cortical segments detected only using segment with 1826 vertices erasing segment 1 (vno[0] = 68039) erasing segment 2 (vno[0] = 79783) erasing segment 3 (vno[0] = 90996) erasing segment 4 (vno[0] = 96147) erasing segment 5 (vno[0] = 98395) erasing segment 6 (vno[0] = 99405) erasing segment 7 (vno[0] = 100356) erasing segment 8 (vno[0] = 102218) erasing segment 9 (vno[0] = 102304) erasing segment 10 (vno[0] = 104108) erasing segment 11 (vno[0] = 105976) erasing segment 12 (vno[0] = 109996) erasing segment 13 (vno[0] = 142140) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label/rh.cortex.label writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area vertex spacing 0.87 +- 0.28 (0.05-->7.96) (max @ vno 74092 --> 86329) face area 0.32 +- 0.18 (0.00-->6.11) refinement took 6.4 minutes #-------------------------------------------- #@# Smooth2 rh Thu Jul 7 02:06:20 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Jul 7 02:06:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.4 mm, total surface area = 83271 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.122 (target=0.015) step 005: RMS=0.088 (target=0.015) step 010: RMS=0.066 (target=0.015) step 015: RMS=0.054 (target=0.015) step 020: RMS=0.046 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.034 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.017 (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 323 vertices thresholded to be in k1 ~ [-0.21 0.32], k2 ~ [-0.08 0.08] total integrated curvature = 0.388*4pi (4.874) --> 1 handles ICI = 1.4, FI = 8.3, variation=147.957 166 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 174 vertices thresholded to be in [-0.11 0.17] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.021 done. #-------------------------------------------- #@# Sphere rh Thu Jul 7 02:08:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.21 hours scaling brain by 0.291... pass 1: epoch 1 of 3 starting distance error %20.20 pass 1: epoch 2 of 3 starting distance error %20.13 unfolding complete - removing small folds... starting distance error %20.04 removing remaining folds... final distance error %20.05 #-------------------------------------------- #@# Surf Reg rh Thu Jul 7 03:21:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.603 curvature mean = 0.023, std = 0.929 curvature mean = 0.023, std = 0.862 curvature mean = 0.004, std = 0.947 curvature mean = 0.011, std = 0.942 curvature mean = 0.003, std = 0.958 curvature mean = 0.005, std = 0.974 curvature mean = 0.000, std = 0.957 curvature mean = 0.001, std = 0.989 curvature mean = -0.030, std = 0.330 curvature mean = 0.006, std = 0.070 curvature mean = 0.076, std = 0.291 curvature mean = 0.006, std = 0.083 curvature mean = 0.040, std = 0.464 curvature mean = 0.006, std = 0.089 curvature mean = 0.023, std = 0.597 curvature mean = 0.006, std = 0.091 curvature mean = 0.008, std = 0.714 expanding nbhd size to 1 1114: 1 negative triangles #-------------------------------------------- #@# Jacobian white rh Thu Jul 7 04:16:23 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Jul 7 04:16:25 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Jul 7 04:16:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1336 labels changed using aseg relabeling using gibbs priors... 000: 3068 changed, 142899 examined... 001: 716 changed, 13154 examined... 002: 199 changed, 3973 examined... 003: 70 changed, 1145 examined... 004: 28 changed, 420 examined... 005: 12 changed, 168 examined... 006: 6 changed, 67 examined... 007: 4 changed, 36 examined... 008: 1 changed, 19 examined... 009: 0 changed, 7 examined... 175 labels changed using aseg 000: 106 total segments, 65 labels (463 vertices) changed 001: 45 total segments, 6 labels (27 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1773 vertices marked for relabeling... 1773 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Jul 7 04:17:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 21503 bright wm thresholded. 2109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 93.6 +- 10.1 [70.0 --> 110.0] GM (78.0) : 76.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.7 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 45.4 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.1 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=105, GM=70 using class modes intead of means.... mean inside = 95.5, mean outside = 76.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->5.96) (max @ vno 74092 --> 86329) face area 0.27 +- 0.14 (0.00-->5.79) mean absolute distance = 0.93 +- 1.20 5012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 305 points - only 6.89% unknown removing 2 vertex label from ripped group deleting segment 6 with 125 points - only 0.00% unknown deleting segment 7 with 157 points - only 14.65% unknown mean border=82.6, 188 (188) missing vertices, mean dist 0.2 [1.1 (%34.3)->0.8 (%65.7))] %33 local maxima, %63 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.29 (0.08-->7.86) (max @ vno 74092 --> 86329) face area 0.27 +- 0.15 (0.00-->4.69) mean absolute distance = 0.47 +- 0.86 5442 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6089038.5, rms=10.93 001: dt: 0.5000, sse=7128632.0, rms=7.69 002: dt: 0.5000, sse=7759228.0, rms=5.94 003: dt: 0.5000, sse=8263533.0, rms=5.01 004: dt: 0.5000, sse=8545507.0, rms=4.52 005: dt: 0.5000, sse=8741570.0, rms=4.24 006: dt: 0.5000, sse=8813797.0, rms=4.08 007: dt: 0.5000, sse=8890295.0, rms=3.96 008: dt: 0.5000, sse=8913022.0, rms=3.91 009: dt: 0.5000, sse=8910272.0, rms=3.85 rms = 3.84, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8929653.0, rms=3.84 011: dt: 0.2500, sse=5820465.0, rms=2.81 012: dt: 0.2500, sse=5458159.0, rms=2.50 013: dt: 0.2500, sse=5200404.5, rms=2.44 rms = 2.40, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5143673.0, rms=2.40 015: dt: 0.1250, sse=4978326.0, rms=2.29 rms = 2.28, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4936033.5, rms=2.28 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 3 with 44 points - only 0.00% unknown deleting segment 5 with 231 points - only 9.09% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 209 points - only 12.92% unknown deleting segment 12 with 6 points - only 16.67% unknown deleting segment 13 with 15 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown mean border=85.0, 278 (90) missing vertices, mean dist -0.3 [0.6 (%60.4)->0.3 (%39.6))] %46 local maxima, %50 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 0.88 +- 0.28 (0.08-->7.94) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.63) mean absolute distance = 0.36 +- 0.53 4731 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5423628.0, rms=4.29 017: dt: 0.5000, sse=6010886.5, rms=3.26 rms = 3.48, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5529973.0, rms=2.60 019: dt: 0.2500, sse=5377876.0, rms=2.21 020: dt: 0.2500, sse=5241144.0, rms=2.04 021: dt: 0.2500, sse=5188928.0, rms=1.98 rms = 1.96, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5149818.5, rms=1.96 023: dt: 0.1250, sse=5051597.5, rms=1.88 rms = 1.88, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5013620.5, rms=1.88 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 42 points - only 0.00% unknown deleting segment 2 with 259 points - only 8.11% unknown removing 1 vertex label from ripped group deleting segment 4 with 40 points - only 0.00% unknown deleting segment 5 with 237 points - only 12.24% unknown deleting segment 6 with 41 points - only 9.76% unknown deleting segment 7 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown mean border=87.5, 294 (77) missing vertices, mean dist -0.2 [0.4 (%65.4)->0.2 (%34.6))] %67 local maxima, %29 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 0.87 +- 0.28 (0.07-->7.98) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.60) mean absolute distance = 0.28 +- 0.42 4232 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5306925.0, rms=3.85 025: dt: 0.5000, sse=5704596.0, rms=2.98 rms = 3.35, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5319649.0, rms=2.22 027: dt: 0.2500, sse=5318920.0, rms=1.87 028: dt: 0.2500, sse=5259179.5, rms=1.79 rms = 1.79, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5236060.5, rms=1.79 030: dt: 0.1250, sse=5124335.0, rms=1.70 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5086908.5, rms=1.70 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 274 points - only 7.66% unknown removing 1 vertex label from ripped group deleting segment 5 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 237 points - only 11.39% unknown deleting segment 8 with 35 points - only 11.43% unknown deleting segment 9 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=88.6, 308 (61) missing vertices, mean dist -0.1 [0.3 (%56.1)->0.2 (%43.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5130541.0, rms=2.23 rms = 2.30, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5276731.0, rms=1.64 033: dt: 0.2500, sse=5595339.5, rms=1.31 rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5586387.5, rms=1.30 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 75 points - only 28.00% unknown deleting segment 3 with 27 points - only 40.74% unknown deleting segment 4 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=58.7, 215 (215) missing vertices, mean dist 1.7 [0.3 (%0.0)->1.9 (%100.0))] %37 local maxima, %51 large gradients and % 9 min vals, 350 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=26679052.0, rms=29.55 001: dt: 0.5000, sse=20310612.0, rms=25.25 002: dt: 0.5000, sse=15669898.0, rms=21.57 003: dt: 0.5000, sse=12957546.0, rms=18.67 004: dt: 0.5000, sse=11617793.0, rms=16.33 005: dt: 0.5000, sse=10590400.0, rms=14.36 006: dt: 0.5000, sse=9849688.0, rms=12.66 007: dt: 0.5000, sse=9262034.0, rms=11.11 008: dt: 0.5000, sse=8832515.0, rms=9.64 009: dt: 0.5000, sse=8597882.0, rms=8.39 010: dt: 0.5000, sse=8592985.0, rms=7.43 011: dt: 0.5000, sse=8640643.0, rms=6.80 012: dt: 0.5000, sse=8719318.0, rms=6.40 013: dt: 0.5000, sse=8793360.0, rms=6.17 014: dt: 0.5000, sse=8853058.0, rms=5.99 015: dt: 0.5000, sse=8892565.0, rms=5.90 016: dt: 0.5000, sse=8902767.0, rms=5.81 017: dt: 0.5000, sse=8932318.0, rms=5.76 018: dt: 0.5000, sse=8902494.0, rms=5.70 rms = 5.66, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=8949728.0, rms=5.66 020: dt: 0.2500, sse=6151680.5, rms=4.55 021: dt: 0.2500, sse=5899281.0, rms=4.23 rms = 4.18, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5669862.0, rms=4.18 023: dt: 0.1250, sse=5204998.0, rms=3.81 024: dt: 0.1250, sse=5134826.0, rms=3.75 rms = 3.75, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5093360.0, rms=3.75 positioning took 2.8 minutes mean border=54.8, 652 (37) missing vertices, mean dist 0.2 [0.2 (%37.7)->0.5 (%62.3))] %55 local maxima, %34 large gradients and % 7 min vals, 102 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=6288619.5, rms=6.98 026: dt: 0.5000, sse=6524961.0, rms=6.13 027: dt: 0.5000, sse=8296397.5, rms=5.98 rms = 6.03, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6682149.0, rms=4.80 029: dt: 0.2500, sse=6075032.0, rms=4.43 030: dt: 0.2500, sse=6121183.0, rms=4.32 031: dt: 0.2500, sse=6088259.5, rms=4.27 rms = 4.25, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6127479.5, rms=4.25 033: dt: 0.1250, sse=5635081.5, rms=3.78 034: dt: 0.1250, sse=5587532.0, rms=3.68 rms = 3.67, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5560582.0, rms=3.67 positioning took 1.2 minutes mean border=52.1, 750 (22) missing vertices, mean dist 0.2 [0.2 (%35.3)->0.3 (%64.7))] %66 local maxima, %22 large gradients and % 7 min vals, 140 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=5960273.0, rms=5.21 rms = 5.82, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5677202.0, rms=4.36 037: dt: 0.2500, sse=5631901.0, rms=3.99 038: dt: 0.2500, sse=5884733.0, rms=3.87 rms = 3.89, time step reduction 2 of 3 to 0.125... 039: dt: 0.1250, sse=5748531.0, rms=3.71 040: dt: 0.1250, sse=5629837.5, rms=3.48 041: dt: 0.1250, sse=5572688.5, rms=3.43 rms = 3.41, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5568650.5, rms=3.41 positioning took 0.9 minutes mean border=50.8, 1210 (19) missing vertices, mean dist 0.1 [0.2 (%42.5)->0.3 (%57.5))] %70 local maxima, %19 large gradients and % 7 min vals, 123 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5637445.0, rms=3.78 rms = 5.13, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=5529294.0, rms=3.42 044: dt: 0.2500, sse=5749075.5, rms=3.33 rms = 3.36, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=5681971.0, rms=3.26 046: dt: 0.1250, sse=5627612.0, rms=3.17 rms = 3.13, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5638414.0, rms=3.13 positioning took 0.7 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area.pial vertex spacing 0.98 +- 0.43 (0.01-->7.92) (max @ vno 75151 --> 74088) face area 0.39 +- 0.31 (0.00-->10.51) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed thickness calculation complete, 199:413 truncations. 72812 vertices at 0 distance 92394 vertices at 1 distance 70164 vertices at 2 distance 26252 vertices at 3 distance 7995 vertices at 4 distance 2446 vertices at 5 distance 966 vertices at 6 distance 408 vertices at 7 distance 240 vertices at 8 distance 151 vertices at 9 distance 97 vertices at 10 distance 73 vertices at 11 distance 48 vertices at 12 distance 35 vertices at 13 distance 25 vertices at 14 distance 17 vertices at 15 distance 20 vertices at 16 distance 27 vertices at 17 distance 29 vertices at 18 distance 24 vertices at 19 distance 35 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.thickness positioning took 12.7 minutes #-------------------------------------------- #@# Surf Volume rh Thu Jul 7 04:30:05 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Thu Jul 7 04:30:05 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1278 840 1728 1.936 0.479 0.124 0.040 16 2.1 bankssts 1077 685 1867 2.358 0.741 0.165 0.094 28 3.7 caudalanteriorcingulate 2885 1818 4173 2.094 0.452 0.164 0.110 92 15.1 caudalmiddlefrontal 2347 1434 2681 1.689 0.418 0.174 3.167 187 8.9 cuneus 457 317 1581 3.058 1.004 0.186 0.092 10 1.7 entorhinal 4689 3064 8055 2.283 0.635 0.155 0.096 121 15.2 fusiform 8048 4895 10703 1.976 0.505 0.145 0.098 267 30.7 inferiorparietal 5205 3463 9981 2.322 0.689 0.175 0.123 333 20.8 inferiortemporal 1956 1201 2585 1.909 0.752 0.166 0.115 53 7.4 isthmuscingulate 7228 4603 10897 2.054 0.529 0.170 0.084 231 25.9 lateraloccipital 4160 2613 6485 2.199 0.623 0.186 0.146 527 28.7 lateralorbitofrontal 4918 3086 6335 1.805 0.575 0.176 0.088 123 18.1 lingual 2523 1687 3933 2.003 0.688 0.190 0.151 154 11.7 medialorbitofrontal 5084 3375 9316 2.253 0.643 0.160 0.089 134 16.5 middletemporal 1275 785 2110 2.257 0.836 0.121 0.064 16 3.3 parahippocampal 2357 1433 3482 2.176 0.513 0.166 0.271 342 42.0 paracentral 2669 1790 4478 2.192 0.446 0.156 0.080 51 7.9 parsopercularis 1233 837 2486 2.317 0.640 0.171 0.150 35 6.3 parsorbitalis 2224 1548 3873 2.151 0.508 0.189 0.122 74 10.5 parstriangularis 2399 1525 2277 1.590 0.416 0.177 0.101 56 9.6 pericalcarine 7220 4573 9490 1.874 0.539 0.155 0.102 171 26.5 postcentral 1807 1172 2889 2.196 0.642 0.166 0.117 64 7.8 posteriorcingulate 8033 5203 13244 2.297 0.533 0.159 0.186 378 32.1 precentral 6378 4069 9005 2.081 0.481 0.145 0.069 170 18.3 precuneus 1357 827 2187 2.163 0.638 0.171 0.176 76 6.3 rostralanteriorcingulate 9064 6129 14919 2.039 0.586 0.189 0.110 347 37.5 rostralmiddlefrontal 10247 6731 19221 2.364 0.636 0.184 0.157 372 52.4 superiorfrontal 8837 5404 12654 2.064 0.500 0.145 0.099 673 40.8 superiorparietal 5564 3675 9751 2.342 0.579 0.157 0.076 241 19.4 superiortemporal 7043 4464 10622 2.187 0.487 0.139 0.179 259 22.2 supramarginal 448 282 884 2.291 0.596 0.210 0.167 22 2.6 frontalpole 589 411 1870 3.122 0.891 0.232 0.193 40 4.3 temporalpole 576 349 1039 2.563 0.414 0.168 0.091 12 2.2 transversetemporal 3521 2230 6729 2.760 0.845 0.156 0.126 224 19.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Jul 7 04:30:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 7 labels changed using aseg relabeling using gibbs priors... 000: 10080 changed, 142899 examined... 001: 2404 changed, 38443 examined... 002: 717 changed, 12274 examined... 003: 334 changed, 3939 examined... 004: 167 changed, 1846 examined... 005: 81 changed, 888 examined... 006: 44 changed, 444 examined... 007: 15 changed, 243 examined... 008: 5 changed, 91 examined... 009: 3 changed, 34 examined... 010: 3 changed, 22 examined... 011: 2 changed, 18 examined... 012: 1 changed, 10 examined... 013: 1 changed, 5 examined... 014: 1 changed, 6 examined... 015: 0 changed, 7 examined... 2 labels changed using aseg 000: 333 total segments, 247 labels (2702 vertices) changed 001: 102 total segments, 18 labels (101 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 152 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1318 vertices marked for relabeling... 1318 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Jul 7 04:31:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1271 828 1999 1.959 0.593 0.181 0.105 39 5.2 G_and_S_frontomargin 1344 864 2166 2.157 0.538 0.155 0.067 22 3.8 G_and_S_occipital_inf 1568 835 2084 2.073 0.493 0.172 0.197 74 9.7 G_and_S_paracentral 1493 1001 2715 2.313 0.565 0.166 0.075 30 4.7 G_and_S_subcentral 1153 774 2146 2.160 0.563 0.213 0.141 60 5.7 G_and_S_transv_frontopol 3342 2173 5306 2.127 0.565 0.165 0.121 117 13.7 G_and_S_cingul-Ant 1526 968 2653 2.454 0.517 0.152 0.086 34 5.3 G_and_S_cingul-Mid-Ant 1349 896 2313 2.332 0.539 0.146 0.070 21 3.3 G_and_S_cingul-Mid-Post 849 494 1353 2.237 0.664 0.215 0.216 53 7.3 G_cingul-Post-dorsal 329 209 675 2.687 0.615 0.213 0.223 14 1.4 G_cingul-Post-ventral 2009 1237 2343 1.666 0.436 0.185 0.102 66 8.8 G_cuneus 1584 1058 3161 2.334 0.518 0.177 0.096 37 5.8 G_front_inf-Opercular 377 245 846 2.641 0.494 0.204 0.249 16 3.0 G_front_inf-Orbital 1184 852 2427 2.255 0.481 0.230 0.167 62 7.5 G_front_inf-Triangul 3961 2622 7928 2.304 0.537 0.214 0.152 190 26.2 G_front_middle 6751 4446 14336 2.500 0.648 0.208 0.264 612 72.6 G_front_sup 554 360 1191 2.786 0.877 0.189 0.155 37 3.5 G_Ins_lg_and_S_cent_ins 746 464 1969 3.181 0.854 0.193 0.117 25 4.0 G_insular_short 2134 1282 4050 2.431 0.412 0.163 0.106 88 7.5 G_occipital_middle 1436 867 2081 2.069 0.478 0.158 0.074 30 4.3 G_occipital_sup 2057 1288 3963 2.412 0.575 0.176 0.149 90 9.1 G_oc-temp_lat-fusifor 3185 1968 4503 1.890 0.664 0.190 0.104 96 13.7 G_oc-temp_med-Lingual 1274 860 3174 2.648 0.937 0.158 0.092 24 4.6 G_oc-temp_med-Parahip 2776 1783 5751 2.384 0.664 0.200 0.149 120 16.8 G_orbital 3183 1830 4651 2.050 0.498 0.153 0.126 134 15.2 G_pariet_inf-Angular 3330 2029 5940 2.346 0.505 0.159 0.336 224 16.5 G_pariet_inf-Supramar 3477 2051 5823 2.255 0.489 0.159 0.150 548 27.1 G_parietal_sup 2875 1677 3872 1.899 0.526 0.178 0.146 110 15.5 G_postcentral 2970 1910 6076 2.505 0.482 0.195 0.365 271 18.5 G_precentral 2956 1779 4854 2.207 0.456 0.165 0.110 158 13.8 G_precuneus 502 346 989 2.119 0.761 0.256 0.186 42 3.0 G_rectus 407 265 652 2.464 0.856 0.240 0.475 80 3.3 G_subcallosal 398 255 835 2.652 0.390 0.187 0.108 10 1.7 G_temp_sup-G_T_transv 2116 1425 4543 2.456 0.542 0.194 0.101 178 9.4 G_temp_sup-Lateral 555 353 1198 2.882 0.669 0.164 0.104 17 2.9 G_temp_sup-Plan_polar 732 513 1208 2.241 0.502 0.125 0.045 18 1.1 G_temp_sup-Plan_tempo 3048 2042 6711 2.455 0.678 0.198 0.161 169 16.0 G_temporal_inf 2475 1663 5583 2.489 0.548 0.173 0.087 74 8.0 G_temporal_middle 398 274 514 1.932 0.432 0.136 0.045 4 0.8 Lat_Fis-ant-Horizont 143 102 211 1.913 0.429 0.130 0.039 1 0.2 Lat_Fis-ant-Vertical 1555 1003 2100 2.309 0.541 0.127 0.052 26 4.0 Lat_Fis-post 3557 2253 4743 1.827 0.540 0.188 0.108 105 15.4 Pole_occipital 1829 1301 5346 2.928 0.763 0.214 0.169 83 10.2 Pole_temporal 2338 1488 2342 1.714 0.491 0.160 0.076 39 7.4 S_calcarine 3484 2277 3848 1.820 0.587 0.140 0.099 92 10.8 S_central 1377 954 1941 1.978 0.430 0.128 0.040 13 2.4 S_cingul-Marginalis 726 431 1020 2.450 0.474 0.135 0.115 113 5.2 S_circular_insula_ant 1411 893 2133 2.460 0.798 0.115 0.055 22 4.4 S_circular_insula_inf 1559 947 1830 2.219 0.364 0.116 0.066 22 2.8 S_circular_insula_sup 904 603 1482 2.264 0.782 0.167 0.114 154 3.0 S_collat_transv_ant 536 343 632 1.911 0.392 0.162 0.101 78 2.9 S_collat_transv_post 2540 1787 3414 1.861 0.435 0.160 0.089 85 8.5 S_front_inf 2045 1355 2540 1.795 0.516 0.168 0.087 62 6.2 S_front_middle 2187 1392 3025 2.077 0.515 0.149 0.076 35 7.9 S_front_sup 969 627 967 1.766 0.409 0.135 0.045 11 1.9 S_interm_prim-Jensen 3052 1967 3478 1.809 0.442 0.121 0.050 32 7.0 S_intrapariet_and_P_trans 1251 830 1583 1.898 0.471 0.157 0.057 18 2.8 S_oc_middle_and_Lunatus 1385 889 1609 1.833 0.408 0.135 0.073 31 5.0 S_oc_sup_and_transversal 791 530 992 1.986 0.408 0.129 0.039 6 1.4 S_occipital_ant 1069 695 1229 1.929 0.429 0.140 0.053 13 2.2 S_oc-temp_lat 2441 1590 2862 1.884 0.522 0.116 0.038 18 3.9 S_oc-temp_med_and_Lingual 493 336 595 1.811 0.482 0.179 0.102 11 1.6 S_orbital_lateral 755 525 1111 2.135 0.893 0.165 0.132 33 4.8 S_orbital_med-olfact 1645 1061 2144 1.930 0.458 0.166 0.142 410 13.3 S_orbital-H_Shaped 2637 1678 3028 1.944 0.463 0.132 2.785 159 5.2 S_parieto_occipital 2031 1234 1908 1.663 0.716 0.143 0.063 38 5.2 S_pericallosal 3786 2515 4836 1.999 0.432 0.122 0.039 35 6.1 S_postcentral 1765 1147 2614 2.218 0.413 0.128 0.050 19 3.5 S_precentral-inf-part 1635 1057 2101 2.113 0.401 0.129 0.045 14 3.3 S_precentral-sup-part 341 207 311 1.531 0.425 0.143 0.051 5 0.8 S_suborbital 1188 807 1607 1.904 0.473 0.152 0.056 18 2.6 S_subparietal 1863 1192 2120 1.842 0.448 0.124 0.038 18 3.0 S_temporal_inf 5447 3534 6832 1.932 0.501 0.128 0.051 84 11.7 S_temporal_sup 287 179 416 2.352 0.551 0.131 0.039 3 0.5 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Thu Jul 7 04:31:39 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD08 SUBJECTS_DIR is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc 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 = 10 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Jul 7 04:46:25 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 sysname Linux hostname compute-0-38 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 258972.108938, pTot = 454322.668305 c = 195350.559367 rh surface-based volumes (mm3): wTot = 260471.231776, pTot = 466432.139438 c = 205960.907661 Computing SupraTentVolCor SupraTentVolCor = 58285.000 SupraTentVol = 979039.808 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 15145 15145 4 5 Left-Inf-Lat-Vent 1149 1149 5 7 Left-Cerebellum-White-Matter 17556 17556 6 8 Left-Cerebellum-Cortex 44861 44861 7 10 Left-Thalamus-Proper 6807 6807 8 11 Left-Caudate 3464 3464 9 12 Left-Putamen 4740 4740 10 13 Left-Pallidum 1933 1933 11 14 3rd-Ventricle 1427 1427 12 15 4th-Ventricle 2955 2955 13 16 Brain-Stem 23899 23899 14 17 Left-Hippocampus 3066 3066 15 18 Left-Amygdala 1242 1242 16 24 CSF 1107 1107 17 26 Left-Accumbens-area 420 420 18 28 Left-VentralDC 3845 3845 19 30 Left-vessel 241 241 20 31 Left-choroid-plexus 1635 1635 23 43 Right-Lateral-Ventricle 14333 14333 24 44 Right-Inf-Lat-Vent 743 743 25 46 Right-Cerebellum-White-Matter 17594 17594 26 47 Right-Cerebellum-Cortex 46152 46152 27 49 Right-Thalamus-Proper 7471 7471 28 50 Right-Caudate 3761 3761 29 51 Right-Putamen 4453 4453 30 52 Right-Pallidum 1684 1684 31 53 Right-Hippocampus 3348 3348 32 54 Right-Amygdala 1305 1305 33 58 Right-Accumbens-area 464 464 34 60 Right-VentralDC 3973 3973 35 62 Right-vessel 222 222 36 63 Right-choroid-plexus 2130 2130 37 72 5th-Ventricle 12 12 38 77 WM-hypointensities 2083 2083 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 65 65 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 233 233 45 251 CC_Posterior 1216 1216 46 252 CC_Mid_Posterior 384 384 47 253 CC_Central 339 339 48 254 CC_Mid_Anterior 390 390 49 255 CC_Anterior 874 874 Reporting on 45 segmentations SubCortGrayVol = 166888 #----------------------------------------- #@# AParc-to-ASeg Thu Jul 7 04:57:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Jul 7 04:59:51 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8815 vertices from left hemi Ripped 8203 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 834030 Used brute-force search on 110 voxels Fixing Parahip LH WM Found 18 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1.000000 5 k 1354.000000 6 k 1.000000 7 k 2.000000 8 k 2.000000 9 k 1.000000 10 k 1.000000 11 k 13.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 15 k 2.000000 16 k 3.000000 17 k 1.000000 Fixing Parahip RH WM Found 16 clusters 0 k 1.000000 1 k 1808.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2.000000 10 k 2.000000 11 k 2.000000 12 k 1.000000 13 k 2.000000 14 k 2.000000 15 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-38 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1547561 # brainmaskvolume 1547561.0 # nbrainsegvoxels 243367 # brainsegvolume 243367.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 2776 2776 2 3002 wm-lh-caudalanteriorcingulate 2720 2720 3 3003 wm-lh-caudalmiddlefrontal 5961 5961 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2294 2294 6 3006 wm-lh-entorhinal 820 820 7 3007 wm-lh-fusiform 5595 5595 8 3008 wm-lh-inferiorparietal 8388 8388 9 3009 wm-lh-inferiortemporal 6212 6212 10 3010 wm-lh-isthmuscingulate 4114 4114 11 3011 wm-lh-lateraloccipital 8928 8928 12 3012 wm-lh-lateralorbitofrontal 6713 6713 13 3013 wm-lh-lingual 6305 6305 14 3014 wm-lh-medialorbitofrontal 3779 3779 15 3015 wm-lh-middletemporal 4678 4678 16 3016 wm-lh-parahippocampal 1476 1476 17 3017 wm-lh-paracentral 2933 2933 18 3018 wm-lh-parsopercularis 4019 4019 19 3019 wm-lh-parsorbitalis 843 843 20 3020 wm-lh-parstriangularis 2889 2889 21 3021 wm-lh-pericalcarine 2819 2819 22 3022 wm-lh-postcentral 7567 7567 23 3023 wm-lh-posteriorcingulate 4309 4309 24 3024 wm-lh-precentral 12490 12490 25 3025 wm-lh-precuneus 9183 9183 26 3026 wm-lh-rostralanteriorcingulate 2695 2695 27 3027 wm-lh-rostralmiddlefrontal 10374 10374 28 3028 wm-lh-superiorfrontal 17013 17013 29 3029 wm-lh-superiorparietal 11728 11728 30 3030 wm-lh-superiortemporal 7345 7345 31 3031 wm-lh-supramarginal 8947 8947 32 3032 wm-lh-frontalpole 260 260 33 3033 wm-lh-temporalpole 583 583 34 3034 wm-lh-transversetemporal 1023 1023 35 3035 wm-lh-insula 9565 9565 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2116 2116 120 4002 wm-rh-caudalanteriorcingulate 2915 2915 121 4003 wm-rh-caudalmiddlefrontal 4665 4665 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1879 1879 124 4006 wm-rh-entorhinal 597 597 125 4007 wm-rh-fusiform 7225 7225 126 4008 wm-rh-inferiorparietal 9817 9817 127 4009 wm-rh-inferiortemporal 5479 5479 128 4010 wm-rh-isthmuscingulate 4186 4186 129 4011 wm-rh-lateraloccipital 8847 8847 130 4012 wm-rh-lateralorbitofrontal 7030 7030 131 4013 wm-rh-lingual 5459 5459 132 4014 wm-rh-medialorbitofrontal 3461 3461 133 4015 wm-rh-middletemporal 6342 6342 134 4016 wm-rh-parahippocampal 1895 1895 135 4017 wm-rh-paracentral 3504 3504 136 4018 wm-rh-parsopercularis 3687 3687 137 4019 wm-rh-parsorbitalis 1100 1100 138 4020 wm-rh-parstriangularis 3066 3066 139 4021 wm-rh-pericalcarine 2768 2768 140 4022 wm-rh-postcentral 8134 8134 141 4023 wm-rh-posteriorcingulate 4048 4048 142 4024 wm-rh-precentral 14551 14551 143 4025 wm-rh-precuneus 10490 10490 144 4026 wm-rh-rostralanteriorcingulate 2285 2285 145 4027 wm-rh-rostralmiddlefrontal 12145 12145 146 4028 wm-rh-superiorfrontal 15641 15641 147 4029 wm-rh-superiorparietal 11048 11048 148 4030 wm-rh-superiortemporal 7531 7531 149 4031 wm-rh-supramarginal 10131 10131 150 4032 wm-rh-frontalpole 310 310 151 4033 wm-rh-temporalpole 607 607 152 4034 wm-rh-transversetemporal 775 775 153 4035 wm-rh-insula 8431 8431 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 32709 32709 237 5002 Right-UnsegmentedWhiteMatter 32447 32447 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label #-------------------------------------------- #@# BA Labels lh Thu Jul 7 05:17:43 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD08 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD08 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label Linux compute-0-38 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AD08 exited with ERRORS at Thu Jul 7 05:17:43 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Jul 11 15:19:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon3 -no-isrunning -subjid AD08 subjid AD08 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-39 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 2203516 22400880 8 194776 920756 -/+ buffers/cache: 1087984 23516412 Swap: 67108860 79160 67029700 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:52-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:19:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-39 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Sphere lh Mon Jul 11 15:19:55 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.20 hours scaling brain by 0.295... pass 1: epoch 1 of 3 starting distance error %19.00 pass 1: epoch 2 of 3 starting distance error %18.92 unfolding complete - removing small folds... starting distance error %18.87 removing remaining folds... final distance error %18.90 #-------------------------------------------- #@# Surf Reg lh Mon Jul 11 16:31:49 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.580 curvature mean = 0.024, std = 0.938 curvature mean = 0.028, std = 0.863 curvature mean = -0.017, std = 0.959 curvature mean = 0.012, std = 0.942 curvature mean = -0.019, std = 0.971 curvature mean = 0.005, std = 0.974 curvature mean = -0.023, std = 0.973 curvature mean = 0.001, std = 0.989 curvature mean = -0.034, std = 0.331 curvature mean = 0.001, std = 0.068 curvature mean = 0.076, std = 0.297 curvature mean = 0.000, std = 0.081 curvature mean = 0.040, std = 0.471 curvature mean = 0.000, std = 0.087 curvature mean = 0.024, std = 0.604 curvature mean = 0.001, std = 0.089 curvature mean = 0.009, std = 0.718 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Mon Jul 11 17:17:09 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 Mon Jul 11 17:17:12 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Jul 11 17:17:14 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1246 labels changed using aseg relabeling using gibbs priors... 000: 3127 changed, 140242 examined... 001: 720 changed, 13258 examined... 002: 176 changed, 4054 examined... 003: 57 changed, 1023 examined... 004: 22 changed, 339 examined... 005: 12 changed, 129 examined... 006: 4 changed, 69 examined... 007: 6 changed, 23 examined... 008: 4 changed, 27 examined... 009: 0 changed, 18 examined... 273 labels changed using aseg 000: 126 total segments, 82 labels (389 vertices) changed 001: 42 total segments, 4 labels (15 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1957 vertices marked for relabeling... 1957 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 55 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Jul 11 17:18:10 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 20465 bright wm thresholded. 2114 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 94.0 +- 8.5 [70.0 --> 110.0] GM (79.0) : 76.6 +- 14.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 110.5 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 34.4 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 19.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=64 using class modes intead of means.... mean inside = 91.2, mean outside = 69.9 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->3.63) (max @ vno 8665 --> 139077) face area 0.27 +- 0.13 (0.00-->1.78) mean absolute distance = 0.93 +- 1.28 5350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 3 with 442 points - only 1.36% unknown removing 4 vertex label from ripped group deleting segment 7 with 37 points - only 0.00% unknown mean border=78.0, 152 (152) missing vertices, mean dist 0.1 [1.1 (%38.8)->0.8 (%61.2))] %37 local maxima, %58 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.28 (0.09-->3.76) (max @ vno 68809 --> 65116) face area 0.27 +- 0.14 (0.00-->1.99) mean absolute distance = 0.50 +- 0.87 5842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6552842.0, rms=12.07 001: dt: 0.5000, sse=7454261.0, rms=8.41 002: dt: 0.5000, sse=7951210.5, rms=6.34 003: dt: 0.5000, sse=8404685.0, rms=5.23 004: dt: 0.5000, sse=8672549.0, rms=4.64 005: dt: 0.5000, sse=8929870.0, rms=4.34 006: dt: 0.5000, sse=8992582.0, rms=4.19 007: dt: 0.5000, sse=9132031.0, rms=4.10 008: dt: 0.5000, sse=9099035.0, rms=4.04 rms = 4.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9164616.0, rms=4.00 010: dt: 0.2500, sse=6044842.5, rms=2.96 011: dt: 0.2500, sse=5692483.5, rms=2.60 012: dt: 0.2500, sse=5434416.0, rms=2.53 013: dt: 0.2500, sse=5347533.5, rms=2.47 rms = 2.45, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5268282.0, rms=2.45 015: dt: 0.1250, sse=5100403.0, rms=2.32 rms = 2.31, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=5060169.0, rms=2.31 positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 328 points - only 1.83% unknown deleting segment 9 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 59 points - only 35.59% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown mean border=80.5, 180 (36) missing vertices, mean dist -0.3 [0.7 (%59.0)->0.3 (%41.0))] %50 local maxima, %45 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 +- 0.27 (0.08-->3.62) (max @ vno 4941 --> 139077) face area 0.34 +- 0.17 (0.00-->2.39) mean absolute distance = 0.38 +- 0.54 4488 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5638249.0, rms=4.73 017: dt: 0.5000, sse=6309014.0, rms=3.52 rms = 3.76, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5758217.5, rms=2.77 019: dt: 0.2500, sse=5560744.0, rms=2.36 020: dt: 0.2500, sse=5422151.0, rms=2.16 021: dt: 0.2500, sse=5377637.0, rms=2.08 rms = 2.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5322279.5, rms=2.04 023: dt: 0.1250, sse=5207634.5, rms=1.94 rms = 1.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5159747.0, rms=1.92 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 338 points - only 1.78% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 48 points - only 33.33% unknown removing 3 vertex label from ripped group deleting segment 13 with 13 points - only 0.00% unknown deleting segment 14 with 5 points - only 40.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=83.3, 168 (23) missing vertices, mean dist -0.2 [0.5 (%65.7)->0.2 (%34.3))] %69 local maxima, %26 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 0.88 +- 0.27 (0.09-->3.70) (max @ vno 110092 --> 109304) face area 0.33 +- 0.17 (0.00-->2.57) mean absolute distance = 0.29 +- 0.42 4206 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5524511.0, rms=4.26 025: dt: 0.5000, sse=6001023.5, rms=3.30 rms = 3.64, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5551531.0, rms=2.40 027: dt: 0.2500, sse=5516627.5, rms=2.01 028: dt: 0.2500, sse=5457070.5, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5421263.0, rms=1.85 030: dt: 0.1250, sse=5273728.0, rms=1.71 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5227965.5, rms=1.70 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 401 points - only 1.50% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 8 with 27 points - only 29.63% unknown deleting segment 9 with 25 points - only 36.00% unknown deleting segment 10 with 30 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 mean border=84.6, 186 (20) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.2 (%42.6))] %77 local maxima, %18 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=5300406.0, rms=2.45 rms = 2.56, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5452801.0, rms=1.75 033: dt: 0.2500, sse=5790372.0, rms=1.30 rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.29, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5776684.0, rms=1.29 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 6 with 12 points - only 50.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 33.33% unknown smoothing surface for 5 iterations... mean border=51.8, 194 (194) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %30 local maxima, %53 large gradients and %13 min vals, 384 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=30757508.0, rms=32.32 001: dt: 0.5000, sse=23489058.0, rms=27.79 002: dt: 0.5000, sse=18131408.0, rms=23.92 003: dt: 0.5000, sse=14754232.0, rms=20.79 004: dt: 0.5000, sse=12853140.0, rms=18.22 005: dt: 0.5000, sse=11433724.0, rms=15.93 006: dt: 0.5000, sse=10400128.0, rms=13.86 007: dt: 0.5000, sse=9520772.0, rms=11.91 008: dt: 0.5000, sse=8996410.0, rms=10.15 009: dt: 0.5000, sse=8662828.0, rms=8.73 010: dt: 0.5000, sse=8726024.0, rms=7.75 011: dt: 0.5000, sse=8693177.0, rms=7.11 012: dt: 0.5000, sse=8836631.0, rms=6.74 013: dt: 0.5000, sse=8856195.0, rms=6.51 014: dt: 0.5000, sse=8937619.0, rms=6.38 015: dt: 0.5000, sse=8963670.0, rms=6.26 016: dt: 0.5000, sse=8991374.0, rms=6.21 017: dt: 0.5000, sse=9004687.0, rms=6.15 rms = 6.10, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=9004395.0, rms=6.10 019: dt: 0.2500, sse=6180831.5, rms=4.84 020: dt: 0.2500, sse=5974802.5, rms=4.47 rms = 4.46, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5785029.5, rms=4.46 022: dt: 0.1250, sse=5117638.0, rms=3.87 023: dt: 0.1250, sse=5039741.0, rms=3.77 rms = 3.76, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4995385.0, rms=3.76 positioning took 3.0 minutes mean border=48.9, 816 (39) missing vertices, mean dist 0.2 [0.1 (%44.7)->0.5 (%55.3))] %45 local maxima, %39 large gradients and %11 min vals, 150 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=5835728.5, rms=6.08 rms = 6.20, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5551875.0, rms=5.29 026: dt: 0.2500, sse=5410220.0, rms=4.77 027: dt: 0.2500, sse=5742131.0, rms=4.60 rms = 4.55, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5866132.5, rms=4.55 029: dt: 0.1250, sse=5379359.0, rms=4.06 030: dt: 0.1250, sse=5365952.0, rms=3.92 rms = 3.87, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5349754.0, rms=3.87 positioning took 0.9 minutes mean border=46.5, 908 (32) missing vertices, mean dist 0.1 [0.1 (%40.8)->0.3 (%59.2))] %59 local maxima, %26 large gradients and %11 min vals, 171 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=5666460.0, rms=5.12 rms = 6.17, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5432502.5, rms=4.37 033: dt: 0.2500, sse=5501489.0, rms=4.11 034: dt: 0.2500, sse=5780536.5, rms=4.04 rms = 4.10, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=5631257.0, rms=3.87 036: dt: 0.1250, sse=5520276.0, rms=3.61 037: dt: 0.1250, sse=5466238.0, rms=3.55 rms = 3.52, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5476543.0, rms=3.52 positioning took 1.0 minutes mean border=45.1, 1489 (31) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))] %63 local maxima, %21 large gradients and %11 min vals, 157 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5556611.0, rms=3.92 rms = 5.55, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5418418.0, rms=3.51 040: dt: 0.2500, sse=5668201.0, rms=3.44 rms = 3.50, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=5588358.0, rms=3.36 042: dt: 0.1250, sse=5531272.0, rms=3.24 043: dt: 0.1250, sse=5528230.0, rms=3.19 rms = 3.16, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5555913.0, rms=3.16 positioning took 0.8 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.03-->5.98) (max @ vno 98271 --> 97182) face area 0.39 +- 0.29 (0.00-->5.10) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed thickness calculation complete, 144:197 truncations. 69914 vertices at 0 distance 94273 vertices at 1 distance 69175 vertices at 2 distance 24600 vertices at 3 distance 6812 vertices at 4 distance 2060 vertices at 5 distance 777 vertices at 6 distance 337 vertices at 7 distance 167 vertices at 8 distance 108 vertices at 9 distance 69 vertices at 10 distance 62 vertices at 11 distance 46 vertices at 12 distance 28 vertices at 13 distance 32 vertices at 14 distance 18 vertices at 15 distance 14 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 9 vertices at 19 distance 13 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.thickness positioning took 13.3 minutes #-------------------------------------------- #@# Surf Volume lh Mon Jul 11 17:31:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Mon Jul 11 17:31:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1779 1158 2315 1.949 0.513 0.154 0.077 35 5.9 bankssts 1179 775 2203 2.547 0.750 0.185 0.093 34 4.4 caudalanteriorcingulate 2942 2008 5204 2.210 0.597 0.190 0.458 1009 23.4 caudalmiddlefrontal 2535 1550 2612 1.622 0.395 0.169 0.089 100 10.8 cuneus 663 432 1543 2.697 0.940 0.190 0.231 27 8.9 entorhinal 4145 2828 8072 2.405 0.593 0.176 0.099 353 19.7 fusiform 7388 4410 8816 1.807 0.527 0.149 0.089 187 25.9 inferiorparietal 4349 2992 7524 2.167 0.581 0.179 0.098 112 17.0 inferiortemporal 1895 1230 2235 1.741 0.653 0.182 0.194 113 13.8 isthmuscingulate 7202 4601 9697 1.920 0.499 0.170 0.086 147 25.5 lateraloccipital 4024 2652 6615 2.202 0.592 0.182 0.107 134 18.8 lateralorbitofrontal 5638 3650 7262 1.791 0.524 0.181 0.093 135 22.6 lingual 3097 1957 4260 2.009 0.770 0.182 0.220 237 26.1 medialorbitofrontal 4546 3079 8073 2.203 0.532 0.174 0.116 159 18.8 middletemporal 1058 697 2305 2.599 0.773 0.172 0.112 31 5.0 parahippocampal 2099 1250 3034 2.257 0.461 0.157 0.104 46 8.9 paracentral 2680 1901 4893 2.243 0.482 0.163 0.085 81 8.7 parsopercularis 1089 707 2079 2.251 0.461 0.216 0.133 42 5.6 parsorbitalis 1807 1215 2650 1.996 0.444 0.165 0.076 35 5.4 parstriangularis 1880 1190 1847 1.686 0.437 0.164 0.086 37 7.0 pericalcarine 7661 4625 10504 2.023 0.629 0.153 0.106 698 34.4 postcentral 1901 1277 2814 2.081 0.646 0.172 0.163 48 5.8 posteriorcingulate 7621 4806 11851 2.289 0.541 0.170 0.209 950 33.7 precentral 6672 4208 7644 1.749 0.479 0.157 0.103 278 25.0 precuneus 1368 907 2600 2.517 0.636 0.179 0.097 44 5.2 rostralanteriorcingulate 7308 5129 12270 2.011 0.571 0.197 0.127 254 36.3 rostralmiddlefrontal 10486 7229 20143 2.348 0.652 0.194 0.143 469 61.5 superiorfrontal 8720 5060 10251 1.889 0.512 0.145 0.131 457 39.7 superiorparietal 5525 3674 10173 2.372 0.555 0.143 0.097 91 14.4 superiortemporal 6454 3971 8928 2.068 0.589 0.145 0.086 321 24.3 supramarginal 345 232 628 2.141 0.427 0.222 0.155 14 2.0 frontalpole 684 455 2287 3.355 0.691 0.195 0.130 18 4.4 temporalpole 827 473 1189 2.262 0.371 0.160 0.089 18 3.1 transversetemporal 3860 2557 7204 2.667 0.698 0.171 0.115 117 15.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Jul 11 17:31:47 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 35 labels changed using aseg relabeling using gibbs priors... 000: 9190 changed, 140242 examined... 001: 2246 changed, 35157 examined... 002: 641 changed, 11612 examined... 003: 240 changed, 3580 examined... 004: 119 changed, 1386 examined... 005: 54 changed, 673 examined... 006: 34 changed, 341 examined... 007: 10 changed, 164 examined... 008: 9 changed, 56 examined... 009: 4 changed, 45 examined... 010: 2 changed, 26 examined... 011: 3 changed, 12 examined... 012: 4 changed, 20 examined... 013: 1 changed, 16 examined... 014: 0 changed, 7 examined... 7 labels changed using aseg 000: 292 total segments, 211 labels (2597 vertices) changed 001: 98 total segments, 18 labels (126 vertices) changed 002: 81 total segments, 1 labels (1 vertices) changed 003: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 106 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1111 vertices marked for relabeling... 1111 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 3 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Jul 11 17:32:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1457 1006 2220 1.922 0.487 0.211 0.121 51 7.9 G_and_S_frontomargin 1543 1030 2232 1.964 0.497 0.152 0.058 21 3.7 G_and_S_occipital_inf 1650 923 2236 2.125 0.515 0.188 0.198 110 15.1 G_and_S_paracentral 1707 1121 3324 2.496 0.543 0.158 0.072 28 4.7 G_and_S_subcentral 640 435 1215 2.137 0.455 0.234 0.167 27 4.4 G_and_S_transv_frontopol 2552 1737 4262 2.182 0.628 0.167 0.080 61 8.1 G_and_S_cingul-Ant 1605 1067 2629 2.370 0.542 0.165 0.084 36 5.4 G_and_S_cingul-Mid-Ant 1528 998 2519 2.335 0.471 0.160 0.166 28 5.0 G_and_S_cingul-Mid-Post 626 429 986 1.950 0.619 0.223 0.179 25 3.1 G_cingul-Post-dorsal 372 240 506 1.852 0.644 0.202 0.151 23 1.6 G_cingul-Post-ventral 2244 1365 2403 1.584 0.388 0.182 0.108 103 11.5 G_cuneus 1795 1237 3544 2.349 0.473 0.176 0.102 71 6.7 G_front_inf-Opercular 377 242 761 2.369 0.460 0.197 0.116 12 1.8 G_front_inf-Orbital 1028 682 1917 2.197 0.429 0.187 0.101 29 3.9 G_front_inf-Triangul 3375 2339 7098 2.297 0.633 0.218 0.182 155 27.7 G_front_middle 7082 4814 15424 2.519 0.664 0.217 0.189 433 53.4 G_front_sup 793 480 1602 2.853 0.843 0.226 0.171 52 5.4 G_Ins_lg_and_S_cent_ins 693 489 1976 3.138 0.675 0.210 0.118 21 3.1 G_insular_short 2202 1373 3950 2.272 0.519 0.177 0.096 54 7.8 G_occipital_middle 1653 921 2045 1.922 0.527 0.144 0.137 218 6.7 G_occipital_sup 1654 1088 3698 2.567 0.510 0.182 0.087 40 6.0 G_oc-temp_lat-fusifor 4202 2627 5564 1.796 0.544 0.193 0.111 124 19.8 G_oc-temp_med-Lingual 1355 888 3212 2.719 0.844 0.201 0.198 60 13.6 G_oc-temp_med-Parahip 2779 1837 5213 2.166 0.634 0.215 0.148 135 17.7 G_orbital 2542 1327 2870 1.825 0.497 0.167 0.138 95 13.8 G_pariet_inf-Angular 3511 2071 5655 2.257 0.600 0.157 0.099 228 14.4 G_pariet_inf-Supramar 3661 1915 4601 1.995 0.522 0.157 0.192 184 22.5 G_parietal_sup 3014 1585 4051 2.070 0.565 0.156 0.146 136 18.0 G_postcentral 3022 1710 5448 2.520 0.542 0.185 0.357 833 18.6 G_precentral 3485 2102 4186 1.738 0.504 0.174 0.141 234 17.5 G_precuneus 1014 640 1732 2.038 0.641 0.222 0.292 117 8.4 G_rectus 654 393 786 2.035 0.891 0.196 0.407 96 14.0 G_subcallosal 649 362 1042 2.337 0.353 0.172 0.101 17 2.9 G_temp_sup-G_T_transv 2323 1527 5603 2.649 0.574 0.180 0.184 66 9.4 G_temp_sup-Lateral 563 386 1307 2.972 0.603 0.144 0.103 9 2.4 G_temp_sup-Plan_polar 1028 662 1588 2.090 0.485 0.129 0.052 17 2.2 G_temp_sup-Plan_tempo 2145 1497 4635 2.353 0.600 0.204 0.126 79 11.2 G_temporal_inf 3055 2021 5972 2.281 0.522 0.194 0.152 146 16.0 G_temporal_middle 362 244 387 1.746 0.491 0.139 0.046 3 0.7 Lat_Fis-ant-Horizont 326 224 433 1.991 0.410 0.139 0.052 3 0.7 Lat_Fis-ant-Vertical 1208 810 1453 2.065 0.465 0.136 0.046 11 2.4 Lat_Fis-post 2465 1513 3120 1.836 0.483 0.191 0.114 71 11.7 Pole_occipital 1625 1126 4415 2.786 0.835 0.198 0.115 41 7.6 Pole_temporal 2331 1517 2473 1.787 0.551 0.156 0.076 39 7.6 S_calcarine 2994 2119 3378 1.754 0.561 0.154 0.123 81 9.3 S_central 1123 776 1398 1.983 0.417 0.115 0.032 8 1.6 S_cingul-Marginalis 555 367 855 2.444 0.411 0.132 0.054 5 1.3 S_circular_insula_ant 1620 1069 2271 2.315 0.504 0.109 0.072 20 3.0 S_circular_insula_inf 1906 1267 2683 2.378 0.421 0.131 0.047 17 3.8 S_circular_insula_sup 741 531 1355 2.314 0.773 0.185 0.194 282 8.5 S_collat_transv_ant 531 349 488 1.697 0.327 0.167 0.062 7 1.4 S_collat_transv_post 1621 1137 2105 1.822 0.459 0.146 0.065 19 4.3 S_front_inf 1819 1281 2713 1.931 0.517 0.178 0.116 58 7.2 S_front_middle 2316 1622 3560 2.021 0.516 0.170 0.493 965 11.3 S_front_sup 288 189 267 1.599 0.370 0.170 0.078 5 1.0 S_interm_prim-Jensen 2580 1631 2572 1.668 0.439 0.134 0.046 31 4.9 S_intrapariet_and_P_trans 986 673 1260 1.908 0.432 0.142 0.046 10 1.8 S_oc_middle_and_Lunatus 1439 947 1611 1.829 0.337 0.122 0.037 11 2.2 S_oc_sup_and_transversal 815 551 1058 2.000 0.448 0.150 0.054 10 2.0 S_occipital_ant 753 509 978 2.116 0.400 0.140 0.052 7 1.7 S_oc-temp_lat 1957 1378 2765 2.112 0.466 0.138 0.045 18 3.7 S_oc-temp_med_and_Lingual 406 291 605 1.869 0.441 0.167 0.061 7 1.1 S_orbital_lateral 1027 663 1349 2.192 0.737 0.149 0.082 20 3.2 S_orbital_med-olfact 1525 1024 2319 2.165 0.521 0.176 0.085 34 5.3 S_orbital-H_Shaped 2309 1460 2407 1.743 0.444 0.132 0.045 27 4.4 S_parieto_occipital 1611 1000 1510 1.825 0.938 0.162 0.128 57 5.4 S_pericallosal 4059 2687 4757 1.852 0.500 0.129 0.066 548 13.5 S_postcentral 1427 993 2124 2.133 0.439 0.150 0.060 21 3.6 S_precentral-inf-part 1434 963 1845 2.068 0.460 0.148 0.061 17 4.0 S_precentral-sup-part 560 377 723 2.099 0.866 0.149 0.053 6 1.3 S_suborbital 1235 825 1449 1.733 0.387 0.173 0.165 65 10.3 S_subparietal 1644 1123 1964 1.924 0.430 0.159 0.064 28 4.4 S_temporal_inf 5920 3854 6619 1.769 0.474 0.133 0.061 96 15.0 S_temporal_sup 331 226 443 2.183 0.510 0.154 0.051 4 0.7 S_temporal_transverse #-------------------------------------------- #@# Sphere rh Mon Jul 11 17:33:10 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.21 hours scaling brain by 0.291... pass 1: epoch 1 of 3 starting distance error %20.20 pass 1: epoch 2 of 3 starting distance error %20.13 unfolding complete - removing small folds... starting distance error %20.04 removing remaining folds... final distance error %20.05 #-------------------------------------------- #@# Surf Reg rh Mon Jul 11 18:45:41 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.603 curvature mean = 0.023, std = 0.929 curvature mean = 0.023, std = 0.862 curvature mean = 0.004, std = 0.947 curvature mean = 0.011, std = 0.942 curvature mean = 0.003, std = 0.958 curvature mean = 0.005, std = 0.974 curvature mean = 0.000, std = 0.957 curvature mean = 0.001, std = 0.989 curvature mean = -0.030, std = 0.330 curvature mean = 0.006, std = 0.070 curvature mean = 0.076, std = 0.291 curvature mean = 0.006, std = 0.083 curvature mean = 0.040, std = 0.464 curvature mean = 0.006, std = 0.089 curvature mean = 0.023, std = 0.597 curvature mean = 0.006, std = 0.091 curvature mean = 0.008, std = 0.714 expanding nbhd size to 1 1114: 1 negative triangles #-------------------------------------------- #@# Jacobian white rh Mon Jul 11 19:40:36 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 Mon Jul 11 19:40:39 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Mon Jul 11 19:40:41 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1336 labels changed using aseg relabeling using gibbs priors... 000: 3068 changed, 142899 examined... 001: 716 changed, 13154 examined... 002: 199 changed, 3973 examined... 003: 70 changed, 1145 examined... 004: 28 changed, 420 examined... 005: 12 changed, 168 examined... 006: 6 changed, 67 examined... 007: 4 changed, 36 examined... 008: 1 changed, 19 examined... 009: 0 changed, 7 examined... 175 labels changed using aseg 000: 106 total segments, 65 labels (463 vertices) changed 001: 45 total segments, 6 labels (27 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1773 vertices marked for relabeling... 1773 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf rh Mon Jul 11 19:41:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 21503 bright wm thresholded. 2109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 93.6 +- 10.1 [70.0 --> 110.0] GM (78.0) : 76.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.7 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 45.4 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.1 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=105, GM=70 using class modes intead of means.... mean inside = 95.5, mean outside = 76.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->5.96) (max @ vno 74092 --> 86329) face area 0.27 +- 0.14 (0.00-->5.79) mean absolute distance = 0.93 +- 1.20 5012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 305 points - only 6.89% unknown removing 2 vertex label from ripped group deleting segment 6 with 125 points - only 0.00% unknown deleting segment 7 with 157 points - only 14.65% unknown mean border=82.6, 188 (188) missing vertices, mean dist 0.2 [1.1 (%34.3)->0.8 (%65.7))] %33 local maxima, %63 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.29 (0.08-->7.86) (max @ vno 74092 --> 86329) face area 0.27 +- 0.15 (0.00-->4.69) mean absolute distance = 0.47 +- 0.86 5442 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6089038.5, rms=10.93 001: dt: 0.5000, sse=7128632.0, rms=7.69 002: dt: 0.5000, sse=7759228.0, rms=5.94 003: dt: 0.5000, sse=8263533.0, rms=5.01 004: dt: 0.5000, sse=8545507.0, rms=4.52 005: dt: 0.5000, sse=8741570.0, rms=4.24 006: dt: 0.5000, sse=8813797.0, rms=4.08 007: dt: 0.5000, sse=8890295.0, rms=3.96 008: dt: 0.5000, sse=8913022.0, rms=3.91 009: dt: 0.5000, sse=8910272.0, rms=3.85 rms = 3.84, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8929653.0, rms=3.84 011: dt: 0.2500, sse=5820465.0, rms=2.81 012: dt: 0.2500, sse=5458159.0, rms=2.50 013: dt: 0.2500, sse=5200404.5, rms=2.44 rms = 2.40, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5143673.0, rms=2.40 015: dt: 0.1250, sse=4978326.0, rms=2.29 rms = 2.28, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4936033.5, rms=2.28 positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 3 with 44 points - only 0.00% unknown deleting segment 5 with 231 points - only 9.09% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 209 points - only 12.92% unknown deleting segment 12 with 6 points - only 16.67% unknown deleting segment 13 with 15 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown mean border=85.0, 278 (90) missing vertices, mean dist -0.3 [0.6 (%60.4)->0.3 (%39.6))] %46 local maxima, %50 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 0.88 +- 0.28 (0.08-->7.94) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.63) mean absolute distance = 0.36 +- 0.53 4731 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5423628.0, rms=4.29 017: dt: 0.5000, sse=6010886.5, rms=3.26 rms = 3.48, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5529973.0, rms=2.60 019: dt: 0.2500, sse=5377876.0, rms=2.21 020: dt: 0.2500, sse=5241144.0, rms=2.04 021: dt: 0.2500, sse=5188928.0, rms=1.98 rms = 1.96, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5149818.5, rms=1.96 023: dt: 0.1250, sse=5051597.5, rms=1.88 rms = 1.88, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5013620.5, rms=1.88 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 42 points - only 0.00% unknown deleting segment 2 with 259 points - only 8.11% unknown removing 1 vertex label from ripped group deleting segment 4 with 40 points - only 0.00% unknown deleting segment 5 with 237 points - only 12.24% unknown deleting segment 6 with 41 points - only 9.76% unknown deleting segment 7 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown mean border=87.5, 294 (77) missing vertices, mean dist -0.2 [0.4 (%65.4)->0.2 (%34.6))] %67 local maxima, %29 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 0.87 +- 0.28 (0.07-->7.98) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.60) mean absolute distance = 0.28 +- 0.42 4232 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5306925.0, rms=3.85 025: dt: 0.5000, sse=5704596.0, rms=2.98 rms = 3.35, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5319649.0, rms=2.22 027: dt: 0.2500, sse=5318920.0, rms=1.87 028: dt: 0.2500, sse=5259179.5, rms=1.79 rms = 1.79, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5236060.5, rms=1.79 030: dt: 0.1250, sse=5124335.0, rms=1.70 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5086908.5, rms=1.70 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 274 points - only 7.66% unknown removing 1 vertex label from ripped group deleting segment 5 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 237 points - only 11.39% unknown deleting segment 8 with 35 points - only 11.43% unknown deleting segment 9 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=88.6, 308 (61) missing vertices, mean dist -0.1 [0.3 (%56.1)->0.2 (%43.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5130541.0, rms=2.23 rms = 2.30, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5276731.0, rms=1.64 033: dt: 0.2500, sse=5595339.5, rms=1.31 rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5586387.5, rms=1.30 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 75 points - only 28.00% unknown deleting segment 3 with 27 points - only 40.74% unknown deleting segment 4 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=58.7, 215 (215) missing vertices, mean dist 1.7 [0.3 (%0.0)->1.9 (%100.0))] %37 local maxima, %51 large gradients and % 9 min vals, 350 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=26679052.0, rms=29.55 001: dt: 0.5000, sse=20310612.0, rms=25.25 002: dt: 0.5000, sse=15669898.0, rms=21.57 003: dt: 0.5000, sse=12957546.0, rms=18.67 004: dt: 0.5000, sse=11617793.0, rms=16.33 005: dt: 0.5000, sse=10590400.0, rms=14.36 006: dt: 0.5000, sse=9849688.0, rms=12.66 007: dt: 0.5000, sse=9262034.0, rms=11.11 008: dt: 0.5000, sse=8832515.0, rms=9.64 009: dt: 0.5000, sse=8597882.0, rms=8.39 010: dt: 0.5000, sse=8592985.0, rms=7.43 011: dt: 0.5000, sse=8640643.0, rms=6.80 012: dt: 0.5000, sse=8719318.0, rms=6.40 013: dt: 0.5000, sse=8793360.0, rms=6.17 014: dt: 0.5000, sse=8853058.0, rms=5.99 015: dt: 0.5000, sse=8892565.0, rms=5.90 016: dt: 0.5000, sse=8902767.0, rms=5.81 017: dt: 0.5000, sse=8932318.0, rms=5.76 018: dt: 0.5000, sse=8902494.0, rms=5.70 rms = 5.66, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=8949728.0, rms=5.66 020: dt: 0.2500, sse=6151680.5, rms=4.55 021: dt: 0.2500, sse=5899281.0, rms=4.23 rms = 4.18, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5669862.0, rms=4.18 023: dt: 0.1250, sse=5204998.0, rms=3.81 024: dt: 0.1250, sse=5134826.0, rms=3.75 rms = 3.75, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5093360.0, rms=3.75 positioning took 2.8 minutes mean border=54.8, 652 (37) missing vertices, mean dist 0.2 [0.2 (%37.7)->0.5 (%62.3))] %55 local maxima, %34 large gradients and % 7 min vals, 102 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=6288619.5, rms=6.98 026: dt: 0.5000, sse=6524961.0, rms=6.13 027: dt: 0.5000, sse=8296397.5, rms=5.98 rms = 6.03, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6682149.0, rms=4.80 029: dt: 0.2500, sse=6075032.0, rms=4.43 030: dt: 0.2500, sse=6121183.0, rms=4.32 031: dt: 0.2500, sse=6088259.5, rms=4.27 rms = 4.25, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6127479.5, rms=4.25 033: dt: 0.1250, sse=5635081.5, rms=3.78 034: dt: 0.1250, sse=5587532.0, rms=3.68 rms = 3.67, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5560582.0, rms=3.67 positioning took 1.2 minutes mean border=52.1, 750 (22) missing vertices, mean dist 0.2 [0.2 (%35.3)->0.3 (%64.7))] %66 local maxima, %22 large gradients and % 7 min vals, 140 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=5960273.0, rms=5.21 rms = 5.82, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5677202.0, rms=4.36 037: dt: 0.2500, sse=5631901.0, rms=3.99 038: dt: 0.2500, sse=5884733.0, rms=3.87 rms = 3.89, time step reduction 2 of 3 to 0.125... 039: dt: 0.1250, sse=5748531.0, rms=3.71 040: dt: 0.1250, sse=5629837.5, rms=3.48 041: dt: 0.1250, sse=5572688.5, rms=3.43 rms = 3.41, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5568650.5, rms=3.41 positioning took 0.9 minutes mean border=50.8, 1210 (19) missing vertices, mean dist 0.1 [0.2 (%42.5)->0.3 (%57.5))] %70 local maxima, %19 large gradients and % 7 min vals, 123 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5637445.0, rms=3.78 rms = 5.13, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=5529294.0, rms=3.42 044: dt: 0.2500, sse=5749075.5, rms=3.33 rms = 3.36, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=5681971.0, rms=3.26 046: dt: 0.1250, sse=5627612.0, rms=3.17 rms = 3.13, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5638414.0, rms=3.13 positioning took 0.7 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area.pial vertex spacing 0.98 +- 0.43 (0.01-->7.92) (max @ vno 75151 --> 74088) face area 0.39 +- 0.31 (0.00-->10.51) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed thickness calculation complete, 199:413 truncations. 72812 vertices at 0 distance 92394 vertices at 1 distance 70164 vertices at 2 distance 26252 vertices at 3 distance 7995 vertices at 4 distance 2446 vertices at 5 distance 966 vertices at 6 distance 408 vertices at 7 distance 240 vertices at 8 distance 151 vertices at 9 distance 97 vertices at 10 distance 73 vertices at 11 distance 48 vertices at 12 distance 35 vertices at 13 distance 25 vertices at 14 distance 17 vertices at 15 distance 20 vertices at 16 distance 27 vertices at 17 distance 29 vertices at 18 distance 24 vertices at 19 distance 35 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.thickness positioning took 12.7 minutes #-------------------------------------------- #@# Surf Volume rh Mon Jul 11 19:54:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Mon Jul 11 19:54:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1278 840 1728 1.936 0.479 0.124 0.040 16 2.1 bankssts 1077 685 1867 2.358 0.741 0.165 0.094 28 3.7 caudalanteriorcingulate 2885 1818 4173 2.094 0.452 0.164 0.110 92 15.1 caudalmiddlefrontal 2347 1434 2681 1.689 0.418 0.174 3.167 187 8.9 cuneus 457 317 1581 3.058 1.004 0.186 0.092 10 1.7 entorhinal 4689 3064 8055 2.283 0.635 0.155 0.096 121 15.2 fusiform 8048 4895 10703 1.976 0.505 0.145 0.098 267 30.7 inferiorparietal 5205 3463 9981 2.322 0.689 0.175 0.123 333 20.8 inferiortemporal 1956 1201 2585 1.909 0.752 0.166 0.115 53 7.4 isthmuscingulate 7228 4603 10897 2.054 0.529 0.170 0.084 231 25.9 lateraloccipital 4160 2613 6485 2.199 0.623 0.186 0.146 527 28.7 lateralorbitofrontal 4918 3086 6335 1.805 0.575 0.176 0.088 123 18.1 lingual 2523 1687 3933 2.003 0.688 0.190 0.151 154 11.7 medialorbitofrontal 5084 3375 9316 2.253 0.643 0.160 0.089 134 16.5 middletemporal 1275 785 2110 2.257 0.836 0.121 0.064 16 3.3 parahippocampal 2357 1433 3482 2.176 0.513 0.166 0.271 342 42.0 paracentral 2669 1790 4478 2.192 0.446 0.156 0.080 51 7.9 parsopercularis 1233 837 2486 2.317 0.640 0.171 0.150 35 6.3 parsorbitalis 2224 1548 3873 2.151 0.508 0.189 0.122 74 10.5 parstriangularis 2399 1525 2277 1.590 0.416 0.177 0.101 56 9.6 pericalcarine 7220 4573 9490 1.874 0.539 0.155 0.102 171 26.5 postcentral 1807 1172 2889 2.196 0.642 0.166 0.117 64 7.8 posteriorcingulate 8033 5203 13244 2.297 0.533 0.159 0.186 378 32.1 precentral 6378 4069 9005 2.081 0.481 0.145 0.069 170 18.3 precuneus 1357 827 2187 2.163 0.638 0.171 0.176 76 6.3 rostralanteriorcingulate 9064 6129 14919 2.039 0.586 0.189 0.110 347 37.5 rostralmiddlefrontal 10247 6731 19221 2.364 0.636 0.184 0.157 372 52.4 superiorfrontal 8837 5404 12654 2.064 0.500 0.145 0.099 673 40.8 superiorparietal 5564 3675 9751 2.342 0.579 0.157 0.076 241 19.4 superiortemporal 7043 4464 10622 2.187 0.487 0.139 0.179 259 22.2 supramarginal 448 282 884 2.291 0.596 0.210 0.167 22 2.6 frontalpole 589 411 1870 3.122 0.891 0.232 0.193 40 4.3 temporalpole 576 349 1039 2.563 0.414 0.168 0.091 12 2.2 transversetemporal 3521 2230 6729 2.760 0.845 0.156 0.126 224 19.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Mon Jul 11 19:54:33 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 7 labels changed using aseg relabeling using gibbs priors... 000: 10080 changed, 142899 examined... 001: 2404 changed, 38443 examined... 002: 717 changed, 12274 examined... 003: 334 changed, 3939 examined... 004: 167 changed, 1846 examined... 005: 81 changed, 888 examined... 006: 44 changed, 444 examined... 007: 15 changed, 243 examined... 008: 5 changed, 91 examined... 009: 3 changed, 34 examined... 010: 3 changed, 22 examined... 011: 2 changed, 18 examined... 012: 1 changed, 10 examined... 013: 1 changed, 5 examined... 014: 1 changed, 6 examined... 015: 0 changed, 7 examined... 2 labels changed using aseg 000: 333 total segments, 247 labels (2702 vertices) changed 001: 102 total segments, 18 labels (101 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 152 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1318 vertices marked for relabeling... 1318 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Mon Jul 11 19:55:33 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1271 828 1999 1.959 0.593 0.181 0.105 39 5.2 G_and_S_frontomargin 1344 864 2166 2.157 0.538 0.155 0.067 22 3.8 G_and_S_occipital_inf 1568 835 2084 2.073 0.493 0.172 0.197 74 9.7 G_and_S_paracentral 1493 1001 2715 2.313 0.565 0.166 0.075 30 4.7 G_and_S_subcentral 1153 774 2146 2.160 0.563 0.213 0.141 60 5.7 G_and_S_transv_frontopol 3342 2173 5306 2.127 0.565 0.165 0.121 117 13.7 G_and_S_cingul-Ant 1526 968 2653 2.454 0.517 0.152 0.086 34 5.3 G_and_S_cingul-Mid-Ant 1349 896 2313 2.332 0.539 0.146 0.070 21 3.3 G_and_S_cingul-Mid-Post 849 494 1353 2.237 0.664 0.215 0.216 53 7.3 G_cingul-Post-dorsal 329 209 675 2.687 0.615 0.213 0.223 14 1.4 G_cingul-Post-ventral 2009 1237 2343 1.666 0.436 0.185 0.102 66 8.8 G_cuneus 1584 1058 3161 2.334 0.518 0.177 0.096 37 5.8 G_front_inf-Opercular 377 245 846 2.641 0.494 0.204 0.249 16 3.0 G_front_inf-Orbital 1184 852 2427 2.255 0.481 0.230 0.167 62 7.5 G_front_inf-Triangul 3961 2622 7928 2.304 0.537 0.214 0.152 190 26.2 G_front_middle 6751 4446 14336 2.500 0.648 0.208 0.264 612 72.6 G_front_sup 554 360 1191 2.786 0.877 0.189 0.155 37 3.5 G_Ins_lg_and_S_cent_ins 746 464 1969 3.181 0.854 0.193 0.117 25 4.0 G_insular_short 2134 1282 4050 2.431 0.412 0.163 0.106 88 7.5 G_occipital_middle 1436 867 2081 2.069 0.478 0.158 0.074 30 4.3 G_occipital_sup 2057 1288 3963 2.412 0.575 0.176 0.149 90 9.1 G_oc-temp_lat-fusifor 3185 1968 4503 1.890 0.664 0.190 0.104 96 13.7 G_oc-temp_med-Lingual 1274 860 3174 2.648 0.937 0.158 0.092 24 4.6 G_oc-temp_med-Parahip 2776 1783 5751 2.384 0.664 0.200 0.149 120 16.8 G_orbital 3183 1830 4651 2.050 0.498 0.153 0.126 134 15.2 G_pariet_inf-Angular 3330 2029 5940 2.346 0.505 0.159 0.336 224 16.5 G_pariet_inf-Supramar 3477 2051 5823 2.255 0.489 0.159 0.150 548 27.1 G_parietal_sup 2875 1677 3872 1.899 0.526 0.178 0.146 110 15.5 G_postcentral 2970 1910 6076 2.505 0.482 0.195 0.365 271 18.5 G_precentral 2956 1779 4854 2.207 0.456 0.165 0.110 158 13.8 G_precuneus 502 346 989 2.119 0.761 0.256 0.186 42 3.0 G_rectus 407 265 652 2.464 0.856 0.240 0.475 80 3.3 G_subcallosal 398 255 835 2.652 0.390 0.187 0.108 10 1.7 G_temp_sup-G_T_transv 2116 1425 4543 2.456 0.542 0.194 0.101 178 9.4 G_temp_sup-Lateral 555 353 1198 2.882 0.669 0.164 0.104 17 2.9 G_temp_sup-Plan_polar 732 513 1208 2.241 0.502 0.125 0.045 18 1.1 G_temp_sup-Plan_tempo 3048 2042 6711 2.455 0.678 0.198 0.161 169 16.0 G_temporal_inf 2475 1663 5583 2.489 0.548 0.173 0.087 74 8.0 G_temporal_middle 398 274 514 1.932 0.432 0.136 0.045 4 0.8 Lat_Fis-ant-Horizont 143 102 211 1.913 0.429 0.130 0.039 1 0.2 Lat_Fis-ant-Vertical 1555 1003 2100 2.309 0.541 0.127 0.052 26 4.0 Lat_Fis-post 3557 2253 4743 1.827 0.540 0.188 0.108 105 15.4 Pole_occipital 1829 1301 5346 2.928 0.763 0.214 0.169 83 10.2 Pole_temporal 2338 1488 2342 1.714 0.491 0.160 0.076 39 7.4 S_calcarine 3484 2277 3848 1.820 0.587 0.140 0.099 92 10.8 S_central 1377 954 1941 1.978 0.430 0.128 0.040 13 2.4 S_cingul-Marginalis 726 431 1020 2.450 0.474 0.135 0.115 113 5.2 S_circular_insula_ant 1411 893 2133 2.460 0.798 0.115 0.055 22 4.4 S_circular_insula_inf 1559 947 1830 2.219 0.364 0.116 0.066 22 2.8 S_circular_insula_sup 904 603 1482 2.264 0.782 0.167 0.114 154 3.0 S_collat_transv_ant 536 343 632 1.911 0.392 0.162 0.101 78 2.9 S_collat_transv_post 2540 1787 3414 1.861 0.435 0.160 0.089 85 8.5 S_front_inf 2045 1355 2540 1.795 0.516 0.168 0.087 62 6.2 S_front_middle 2187 1392 3025 2.077 0.515 0.149 0.076 35 7.9 S_front_sup 969 627 967 1.766 0.409 0.135 0.045 11 1.9 S_interm_prim-Jensen 3052 1967 3478 1.809 0.442 0.121 0.050 32 7.0 S_intrapariet_and_P_trans 1251 830 1583 1.898 0.471 0.157 0.057 18 2.8 S_oc_middle_and_Lunatus 1385 889 1609 1.833 0.408 0.135 0.073 31 5.0 S_oc_sup_and_transversal 791 530 992 1.986 0.408 0.129 0.039 6 1.4 S_occipital_ant 1069 695 1229 1.929 0.429 0.140 0.053 13 2.2 S_oc-temp_lat 2441 1590 2862 1.884 0.522 0.116 0.038 18 3.9 S_oc-temp_med_and_Lingual 493 336 595 1.811 0.482 0.179 0.102 11 1.6 S_orbital_lateral 755 525 1111 2.135 0.893 0.165 0.132 33 4.8 S_orbital_med-olfact 1645 1061 2144 1.930 0.458 0.166 0.142 410 13.3 S_orbital-H_Shaped 2637 1678 3028 1.944 0.463 0.132 2.785 159 5.2 S_parieto_occipital 2031 1234 1908 1.663 0.716 0.143 0.063 38 5.2 S_pericallosal 3786 2515 4836 1.999 0.432 0.122 0.039 35 6.1 S_postcentral 1765 1147 2614 2.218 0.413 0.128 0.050 19 3.5 S_precentral-inf-part 1635 1057 2101 2.113 0.401 0.129 0.045 14 3.3 S_precentral-sup-part 341 207 311 1.531 0.425 0.143 0.051 5 0.8 S_suborbital 1188 807 1607 1.904 0.473 0.152 0.056 18 2.6 S_subparietal 1863 1192 2120 1.842 0.448 0.124 0.038 18 3.0 S_temporal_inf 5447 3534 6832 1.932 0.501 0.128 0.051 84 11.7 S_temporal_sup 287 179 416 2.352 0.551 0.131 0.039 3 0.5 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Mon Jul 11 19:55:51 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD08 SUBJECTS_DIR is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc 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 = 10 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Mon Jul 11 20:10:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 sysname Linux hostname compute-0-39 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 258972.108938, pTot = 454322.668305 c = 195350.559367 rh surface-based volumes (mm3): wTot = 260471.231776, pTot = 466432.139438 c = 205960.907661 Computing SupraTentVolCor SupraTentVolCor = 58285.000 SupraTentVol = 979039.808 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 15145 15145 4 5 Left-Inf-Lat-Vent 1149 1149 5 7 Left-Cerebellum-White-Matter 17556 17556 6 8 Left-Cerebellum-Cortex 44861 44861 7 10 Left-Thalamus-Proper 6807 6807 8 11 Left-Caudate 3464 3464 9 12 Left-Putamen 4740 4740 10 13 Left-Pallidum 1933 1933 11 14 3rd-Ventricle 1427 1427 12 15 4th-Ventricle 2955 2955 13 16 Brain-Stem 23899 23899 14 17 Left-Hippocampus 3066 3066 15 18 Left-Amygdala 1242 1242 16 24 CSF 1107 1107 17 26 Left-Accumbens-area 420 420 18 28 Left-VentralDC 3845 3845 19 30 Left-vessel 241 241 20 31 Left-choroid-plexus 1635 1635 23 43 Right-Lateral-Ventricle 14333 14333 24 44 Right-Inf-Lat-Vent 743 743 25 46 Right-Cerebellum-White-Matter 17594 17594 26 47 Right-Cerebellum-Cortex 46152 46152 27 49 Right-Thalamus-Proper 7471 7471 28 50 Right-Caudate 3761 3761 29 51 Right-Putamen 4453 4453 30 52 Right-Pallidum 1684 1684 31 53 Right-Hippocampus 3348 3348 32 54 Right-Amygdala 1305 1305 33 58 Right-Accumbens-area 464 464 34 60 Right-VentralDC 3973 3973 35 62 Right-vessel 222 222 36 63 Right-choroid-plexus 2130 2130 37 72 5th-Ventricle 12 12 38 77 WM-hypointensities 2083 2083 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 65 65 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 233 233 45 251 CC_Posterior 1216 1216 46 252 CC_Mid_Posterior 384 384 47 253 CC_Central 339 339 48 254 CC_Mid_Anterior 390 390 49 255 CC_Anterior 874 874 Reporting on 45 segmentations SubCortGrayVol = 166888 #----------------------------------------- #@# AParc-to-ASeg Mon Jul 11 20:21:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Mon Jul 11 20:24:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8815 vertices from left hemi Ripped 8203 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 834030 Used brute-force search on 110 voxels Fixing Parahip LH WM Found 18 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1.000000 5 k 1354.000000 6 k 1.000000 7 k 2.000000 8 k 2.000000 9 k 1.000000 10 k 1.000000 11 k 13.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 15 k 2.000000 16 k 3.000000 17 k 1.000000 Fixing Parahip RH WM Found 16 clusters 0 k 1.000000 1 k 1808.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2.000000 10 k 2.000000 11 k 2.000000 12 k 1.000000 13 k 2.000000 14 k 2.000000 15 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-39 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1547561 # brainmaskvolume 1547561.0 # nbrainsegvoxels 243367 # brainsegvolume 243367.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 2776 2776 2 3002 wm-lh-caudalanteriorcingulate 2720 2720 3 3003 wm-lh-caudalmiddlefrontal 5961 5961 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2294 2294 6 3006 wm-lh-entorhinal 820 820 7 3007 wm-lh-fusiform 5595 5595 8 3008 wm-lh-inferiorparietal 8388 8388 9 3009 wm-lh-inferiortemporal 6212 6212 10 3010 wm-lh-isthmuscingulate 4114 4114 11 3011 wm-lh-lateraloccipital 8928 8928 12 3012 wm-lh-lateralorbitofrontal 6713 6713 13 3013 wm-lh-lingual 6305 6305 14 3014 wm-lh-medialorbitofrontal 3779 3779 15 3015 wm-lh-middletemporal 4678 4678 16 3016 wm-lh-parahippocampal 1476 1476 17 3017 wm-lh-paracentral 2933 2933 18 3018 wm-lh-parsopercularis 4019 4019 19 3019 wm-lh-parsorbitalis 843 843 20 3020 wm-lh-parstriangularis 2889 2889 21 3021 wm-lh-pericalcarine 2819 2819 22 3022 wm-lh-postcentral 7567 7567 23 3023 wm-lh-posteriorcingulate 4309 4309 24 3024 wm-lh-precentral 12490 12490 25 3025 wm-lh-precuneus 9183 9183 26 3026 wm-lh-rostralanteriorcingulate 2695 2695 27 3027 wm-lh-rostralmiddlefrontal 10374 10374 28 3028 wm-lh-superiorfrontal 17013 17013 29 3029 wm-lh-superiorparietal 11728 11728 30 3030 wm-lh-superiortemporal 7345 7345 31 3031 wm-lh-supramarginal 8947 8947 32 3032 wm-lh-frontalpole 260 260 33 3033 wm-lh-temporalpole 583 583 34 3034 wm-lh-transversetemporal 1023 1023 35 3035 wm-lh-insula 9565 9565 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2116 2116 120 4002 wm-rh-caudalanteriorcingulate 2915 2915 121 4003 wm-rh-caudalmiddlefrontal 4665 4665 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1879 1879 124 4006 wm-rh-entorhinal 597 597 125 4007 wm-rh-fusiform 7225 7225 126 4008 wm-rh-inferiorparietal 9817 9817 127 4009 wm-rh-inferiortemporal 5479 5479 128 4010 wm-rh-isthmuscingulate 4186 4186 129 4011 wm-rh-lateraloccipital 8847 8847 130 4012 wm-rh-lateralorbitofrontal 7030 7030 131 4013 wm-rh-lingual 5459 5459 132 4014 wm-rh-medialorbitofrontal 3461 3461 133 4015 wm-rh-middletemporal 6342 6342 134 4016 wm-rh-parahippocampal 1895 1895 135 4017 wm-rh-paracentral 3504 3504 136 4018 wm-rh-parsopercularis 3687 3687 137 4019 wm-rh-parsorbitalis 1100 1100 138 4020 wm-rh-parstriangularis 3066 3066 139 4021 wm-rh-pericalcarine 2768 2768 140 4022 wm-rh-postcentral 8134 8134 141 4023 wm-rh-posteriorcingulate 4048 4048 142 4024 wm-rh-precentral 14551 14551 143 4025 wm-rh-precuneus 10490 10490 144 4026 wm-rh-rostralanteriorcingulate 2285 2285 145 4027 wm-rh-rostralmiddlefrontal 12145 12145 146 4028 wm-rh-superiorfrontal 15641 15641 147 4029 wm-rh-superiorparietal 11048 11048 148 4030 wm-rh-superiortemporal 7531 7531 149 4031 wm-rh-supramarginal 10131 10131 150 4032 wm-rh-frontalpole 310 310 151 4033 wm-rh-temporalpole 607 607 152 4034 wm-rh-transversetemporal 775 775 153 4035 wm-rh-insula 8431 8431 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 32709 32709 237 5002 Right-UnsegmentedWhiteMatter 32447 32447 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label #-------------------------------------------- #@# BA Labels lh Mon Jul 11 20:41:58 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD08 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD08 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label 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 recon-all -s AD08 exited with ERRORS at Mon Jul 11 20:41:59 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jul 12 10:26:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon3 -no-isrunning -subjid AD08 subjid AD08 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-16 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 128306 total used free shared buffers cached Mem: 32877636 6483892 26393744 4 176308 997196 -/+ buffers/cache: 5310388 27567248 Swap: 67108860 92272 67016588 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:26:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-16 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Sphere lh Tue Jul 12 10:26:49 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.30 hours scaling brain by 0.295... pass 1: epoch 1 of 3 starting distance error %19.00 pass 1: epoch 2 of 3 starting distance error %18.92 unfolding complete - removing small folds... starting distance error %18.87 removing remaining folds... final distance error %18.90 #-------------------------------------------- #@# Surf Reg lh Tue Jul 12 11:44:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.580 curvature mean = 0.024, std = 0.938 curvature mean = 0.028, std = 0.863 curvature mean = -0.017, std = 0.959 curvature mean = 0.012, std = 0.942 curvature mean = -0.019, std = 0.971 curvature mean = 0.005, std = 0.974 curvature mean = -0.023, std = 0.973 curvature mean = 0.001, std = 0.989 curvature mean = -0.034, std = 0.331 curvature mean = 0.001, std = 0.068 curvature mean = 0.076, std = 0.297 curvature mean = 0.000, std = 0.081 curvature mean = 0.040, std = 0.471 curvature mean = 0.000, std = 0.087 curvature mean = 0.024, std = 0.604 curvature mean = 0.001, std = 0.089 curvature mean = 0.009, std = 0.718 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Jul 12 12:31:56 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 Tue Jul 12 12:31:59 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jul 12 12:32:02 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1246 labels changed using aseg relabeling using gibbs priors... 000: 3127 changed, 140242 examined... 001: 720 changed, 13258 examined... 002: 176 changed, 4054 examined... 003: 57 changed, 1023 examined... 004: 22 changed, 339 examined... 005: 12 changed, 129 examined... 006: 4 changed, 69 examined... 007: 6 changed, 23 examined... 008: 4 changed, 27 examined... 009: 0 changed, 18 examined... 273 labels changed using aseg 000: 126 total segments, 82 labels (389 vertices) changed 001: 42 total segments, 4 labels (15 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1957 vertices marked for relabeling... 1957 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 2 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jul 12 12:33:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 20465 bright wm thresholded. 2114 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 94.0 +- 8.5 [70.0 --> 110.0] GM (79.0) : 76.6 +- 14.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 110.5 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 34.4 (was 40) setting MAX_GRAY to 93.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 19.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=64 using class modes intead of means.... mean inside = 91.2, mean outside = 69.9 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->3.63) (max @ vno 8665 --> 139077) face area 0.27 +- 0.13 (0.00-->1.78) mean absolute distance = 0.93 +- 1.28 5350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 3 with 442 points - only 1.36% unknown removing 4 vertex label from ripped group deleting segment 7 with 37 points - only 0.00% unknown mean border=78.0, 152 (152) missing vertices, mean dist 0.1 [1.1 (%38.8)->0.8 (%61.2))] %37 local maxima, %58 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.28 (0.09-->3.76) (max @ vno 68809 --> 65116) face area 0.27 +- 0.14 (0.00-->1.99) mean absolute distance = 0.50 +- 0.87 5842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6552842.0, rms=12.07 001: dt: 0.5000, sse=7454261.0, rms=8.41 002: dt: 0.5000, sse=7951210.5, rms=6.34 003: dt: 0.5000, sse=8404685.0, rms=5.23 004: dt: 0.5000, sse=8672549.0, rms=4.64 005: dt: 0.5000, sse=8929870.0, rms=4.34 006: dt: 0.5000, sse=8992582.0, rms=4.19 007: dt: 0.5000, sse=9132031.0, rms=4.10 008: dt: 0.5000, sse=9099035.0, rms=4.04 rms = 4.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9164616.0, rms=4.00 010: dt: 0.2500, sse=6044842.5, rms=2.96 011: dt: 0.2500, sse=5692483.5, rms=2.60 012: dt: 0.2500, sse=5434416.0, rms=2.53 013: dt: 0.2500, sse=5347533.5, rms=2.47 rms = 2.45, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5268282.0, rms=2.45 015: dt: 0.1250, sse=5100403.0, rms=2.32 rms = 2.31, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=5060169.0, rms=2.31 positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 328 points - only 1.83% unknown deleting segment 9 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 13 with 59 points - only 35.59% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown mean border=80.5, 180 (36) missing vertices, mean dist -0.3 [0.7 (%59.0)->0.3 (%41.0))] %50 local maxima, %45 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 +- 0.27 (0.08-->3.62) (max @ vno 4941 --> 139077) face area 0.34 +- 0.17 (0.00-->2.39) mean absolute distance = 0.38 +- 0.54 4488 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5638249.0, rms=4.73 017: dt: 0.5000, sse=6309014.0, rms=3.52 rms = 3.76, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5758217.5, rms=2.77 019: dt: 0.2500, sse=5560744.0, rms=2.36 020: dt: 0.2500, sse=5422151.0, rms=2.16 021: dt: 0.2500, sse=5377637.0, rms=2.08 rms = 2.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5322279.5, rms=2.04 023: dt: 0.1250, sse=5207634.5, rms=1.94 rms = 1.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5159747.0, rms=1.92 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 338 points - only 1.78% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 48 points - only 33.33% unknown removing 3 vertex label from ripped group deleting segment 13 with 13 points - only 0.00% unknown deleting segment 14 with 5 points - only 40.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=83.3, 168 (23) missing vertices, mean dist -0.2 [0.5 (%65.7)->0.2 (%34.3))] %69 local maxima, %26 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 0.88 +- 0.27 (0.09-->3.70) (max @ vno 110092 --> 109304) face area 0.33 +- 0.17 (0.00-->2.57) mean absolute distance = 0.29 +- 0.42 4206 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5524511.0, rms=4.26 025: dt: 0.5000, sse=6001023.5, rms=3.30 rms = 3.64, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5551531.0, rms=2.40 027: dt: 0.2500, sse=5516627.5, rms=2.01 028: dt: 0.2500, sse=5457070.5, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5421263.0, rms=1.85 030: dt: 0.1250, sse=5273728.0, rms=1.71 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5227965.5, rms=1.70 positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 401 points - only 1.50% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 30 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 8 with 27 points - only 29.63% unknown deleting segment 9 with 25 points - only 36.00% unknown deleting segment 10 with 30 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 mean border=84.6, 186 (20) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.2 (%42.6))] %77 local maxima, %18 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=5300406.0, rms=2.45 rms = 2.56, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5452801.0, rms=1.75 033: dt: 0.2500, sse=5790372.0, rms=1.30 rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.29, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5776684.0, rms=1.29 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 6 with 12 points - only 50.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 33.33% unknown smoothing surface for 5 iterations... mean border=51.8, 194 (194) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %30 local maxima, %53 large gradients and %13 min vals, 384 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=30757508.0, rms=32.32 001: dt: 0.5000, sse=23489058.0, rms=27.79 002: dt: 0.5000, sse=18131408.0, rms=23.92 003: dt: 0.5000, sse=14754232.0, rms=20.79 004: dt: 0.5000, sse=12853140.0, rms=18.22 005: dt: 0.5000, sse=11433724.0, rms=15.93 006: dt: 0.5000, sse=10400128.0, rms=13.86 007: dt: 0.5000, sse=9520772.0, rms=11.91 008: dt: 0.5000, sse=8996410.0, rms=10.15 009: dt: 0.5000, sse=8662828.0, rms=8.73 010: dt: 0.5000, sse=8726024.0, rms=7.75 011: dt: 0.5000, sse=8693177.0, rms=7.11 012: dt: 0.5000, sse=8836631.0, rms=6.74 013: dt: 0.5000, sse=8856195.0, rms=6.51 014: dt: 0.5000, sse=8937619.0, rms=6.38 015: dt: 0.5000, sse=8963670.0, rms=6.26 016: dt: 0.5000, sse=8991374.0, rms=6.21 017: dt: 0.5000, sse=9004687.0, rms=6.15 rms = 6.10, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=9004395.0, rms=6.10 019: dt: 0.2500, sse=6180831.5, rms=4.84 020: dt: 0.2500, sse=5974802.5, rms=4.47 rms = 4.46, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5785029.5, rms=4.46 022: dt: 0.1250, sse=5117638.0, rms=3.87 023: dt: 0.1250, sse=5039741.0, rms=3.77 rms = 3.76, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4995385.0, rms=3.76 positioning took 3.0 minutes mean border=48.9, 816 (39) missing vertices, mean dist 0.2 [0.1 (%44.7)->0.5 (%55.3))] %45 local maxima, %39 large gradients and %11 min vals, 150 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=5835728.5, rms=6.08 rms = 6.20, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5551875.0, rms=5.29 026: dt: 0.2500, sse=5410220.0, rms=4.77 027: dt: 0.2500, sse=5742131.0, rms=4.60 rms = 4.55, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5866132.5, rms=4.55 029: dt: 0.1250, sse=5379359.0, rms=4.06 030: dt: 0.1250, sse=5365952.0, rms=3.92 rms = 3.87, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5349754.0, rms=3.87 positioning took 0.9 minutes mean border=46.5, 908 (32) missing vertices, mean dist 0.1 [0.1 (%40.8)->0.3 (%59.2))] %59 local maxima, %26 large gradients and %11 min vals, 171 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=5666460.0, rms=5.12 rms = 6.17, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5432502.5, rms=4.37 033: dt: 0.2500, sse=5501489.0, rms=4.11 034: dt: 0.2500, sse=5780536.5, rms=4.04 rms = 4.10, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=5631257.0, rms=3.87 036: dt: 0.1250, sse=5520276.0, rms=3.61 037: dt: 0.1250, sse=5466238.0, rms=3.55 rms = 3.52, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5476543.0, rms=3.52 positioning took 0.9 minutes mean border=45.1, 1489 (31) missing vertices, mean dist 0.1 [0.2 (%47.3)->0.3 (%52.7))] %63 local maxima, %21 large gradients and %11 min vals, 157 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5556611.0, rms=3.92 rms = 5.55, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5418418.0, rms=3.51 040: dt: 0.2500, sse=5668201.0, rms=3.44 rms = 3.50, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=5588358.0, rms=3.36 042: dt: 0.1250, sse=5531272.0, rms=3.24 043: dt: 0.1250, sse=5528230.0, rms=3.19 rms = 3.16, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5555913.0, rms=3.16 positioning took 0.8 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.03-->5.98) (max @ vno 98271 --> 97182) face area 0.39 +- 0.29 (0.00-->5.10) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed 0 of 140242 vertices processed 25000 of 140242 vertices processed 50000 of 140242 vertices processed 75000 of 140242 vertices processed 100000 of 140242 vertices processed 125000 of 140242 vertices processed thickness calculation complete, 144:197 truncations. 69914 vertices at 0 distance 94273 vertices at 1 distance 69175 vertices at 2 distance 24600 vertices at 3 distance 6812 vertices at 4 distance 2060 vertices at 5 distance 777 vertices at 6 distance 337 vertices at 7 distance 167 vertices at 8 distance 108 vertices at 9 distance 69 vertices at 10 distance 62 vertices at 11 distance 46 vertices at 12 distance 28 vertices at 13 distance 32 vertices at 14 distance 18 vertices at 15 distance 14 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 9 vertices at 19 distance 13 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.thickness positioning took 13.8 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jul 12 12:46:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Jul 12 12:46:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1779 1158 2315 1.949 0.513 0.154 0.077 35 5.9 bankssts 1179 775 2203 2.547 0.750 0.185 0.093 34 4.4 caudalanteriorcingulate 2942 2008 5204 2.210 0.597 0.190 0.458 1009 23.4 caudalmiddlefrontal 2535 1550 2612 1.622 0.395 0.169 0.089 100 10.8 cuneus 663 432 1543 2.697 0.940 0.190 0.231 27 8.9 entorhinal 4145 2828 8072 2.405 0.593 0.176 0.099 353 19.7 fusiform 7388 4410 8816 1.807 0.527 0.149 0.089 187 25.9 inferiorparietal 4349 2992 7524 2.167 0.581 0.179 0.098 112 17.0 inferiortemporal 1895 1230 2235 1.741 0.653 0.182 0.194 113 13.8 isthmuscingulate 7202 4601 9697 1.920 0.499 0.170 0.086 147 25.5 lateraloccipital 4024 2652 6615 2.202 0.592 0.182 0.107 134 18.8 lateralorbitofrontal 5638 3650 7262 1.791 0.524 0.181 0.093 135 22.6 lingual 3097 1957 4260 2.009 0.770 0.182 0.220 237 26.1 medialorbitofrontal 4546 3079 8073 2.203 0.532 0.174 0.116 159 18.8 middletemporal 1058 697 2305 2.599 0.773 0.172 0.112 31 5.0 parahippocampal 2099 1250 3034 2.257 0.461 0.157 0.104 46 8.9 paracentral 2680 1901 4893 2.243 0.482 0.163 0.085 81 8.7 parsopercularis 1089 707 2079 2.251 0.461 0.216 0.133 42 5.6 parsorbitalis 1807 1215 2650 1.996 0.444 0.165 0.076 35 5.4 parstriangularis 1880 1190 1847 1.686 0.437 0.164 0.086 37 7.0 pericalcarine 7661 4625 10504 2.023 0.629 0.153 0.106 698 34.4 postcentral 1901 1277 2814 2.081 0.646 0.172 0.163 48 5.8 posteriorcingulate 7621 4806 11851 2.289 0.541 0.170 0.209 950 33.7 precentral 6672 4208 7644 1.749 0.479 0.157 0.103 278 25.0 precuneus 1368 907 2600 2.517 0.636 0.179 0.097 44 5.2 rostralanteriorcingulate 7308 5129 12270 2.011 0.571 0.197 0.127 254 36.3 rostralmiddlefrontal 10486 7229 20143 2.348 0.652 0.194 0.143 469 61.5 superiorfrontal 8720 5060 10251 1.889 0.512 0.145 0.131 457 39.7 superiorparietal 5525 3674 10173 2.372 0.555 0.143 0.097 91 14.4 superiortemporal 6454 3971 8928 2.068 0.589 0.145 0.086 321 24.3 supramarginal 345 232 628 2.141 0.427 0.222 0.155 14 2.0 frontalpole 684 455 2287 3.355 0.691 0.195 0.130 18 4.4 temporalpole 827 473 1189 2.262 0.371 0.160 0.089 18 3.1 transversetemporal 3860 2557 7204 2.667 0.698 0.171 0.115 117 15.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jul 12 12:47:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 35 labels changed using aseg relabeling using gibbs priors... 000: 9190 changed, 140242 examined... 001: 2246 changed, 35157 examined... 002: 641 changed, 11612 examined... 003: 240 changed, 3580 examined... 004: 119 changed, 1386 examined... 005: 54 changed, 673 examined... 006: 34 changed, 341 examined... 007: 10 changed, 164 examined... 008: 9 changed, 56 examined... 009: 4 changed, 45 examined... 010: 2 changed, 26 examined... 011: 3 changed, 12 examined... 012: 4 changed, 20 examined... 013: 1 changed, 16 examined... 014: 0 changed, 7 examined... 7 labels changed using aseg 000: 292 total segments, 211 labels (2597 vertices) changed 001: 98 total segments, 18 labels (126 vertices) changed 002: 81 total segments, 1 labels (1 vertices) changed 003: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 106 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1111 vertices marked for relabeling... 1111 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jul 12 12:48:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1457 1006 2220 1.922 0.487 0.211 0.121 51 7.9 G_and_S_frontomargin 1543 1030 2232 1.964 0.497 0.152 0.058 21 3.7 G_and_S_occipital_inf 1650 923 2236 2.125 0.515 0.188 0.198 110 15.1 G_and_S_paracentral 1707 1121 3324 2.496 0.543 0.158 0.072 28 4.7 G_and_S_subcentral 640 435 1215 2.137 0.455 0.234 0.167 27 4.4 G_and_S_transv_frontopol 2552 1737 4262 2.182 0.628 0.167 0.080 61 8.1 G_and_S_cingul-Ant 1605 1067 2629 2.370 0.542 0.165 0.084 36 5.4 G_and_S_cingul-Mid-Ant 1528 998 2519 2.335 0.471 0.160 0.166 28 5.0 G_and_S_cingul-Mid-Post 626 429 986 1.950 0.619 0.223 0.179 25 3.1 G_cingul-Post-dorsal 372 240 506 1.852 0.644 0.202 0.151 23 1.6 G_cingul-Post-ventral 2244 1365 2403 1.584 0.388 0.182 0.108 103 11.5 G_cuneus 1795 1237 3544 2.349 0.473 0.176 0.102 71 6.7 G_front_inf-Opercular 377 242 761 2.369 0.460 0.197 0.116 12 1.8 G_front_inf-Orbital 1028 682 1917 2.197 0.429 0.187 0.101 29 3.9 G_front_inf-Triangul 3375 2339 7098 2.297 0.633 0.218 0.182 155 27.7 G_front_middle 7082 4814 15424 2.519 0.664 0.217 0.189 433 53.4 G_front_sup 793 480 1602 2.853 0.843 0.226 0.171 52 5.4 G_Ins_lg_and_S_cent_ins 693 489 1976 3.138 0.675 0.210 0.118 21 3.1 G_insular_short 2202 1373 3950 2.272 0.519 0.177 0.096 54 7.8 G_occipital_middle 1653 921 2045 1.922 0.527 0.144 0.137 218 6.7 G_occipital_sup 1654 1088 3698 2.567 0.510 0.182 0.087 40 6.0 G_oc-temp_lat-fusifor 4202 2627 5564 1.796 0.544 0.193 0.111 124 19.8 G_oc-temp_med-Lingual 1355 888 3212 2.719 0.844 0.201 0.198 60 13.6 G_oc-temp_med-Parahip 2779 1837 5213 2.166 0.634 0.215 0.148 135 17.7 G_orbital 2542 1327 2870 1.825 0.497 0.167 0.138 95 13.8 G_pariet_inf-Angular 3511 2071 5655 2.257 0.600 0.157 0.099 228 14.4 G_pariet_inf-Supramar 3661 1915 4601 1.995 0.522 0.157 0.192 184 22.5 G_parietal_sup 3014 1585 4051 2.070 0.565 0.156 0.146 136 18.0 G_postcentral 3022 1710 5448 2.520 0.542 0.185 0.357 833 18.6 G_precentral 3485 2102 4186 1.738 0.504 0.174 0.141 234 17.5 G_precuneus 1014 640 1732 2.038 0.641 0.222 0.292 117 8.4 G_rectus 654 393 786 2.035 0.891 0.196 0.407 96 14.0 G_subcallosal 649 362 1042 2.337 0.353 0.172 0.101 17 2.9 G_temp_sup-G_T_transv 2323 1527 5603 2.649 0.574 0.180 0.184 66 9.4 G_temp_sup-Lateral 563 386 1307 2.972 0.603 0.144 0.103 9 2.4 G_temp_sup-Plan_polar 1028 662 1588 2.090 0.485 0.129 0.052 17 2.2 G_temp_sup-Plan_tempo 2145 1497 4635 2.353 0.600 0.204 0.126 79 11.2 G_temporal_inf 3055 2021 5972 2.281 0.522 0.194 0.152 146 16.0 G_temporal_middle 362 244 387 1.746 0.491 0.139 0.046 3 0.7 Lat_Fis-ant-Horizont 326 224 433 1.991 0.410 0.139 0.052 3 0.7 Lat_Fis-ant-Vertical 1208 810 1453 2.065 0.465 0.136 0.046 11 2.4 Lat_Fis-post 2465 1513 3120 1.836 0.483 0.191 0.114 71 11.7 Pole_occipital 1625 1126 4415 2.786 0.835 0.198 0.115 41 7.6 Pole_temporal 2331 1517 2473 1.787 0.551 0.156 0.076 39 7.6 S_calcarine 2994 2119 3378 1.754 0.561 0.154 0.123 81 9.3 S_central 1123 776 1398 1.983 0.417 0.115 0.032 8 1.6 S_cingul-Marginalis 555 367 855 2.444 0.411 0.132 0.054 5 1.3 S_circular_insula_ant 1620 1069 2271 2.315 0.504 0.109 0.072 20 3.0 S_circular_insula_inf 1906 1267 2683 2.378 0.421 0.131 0.047 17 3.8 S_circular_insula_sup 741 531 1355 2.314 0.773 0.185 0.194 282 8.5 S_collat_transv_ant 531 349 488 1.697 0.327 0.167 0.062 7 1.4 S_collat_transv_post 1621 1137 2105 1.822 0.459 0.146 0.065 19 4.3 S_front_inf 1819 1281 2713 1.931 0.517 0.178 0.116 58 7.2 S_front_middle 2316 1622 3560 2.021 0.516 0.170 0.493 965 11.3 S_front_sup 288 189 267 1.599 0.370 0.170 0.078 5 1.0 S_interm_prim-Jensen 2580 1631 2572 1.668 0.439 0.134 0.046 31 4.9 S_intrapariet_and_P_trans 986 673 1260 1.908 0.432 0.142 0.046 10 1.8 S_oc_middle_and_Lunatus 1439 947 1611 1.829 0.337 0.122 0.037 11 2.2 S_oc_sup_and_transversal 815 551 1058 2.000 0.448 0.150 0.054 10 2.0 S_occipital_ant 753 509 978 2.116 0.400 0.140 0.052 7 1.7 S_oc-temp_lat 1957 1378 2765 2.112 0.466 0.138 0.045 18 3.7 S_oc-temp_med_and_Lingual 406 291 605 1.869 0.441 0.167 0.061 7 1.1 S_orbital_lateral 1027 663 1349 2.192 0.737 0.149 0.082 20 3.2 S_orbital_med-olfact 1525 1024 2319 2.165 0.521 0.176 0.085 34 5.3 S_orbital-H_Shaped 2309 1460 2407 1.743 0.444 0.132 0.045 27 4.4 S_parieto_occipital 1611 1000 1510 1.825 0.938 0.162 0.128 57 5.4 S_pericallosal 4059 2687 4757 1.852 0.500 0.129 0.066 548 13.5 S_postcentral 1427 993 2124 2.133 0.439 0.150 0.060 21 3.6 S_precentral-inf-part 1434 963 1845 2.068 0.460 0.148 0.061 17 4.0 S_precentral-sup-part 560 377 723 2.099 0.866 0.149 0.053 6 1.3 S_suborbital 1235 825 1449 1.733 0.387 0.173 0.165 65 10.3 S_subparietal 1644 1123 1964 1.924 0.430 0.159 0.064 28 4.4 S_temporal_inf 5920 3854 6619 1.769 0.474 0.133 0.061 96 15.0 S_temporal_sup 331 226 443 2.183 0.510 0.154 0.051 4 0.7 S_temporal_transverse #-------------------------------------------- #@# Sphere rh Tue Jul 12 12:48:46 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.62 hours scaling brain by 0.291... pass 1: epoch 1 of 3 starting distance error %20.20 pass 1: epoch 2 of 3 starting distance error %20.13 unfolding complete - removing small folds... starting distance error %20.04 removing remaining folds... final distance error %20.05 #-------------------------------------------- #@# Surf Reg rh Tue Jul 12 14:25:51 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.603 curvature mean = 0.023, std = 0.929 curvature mean = 0.023, std = 0.862 curvature mean = 0.004, std = 0.947 curvature mean = 0.011, std = 0.942 curvature mean = 0.003, std = 0.958 curvature mean = 0.005, std = 0.974 curvature mean = 0.000, std = 0.957 curvature mean = 0.001, std = 0.989 curvature mean = -0.030, std = 0.330 curvature mean = 0.006, std = 0.070 curvature mean = 0.076, std = 0.291 curvature mean = 0.006, std = 0.083 curvature mean = 0.040, std = 0.464 curvature mean = 0.006, std = 0.089 curvature mean = 0.023, std = 0.597 curvature mean = 0.006, std = 0.091 curvature mean = 0.008, std = 0.714 expanding nbhd size to 1 1114: 1 negative triangles #-------------------------------------------- #@# Jacobian white rh Tue Jul 12 15:47:50 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 Tue Jul 12 15:47:54 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Jul 12 15:47:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1336 labels changed using aseg relabeling using gibbs priors... 000: 3068 changed, 142899 examined... 001: 716 changed, 13154 examined... 002: 199 changed, 3973 examined... 003: 70 changed, 1145 examined... 004: 28 changed, 420 examined... 005: 12 changed, 168 examined... 006: 6 changed, 67 examined... 007: 4 changed, 36 examined... 008: 1 changed, 19 examined... 009: 0 changed, 7 examined... 175 labels changed using aseg 000: 106 total segments, 65 labels (463 vertices) changed 001: 45 total segments, 6 labels (27 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1773 vertices marked for relabeling... 1773 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Jul 12 15:49:08 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD08 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... 21503 bright wm thresholded. 2109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.orig... computing class statistics... border white: 275373 voxels (1.64%) border gray 304567 voxels (1.82%) WM (93.0): 93.6 +- 10.1 [70.0 --> 110.0] GM (78.0) : 76.6 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.7 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 45.4 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.1 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=105, GM=70 using class modes intead of means.... mean inside = 95.5, mean outside = 76.6 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->5.96) (max @ vno 74092 --> 86329) face area 0.27 +- 0.14 (0.00-->5.79) mean absolute distance = 0.93 +- 1.20 5012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 305 points - only 6.89% unknown removing 2 vertex label from ripped group deleting segment 6 with 125 points - only 0.00% unknown deleting segment 7 with 157 points - only 14.65% unknown mean border=82.6, 188 (188) missing vertices, mean dist 0.2 [1.1 (%34.3)->0.8 (%65.7))] %33 local maxima, %63 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.29 (0.08-->7.86) (max @ vno 74092 --> 86329) face area 0.27 +- 0.15 (0.00-->4.69) mean absolute distance = 0.47 +- 0.86 5442 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6089038.5, rms=10.93 001: dt: 0.5000, sse=7128632.0, rms=7.69 002: dt: 0.5000, sse=7759228.0, rms=5.94 003: dt: 0.5000, sse=8263533.0, rms=5.01 004: dt: 0.5000, sse=8545507.0, rms=4.52 005: dt: 0.5000, sse=8741570.0, rms=4.24 006: dt: 0.5000, sse=8813797.0, rms=4.08 007: dt: 0.5000, sse=8890295.0, rms=3.96 008: dt: 0.5000, sse=8913022.0, rms=3.91 009: dt: 0.5000, sse=8910272.0, rms=3.85 rms = 3.84, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8929653.0, rms=3.84 011: dt: 0.2500, sse=5820465.0, rms=2.81 012: dt: 0.2500, sse=5458159.0, rms=2.50 013: dt: 0.2500, sse=5200404.5, rms=2.44 rms = 2.40, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5143673.0, rms=2.40 015: dt: 0.1250, sse=4978326.0, rms=2.29 rms = 2.28, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4936033.5, rms=2.28 positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 3 with 44 points - only 0.00% unknown deleting segment 5 with 231 points - only 9.09% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 209 points - only 12.92% unknown deleting segment 12 with 6 points - only 16.67% unknown deleting segment 13 with 15 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown mean border=85.0, 278 (90) missing vertices, mean dist -0.3 [0.6 (%60.4)->0.3 (%39.6))] %46 local maxima, %50 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 0.88 +- 0.28 (0.08-->7.94) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.63) mean absolute distance = 0.36 +- 0.53 4731 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5423628.0, rms=4.29 017: dt: 0.5000, sse=6010886.5, rms=3.26 rms = 3.48, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5529973.0, rms=2.60 019: dt: 0.2500, sse=5377876.0, rms=2.21 020: dt: 0.2500, sse=5241144.0, rms=2.04 021: dt: 0.2500, sse=5188928.0, rms=1.98 rms = 1.96, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5149818.5, rms=1.96 023: dt: 0.1250, sse=5051597.5, rms=1.88 rms = 1.88, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5013620.5, rms=1.88 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 42 points - only 0.00% unknown deleting segment 2 with 259 points - only 8.11% unknown removing 1 vertex label from ripped group deleting segment 4 with 40 points - only 0.00% unknown deleting segment 5 with 237 points - only 12.24% unknown deleting segment 6 with 41 points - only 9.76% unknown deleting segment 7 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown mean border=87.5, 294 (77) missing vertices, mean dist -0.2 [0.4 (%65.4)->0.2 (%34.6))] %67 local maxima, %29 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 0.87 +- 0.28 (0.07-->7.98) (max @ vno 74092 --> 86329) face area 0.33 +- 0.18 (0.00-->5.60) mean absolute distance = 0.28 +- 0.42 4232 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5306925.0, rms=3.85 025: dt: 0.5000, sse=5704596.0, rms=2.98 rms = 3.35, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5319649.0, rms=2.22 027: dt: 0.2500, sse=5318920.0, rms=1.87 028: dt: 0.2500, sse=5259179.5, rms=1.79 rms = 1.79, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5236060.5, rms=1.79 030: dt: 0.1250, sse=5124335.0, rms=1.70 rms = 1.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5086908.5, rms=1.70 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown deleting segment 2 with 274 points - only 7.66% unknown removing 1 vertex label from ripped group deleting segment 5 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 237 points - only 11.39% unknown deleting segment 8 with 35 points - only 11.43% unknown deleting segment 9 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=88.6, 308 (61) missing vertices, mean dist -0.1 [0.3 (%56.1)->0.2 (%43.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5130541.0, rms=2.23 rms = 2.30, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5276731.0, rms=1.64 033: dt: 0.2500, sse=5595339.5, rms=1.31 rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5586387.5, rms=1.30 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 75 points - only 28.00% unknown deleting segment 3 with 27 points - only 40.74% unknown deleting segment 4 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=58.7, 215 (215) missing vertices, mean dist 1.7 [0.3 (%0.0)->1.9 (%100.0))] %37 local maxima, %51 large gradients and % 9 min vals, 350 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=26679052.0, rms=29.55 001: dt: 0.5000, sse=20310612.0, rms=25.25 002: dt: 0.5000, sse=15669898.0, rms=21.57 003: dt: 0.5000, sse=12957546.0, rms=18.67 004: dt: 0.5000, sse=11617793.0, rms=16.33 005: dt: 0.5000, sse=10590400.0, rms=14.36 006: dt: 0.5000, sse=9849688.0, rms=12.66 007: dt: 0.5000, sse=9262034.0, rms=11.11 008: dt: 0.5000, sse=8832515.0, rms=9.64 009: dt: 0.5000, sse=8597882.0, rms=8.39 010: dt: 0.5000, sse=8592985.0, rms=7.43 011: dt: 0.5000, sse=8640643.0, rms=6.80 012: dt: 0.5000, sse=8719318.0, rms=6.40 013: dt: 0.5000, sse=8793360.0, rms=6.17 014: dt: 0.5000, sse=8853058.0, rms=5.99 015: dt: 0.5000, sse=8892565.0, rms=5.90 016: dt: 0.5000, sse=8902767.0, rms=5.81 017: dt: 0.5000, sse=8932318.0, rms=5.76 018: dt: 0.5000, sse=8902494.0, rms=5.70 rms = 5.66, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=8949728.0, rms=5.66 020: dt: 0.2500, sse=6151680.5, rms=4.55 021: dt: 0.2500, sse=5899281.0, rms=4.23 rms = 4.18, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5669862.0, rms=4.18 023: dt: 0.1250, sse=5204998.0, rms=3.81 024: dt: 0.1250, sse=5134826.0, rms=3.75 rms = 3.75, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5093360.0, rms=3.75 positioning took 3.3 minutes mean border=54.8, 652 (37) missing vertices, mean dist 0.2 [0.2 (%37.7)->0.5 (%62.3))] %55 local maxima, %34 large gradients and % 7 min vals, 102 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=6288619.5, rms=6.98 026: dt: 0.5000, sse=6524961.0, rms=6.13 027: dt: 0.5000, sse=8296397.5, rms=5.98 rms = 6.03, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6682149.0, rms=4.80 029: dt: 0.2500, sse=6075032.0, rms=4.43 030: dt: 0.2500, sse=6121183.0, rms=4.32 031: dt: 0.2500, sse=6088259.5, rms=4.27 rms = 4.25, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6127479.5, rms=4.25 033: dt: 0.1250, sse=5635081.5, rms=3.78 034: dt: 0.1250, sse=5587532.0, rms=3.68 rms = 3.67, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5560582.0, rms=3.67 positioning took 1.4 minutes mean border=52.1, 750 (22) missing vertices, mean dist 0.2 [0.2 (%35.3)->0.3 (%64.7))] %66 local maxima, %22 large gradients and % 7 min vals, 140 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=5960273.0, rms=5.21 rms = 5.82, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5677202.0, rms=4.36 037: dt: 0.2500, sse=5631901.0, rms=3.99 038: dt: 0.2500, sse=5884733.0, rms=3.87 rms = 3.89, time step reduction 2 of 3 to 0.125... 039: dt: 0.1250, sse=5748531.0, rms=3.71 040: dt: 0.1250, sse=5629837.5, rms=3.48 041: dt: 0.1250, sse=5572688.5, rms=3.43 rms = 3.41, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5568650.5, rms=3.41 positioning took 1.2 minutes mean border=50.8, 1210 (19) missing vertices, mean dist 0.1 [0.2 (%42.5)->0.3 (%57.5))] %70 local maxima, %19 large gradients and % 7 min vals, 123 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5637445.0, rms=3.78 rms = 5.13, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=5529294.0, rms=3.42 044: dt: 0.2500, sse=5749075.5, rms=3.33 rms = 3.36, time step reduction 2 of 3 to 0.125... 045: dt: 0.1250, sse=5681971.0, rms=3.26 046: dt: 0.1250, sse=5627612.0, rms=3.17 rms = 3.13, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5638414.0, rms=3.13 positioning took 0.9 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.area.pial vertex spacing 0.98 +- 0.43 (0.01-->7.92) (max @ vno 75151 --> 74088) face area 0.39 +- 0.31 (0.00-->10.51) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed 0 of 142899 vertices processed 25000 of 142899 vertices processed 50000 of 142899 vertices processed 75000 of 142899 vertices processed 100000 of 142899 vertices processed 125000 of 142899 vertices processed thickness calculation complete, 199:413 truncations. 72812 vertices at 0 distance 92394 vertices at 1 distance 70164 vertices at 2 distance 26252 vertices at 3 distance 7995 vertices at 4 distance 2446 vertices at 5 distance 966 vertices at 6 distance 408 vertices at 7 distance 240 vertices at 8 distance 151 vertices at 9 distance 97 vertices at 10 distance 73 vertices at 11 distance 48 vertices at 12 distance 35 vertices at 13 distance 25 vertices at 14 distance 17 vertices at 15 distance 20 vertices at 16 distance 27 vertices at 17 distance 29 vertices at 18 distance 24 vertices at 19 distance 35 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.thickness positioning took 15.2 minutes #-------------------------------------------- #@# Surf Volume rh Tue Jul 12 16:04:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Tue Jul 12 16:04:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1278 840 1728 1.936 0.479 0.124 0.040 16 2.1 bankssts 1077 685 1867 2.358 0.741 0.165 0.094 28 3.7 caudalanteriorcingulate 2885 1818 4173 2.094 0.452 0.164 0.110 92 15.1 caudalmiddlefrontal 2347 1434 2681 1.689 0.418 0.174 3.167 187 8.9 cuneus 457 317 1581 3.058 1.004 0.186 0.092 10 1.7 entorhinal 4689 3064 8055 2.283 0.635 0.155 0.096 121 15.2 fusiform 8048 4895 10703 1.976 0.505 0.145 0.098 267 30.7 inferiorparietal 5205 3463 9981 2.322 0.689 0.175 0.123 333 20.8 inferiortemporal 1956 1201 2585 1.909 0.752 0.166 0.115 53 7.4 isthmuscingulate 7228 4603 10897 2.054 0.529 0.170 0.084 231 25.9 lateraloccipital 4160 2613 6485 2.199 0.623 0.186 0.146 527 28.7 lateralorbitofrontal 4918 3086 6335 1.805 0.575 0.176 0.088 123 18.1 lingual 2523 1687 3933 2.003 0.688 0.190 0.151 154 11.7 medialorbitofrontal 5084 3375 9316 2.253 0.643 0.160 0.089 134 16.5 middletemporal 1275 785 2110 2.257 0.836 0.121 0.064 16 3.3 parahippocampal 2357 1433 3482 2.176 0.513 0.166 0.271 342 42.0 paracentral 2669 1790 4478 2.192 0.446 0.156 0.080 51 7.9 parsopercularis 1233 837 2486 2.317 0.640 0.171 0.150 35 6.3 parsorbitalis 2224 1548 3873 2.151 0.508 0.189 0.122 74 10.5 parstriangularis 2399 1525 2277 1.590 0.416 0.177 0.101 56 9.6 pericalcarine 7220 4573 9490 1.874 0.539 0.155 0.102 171 26.5 postcentral 1807 1172 2889 2.196 0.642 0.166 0.117 64 7.8 posteriorcingulate 8033 5203 13244 2.297 0.533 0.159 0.186 378 32.1 precentral 6378 4069 9005 2.081 0.481 0.145 0.069 170 18.3 precuneus 1357 827 2187 2.163 0.638 0.171 0.176 76 6.3 rostralanteriorcingulate 9064 6129 14919 2.039 0.586 0.189 0.110 347 37.5 rostralmiddlefrontal 10247 6731 19221 2.364 0.636 0.184 0.157 372 52.4 superiorfrontal 8837 5404 12654 2.064 0.500 0.145 0.099 673 40.8 superiorparietal 5564 3675 9751 2.342 0.579 0.157 0.076 241 19.4 superiortemporal 7043 4464 10622 2.187 0.487 0.139 0.179 259 22.2 supramarginal 448 282 884 2.291 0.596 0.210 0.167 22 2.6 frontalpole 589 411 1870 3.122 0.891 0.232 0.193 40 4.3 temporalpole 576 349 1039 2.563 0.414 0.168 0.091 12 2.2 transversetemporal 3521 2230 6729 2.760 0.845 0.156 0.126 224 19.0 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Jul 12 16:04:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD08 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 7 labels changed using aseg relabeling using gibbs priors... 000: 10080 changed, 142899 examined... 001: 2404 changed, 38443 examined... 002: 717 changed, 12274 examined... 003: 334 changed, 3939 examined... 004: 167 changed, 1846 examined... 005: 81 changed, 888 examined... 006: 44 changed, 444 examined... 007: 15 changed, 243 examined... 008: 5 changed, 91 examined... 009: 3 changed, 34 examined... 010: 3 changed, 22 examined... 011: 2 changed, 18 examined... 012: 1 changed, 10 examined... 013: 1 changed, 5 examined... 014: 1 changed, 6 examined... 015: 0 changed, 7 examined... 2 labels changed using aseg 000: 333 total segments, 247 labels (2702 vertices) changed 001: 102 total segments, 18 labels (101 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 152 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1318 vertices marked for relabeling... 1318 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jul 12 16:05:53 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 AD08 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 1271 828 1999 1.959 0.593 0.181 0.105 39 5.2 G_and_S_frontomargin 1344 864 2166 2.157 0.538 0.155 0.067 22 3.8 G_and_S_occipital_inf 1568 835 2084 2.073 0.493 0.172 0.197 74 9.7 G_and_S_paracentral 1493 1001 2715 2.313 0.565 0.166 0.075 30 4.7 G_and_S_subcentral 1153 774 2146 2.160 0.563 0.213 0.141 60 5.7 G_and_S_transv_frontopol 3342 2173 5306 2.127 0.565 0.165 0.121 117 13.7 G_and_S_cingul-Ant 1526 968 2653 2.454 0.517 0.152 0.086 34 5.3 G_and_S_cingul-Mid-Ant 1349 896 2313 2.332 0.539 0.146 0.070 21 3.3 G_and_S_cingul-Mid-Post 849 494 1353 2.237 0.664 0.215 0.216 53 7.3 G_cingul-Post-dorsal 329 209 675 2.687 0.615 0.213 0.223 14 1.4 G_cingul-Post-ventral 2009 1237 2343 1.666 0.436 0.185 0.102 66 8.8 G_cuneus 1584 1058 3161 2.334 0.518 0.177 0.096 37 5.8 G_front_inf-Opercular 377 245 846 2.641 0.494 0.204 0.249 16 3.0 G_front_inf-Orbital 1184 852 2427 2.255 0.481 0.230 0.167 62 7.5 G_front_inf-Triangul 3961 2622 7928 2.304 0.537 0.214 0.152 190 26.2 G_front_middle 6751 4446 14336 2.500 0.648 0.208 0.264 612 72.6 G_front_sup 554 360 1191 2.786 0.877 0.189 0.155 37 3.5 G_Ins_lg_and_S_cent_ins 746 464 1969 3.181 0.854 0.193 0.117 25 4.0 G_insular_short 2134 1282 4050 2.431 0.412 0.163 0.106 88 7.5 G_occipital_middle 1436 867 2081 2.069 0.478 0.158 0.074 30 4.3 G_occipital_sup 2057 1288 3963 2.412 0.575 0.176 0.149 90 9.1 G_oc-temp_lat-fusifor 3185 1968 4503 1.890 0.664 0.190 0.104 96 13.7 G_oc-temp_med-Lingual 1274 860 3174 2.648 0.937 0.158 0.092 24 4.6 G_oc-temp_med-Parahip 2776 1783 5751 2.384 0.664 0.200 0.149 120 16.8 G_orbital 3183 1830 4651 2.050 0.498 0.153 0.126 134 15.2 G_pariet_inf-Angular 3330 2029 5940 2.346 0.505 0.159 0.336 224 16.5 G_pariet_inf-Supramar 3477 2051 5823 2.255 0.489 0.159 0.150 548 27.1 G_parietal_sup 2875 1677 3872 1.899 0.526 0.178 0.146 110 15.5 G_postcentral 2970 1910 6076 2.505 0.482 0.195 0.365 271 18.5 G_precentral 2956 1779 4854 2.207 0.456 0.165 0.110 158 13.8 G_precuneus 502 346 989 2.119 0.761 0.256 0.186 42 3.0 G_rectus 407 265 652 2.464 0.856 0.240 0.475 80 3.3 G_subcallosal 398 255 835 2.652 0.390 0.187 0.108 10 1.7 G_temp_sup-G_T_transv 2116 1425 4543 2.456 0.542 0.194 0.101 178 9.4 G_temp_sup-Lateral 555 353 1198 2.882 0.669 0.164 0.104 17 2.9 G_temp_sup-Plan_polar 732 513 1208 2.241 0.502 0.125 0.045 18 1.1 G_temp_sup-Plan_tempo 3048 2042 6711 2.455 0.678 0.198 0.161 169 16.0 G_temporal_inf 2475 1663 5583 2.489 0.548 0.173 0.087 74 8.0 G_temporal_middle 398 274 514 1.932 0.432 0.136 0.045 4 0.8 Lat_Fis-ant-Horizont 143 102 211 1.913 0.429 0.130 0.039 1 0.2 Lat_Fis-ant-Vertical 1555 1003 2100 2.309 0.541 0.127 0.052 26 4.0 Lat_Fis-post 3557 2253 4743 1.827 0.540 0.188 0.108 105 15.4 Pole_occipital 1829 1301 5346 2.928 0.763 0.214 0.169 83 10.2 Pole_temporal 2338 1488 2342 1.714 0.491 0.160 0.076 39 7.4 S_calcarine 3484 2277 3848 1.820 0.587 0.140 0.099 92 10.8 S_central 1377 954 1941 1.978 0.430 0.128 0.040 13 2.4 S_cingul-Marginalis 726 431 1020 2.450 0.474 0.135 0.115 113 5.2 S_circular_insula_ant 1411 893 2133 2.460 0.798 0.115 0.055 22 4.4 S_circular_insula_inf 1559 947 1830 2.219 0.364 0.116 0.066 22 2.8 S_circular_insula_sup 904 603 1482 2.264 0.782 0.167 0.114 154 3.0 S_collat_transv_ant 536 343 632 1.911 0.392 0.162 0.101 78 2.9 S_collat_transv_post 2540 1787 3414 1.861 0.435 0.160 0.089 85 8.5 S_front_inf 2045 1355 2540 1.795 0.516 0.168 0.087 62 6.2 S_front_middle 2187 1392 3025 2.077 0.515 0.149 0.076 35 7.9 S_front_sup 969 627 967 1.766 0.409 0.135 0.045 11 1.9 S_interm_prim-Jensen 3052 1967 3478 1.809 0.442 0.121 0.050 32 7.0 S_intrapariet_and_P_trans 1251 830 1583 1.898 0.471 0.157 0.057 18 2.8 S_oc_middle_and_Lunatus 1385 889 1609 1.833 0.408 0.135 0.073 31 5.0 S_oc_sup_and_transversal 791 530 992 1.986 0.408 0.129 0.039 6 1.4 S_occipital_ant 1069 695 1229 1.929 0.429 0.140 0.053 13 2.2 S_oc-temp_lat 2441 1590 2862 1.884 0.522 0.116 0.038 18 3.9 S_oc-temp_med_and_Lingual 493 336 595 1.811 0.482 0.179 0.102 11 1.6 S_orbital_lateral 755 525 1111 2.135 0.893 0.165 0.132 33 4.8 S_orbital_med-olfact 1645 1061 2144 1.930 0.458 0.166 0.142 410 13.3 S_orbital-H_Shaped 2637 1678 3028 1.944 0.463 0.132 2.785 159 5.2 S_parieto_occipital 2031 1234 1908 1.663 0.716 0.143 0.063 38 5.2 S_pericallosal 3786 2515 4836 1.999 0.432 0.122 0.039 35 6.1 S_postcentral 1765 1147 2614 2.218 0.413 0.128 0.050 19 3.5 S_precentral-inf-part 1635 1057 2101 2.113 0.401 0.129 0.045 14 3.3 S_precentral-sup-part 341 207 311 1.531 0.425 0.143 0.051 5 0.8 S_suborbital 1188 807 1607 1.904 0.473 0.152 0.056 18 2.6 S_subparietal 1863 1192 2120 1.842 0.448 0.124 0.038 18 3.0 S_temporal_inf 5447 3534 6832 1.932 0.501 0.128 0.051 84 11.7 S_temporal_sup 287 179 416 2.352 0.551 0.131 0.039 3 0.5 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 12 16:06:14 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD08 SUBJECTS_DIR is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc 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 = 10 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Jul 12 16:25:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD08 sysname Linux hostname compute-0-16 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 258972.108938, pTot = 454322.668305 c = 195350.559367 rh surface-based volumes (mm3): wTot = 260471.231776, pTot = 466432.139438 c = 205960.907661 Computing SupraTentVolCor SupraTentVolCor = 58285.000 SupraTentVol = 979039.808 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 15145 15145 4 5 Left-Inf-Lat-Vent 1149 1149 5 7 Left-Cerebellum-White-Matter 17556 17556 6 8 Left-Cerebellum-Cortex 44861 44861 7 10 Left-Thalamus-Proper 6807 6807 8 11 Left-Caudate 3464 3464 9 12 Left-Putamen 4740 4740 10 13 Left-Pallidum 1933 1933 11 14 3rd-Ventricle 1427 1427 12 15 4th-Ventricle 2955 2955 13 16 Brain-Stem 23899 23899 14 17 Left-Hippocampus 3066 3066 15 18 Left-Amygdala 1242 1242 16 24 CSF 1107 1107 17 26 Left-Accumbens-area 420 420 18 28 Left-VentralDC 3845 3845 19 30 Left-vessel 241 241 20 31 Left-choroid-plexus 1635 1635 23 43 Right-Lateral-Ventricle 14333 14333 24 44 Right-Inf-Lat-Vent 743 743 25 46 Right-Cerebellum-White-Matter 17594 17594 26 47 Right-Cerebellum-Cortex 46152 46152 27 49 Right-Thalamus-Proper 7471 7471 28 50 Right-Caudate 3761 3761 29 51 Right-Putamen 4453 4453 30 52 Right-Pallidum 1684 1684 31 53 Right-Hippocampus 3348 3348 32 54 Right-Amygdala 1305 1305 33 58 Right-Accumbens-area 464 464 34 60 Right-VentralDC 3973 3973 35 62 Right-vessel 222 222 36 63 Right-choroid-plexus 2130 2130 37 72 5th-Ventricle 12 12 38 77 WM-hypointensities 2083 2083 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 65 65 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 233 233 45 251 CC_Posterior 1216 1216 46 252 CC_Mid_Posterior 384 384 47 253 CC_Central 339 339 48 254 CC_Mid_Anterior 390 390 49 255 CC_Anterior 874 874 Reporting on 45 segmentations SubCortGrayVol = 166888 #----------------------------------------- #@# AParc-to-ASeg Tue Jul 12 16:41:45 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 394952 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Jul 12 16:44:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_aparc2aseg --s AD08 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD08 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8815 vertices from left hemi Ripped 8203 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/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 = 834030 Used brute-force search on 110 voxels Fixing Parahip LH WM Found 18 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1.000000 5 k 1354.000000 6 k 1.000000 7 k 2.000000 8 k 2.000000 9 k 1.000000 10 k 1.000000 11 k 13.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 15 k 2.000000 16 k 3.000000 17 k 1.000000 Fixing Parahip RH WM Found 16 clusters 0 k 1.000000 1 k 1808.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2.000000 10 k 2.000000 11 k 2.000000 12 k 1.000000 13 k 2.000000 14 k 2.000000 15 k 1.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD08 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-16 machine x86_64 user fdu0 atlas_icv (eTIV) = 1593014 mm^3 (det: 1.222905 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 232974 rh white matter volume 234361 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1547561 # brainmaskvolume 1547561.0 # nbrainsegvoxels 243367 # brainsegvolume 243367.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 2776 2776 2 3002 wm-lh-caudalanteriorcingulate 2720 2720 3 3003 wm-lh-caudalmiddlefrontal 5961 5961 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2294 2294 6 3006 wm-lh-entorhinal 820 820 7 3007 wm-lh-fusiform 5595 5595 8 3008 wm-lh-inferiorparietal 8388 8388 9 3009 wm-lh-inferiortemporal 6212 6212 10 3010 wm-lh-isthmuscingulate 4114 4114 11 3011 wm-lh-lateraloccipital 8928 8928 12 3012 wm-lh-lateralorbitofrontal 6713 6713 13 3013 wm-lh-lingual 6305 6305 14 3014 wm-lh-medialorbitofrontal 3779 3779 15 3015 wm-lh-middletemporal 4678 4678 16 3016 wm-lh-parahippocampal 1476 1476 17 3017 wm-lh-paracentral 2933 2933 18 3018 wm-lh-parsopercularis 4019 4019 19 3019 wm-lh-parsorbitalis 843 843 20 3020 wm-lh-parstriangularis 2889 2889 21 3021 wm-lh-pericalcarine 2819 2819 22 3022 wm-lh-postcentral 7567 7567 23 3023 wm-lh-posteriorcingulate 4309 4309 24 3024 wm-lh-precentral 12490 12490 25 3025 wm-lh-precuneus 9183 9183 26 3026 wm-lh-rostralanteriorcingulate 2695 2695 27 3027 wm-lh-rostralmiddlefrontal 10374 10374 28 3028 wm-lh-superiorfrontal 17013 17013 29 3029 wm-lh-superiorparietal 11728 11728 30 3030 wm-lh-superiortemporal 7345 7345 31 3031 wm-lh-supramarginal 8947 8947 32 3032 wm-lh-frontalpole 260 260 33 3033 wm-lh-temporalpole 583 583 34 3034 wm-lh-transversetemporal 1023 1023 35 3035 wm-lh-insula 9565 9565 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2116 2116 120 4002 wm-rh-caudalanteriorcingulate 2915 2915 121 4003 wm-rh-caudalmiddlefrontal 4665 4665 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1879 1879 124 4006 wm-rh-entorhinal 597 597 125 4007 wm-rh-fusiform 7225 7225 126 4008 wm-rh-inferiorparietal 9817 9817 127 4009 wm-rh-inferiortemporal 5479 5479 128 4010 wm-rh-isthmuscingulate 4186 4186 129 4011 wm-rh-lateraloccipital 8847 8847 130 4012 wm-rh-lateralorbitofrontal 7030 7030 131 4013 wm-rh-lingual 5459 5459 132 4014 wm-rh-medialorbitofrontal 3461 3461 133 4015 wm-rh-middletemporal 6342 6342 134 4016 wm-rh-parahippocampal 1895 1895 135 4017 wm-rh-paracentral 3504 3504 136 4018 wm-rh-parsopercularis 3687 3687 137 4019 wm-rh-parsorbitalis 1100 1100 138 4020 wm-rh-parstriangularis 3066 3066 139 4021 wm-rh-pericalcarine 2768 2768 140 4022 wm-rh-postcentral 8134 8134 141 4023 wm-rh-posteriorcingulate 4048 4048 142 4024 wm-rh-precentral 14551 14551 143 4025 wm-rh-precuneus 10490 10490 144 4026 wm-rh-rostralanteriorcingulate 2285 2285 145 4027 wm-rh-rostralmiddlefrontal 12145 12145 146 4028 wm-rh-superiorfrontal 15641 15641 147 4029 wm-rh-superiorparietal 11048 11048 148 4030 wm-rh-superiortemporal 7531 7531 149 4031 wm-rh-supramarginal 10131 10131 150 4032 wm-rh-frontalpole 310 310 151 4033 wm-rh-temporalpole 607 607 152 4034 wm-rh-transversetemporal 775 775 153 4035 wm-rh-insula 8431 8431 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 32709 32709 237 5002 Right-UnsegmentedWhiteMatter 32447 32447 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD08/label #-------------------------------------------- #@# BA Labels lh Tue Jul 12 17:06:14 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD08 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD08 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/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label Linux compute-0-16 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 recon-all -s AD08 exited with ERRORS at Tue Jul 12 17:06:15 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting