Tue Jun 14 16:42:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 /usr/local/freesurfer/stable6//bin/recon-all -all -nuintensitycor-3T -subjid AD18 -i /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD18/AD18_MR.nii subjid AD18 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-0-102 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 5209756 27667496 168 145336 3859088 -/+ buffers/cache: 1205332 31671920 Swap: 67108860 98312 67010548 pbsjob 11789921.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: 2016/06/14-20:42:42-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:43-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-0-102 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: 2016/06/14-20:42:44-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-0-102 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: 2016/06/14-20:42:44-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-0-102 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: 2016/06/14-20:42:44-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-0-102 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/AD18 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD18/AD18_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/orig/001.mgz mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD18/AD18_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/AD18_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/AD18/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jun 14 16:42:50 EDT 2016 Found 1 runs /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/mri/orig/001.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/transforms/talairach.xfm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/orig.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jun 14 16:43:03 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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-0-102 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 16:43:03 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.8077 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8077/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8077/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.8077/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jun 14 16:43:08 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.8077/nu0.mnc ./tmp.mri_nu_correct.mni.8077/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8077/0/ -iterations 1000 -distance 50 [fdu0@compute-0-102:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/] [2016-06-14 16:43:08] 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.8077/0/ ./tmp.mri_nu_correct.mni.8077/nu0.mnc ./tmp.mri_nu_correct.mni.8077/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 45 CV of field change: 0.000948076 mri_convert ./tmp.mri_nu_correct.mni.8077/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.8077/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.8077/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 16:44:41 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 16:44:41 EDT 2016 Ended at Tue Jun 14 16:45:58 EDT 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jun 14 16:46:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5700, pval=0.2115 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6//bin/extract_talairach_avi_QA.awk /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/transforms/talairach_avi.log TalAviQA: 0.97464 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Jun 14 16:46:00 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/AD18/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-0-102 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 16:46:00 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.9033 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9033/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9033/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.9033/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jun 14 16:46:04 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.9033/nu0.mnc ./tmp.mri_nu_correct.mni.9033/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9033/0/ -iterations 1000 -distance 50 [fdu0@compute-0-102:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/] [2016-06-14 16:46:04] 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.9033/0/ ./tmp.mri_nu_correct.mni.9033/nu0.mnc ./tmp.mri_nu_correct.mni.9033/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 45 CV of field change: 0.000948076 mri_binarize --i ./tmp.mri_nu_correct.mni.9033/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9033/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/AD18/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9033/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9033/ones.mgz sysname Linux hostname compute-0-102 machine x86_64 user fdu0 input ./tmp.mri_nu_correct.mni.9033/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9033/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.9033/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9033/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9033/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.9033/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9033/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9033/input.mean.dat sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9033/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.9033/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9033/ones.mgz --i ./tmp.mri_nu_correct.mni.9033/nu1.mnc --sum ./tmp.mri_nu_correct.mni.9033/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9033/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.9033/ones.mgz --i ./tmp.mri_nu_correct.mni.9033/nu1.mnc --sum ./tmp.mri_nu_correct.mni.9033/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9033/output.mean.dat sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9033/ones.mgz Loading ./tmp.mri_nu_correct.mni.9033/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.9033/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9033/nu1.mnc ./tmp.mri_nu_correct.mni.9033/nu1.mnc mul .99576670281188956003 Saving result to './tmp.mri_nu_correct.mni.9033/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9033/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.9033/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.9033/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 10 seconds. mapping ( 5, 113) to ( 3, 110) Tue Jun 14 16:48:15 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Jun 14 16:48:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 1.07129 0.04476 0.00977 -1.14683; -0.06681 1.02788 0.47520 12.53826; 0.01426 -0.44368 1.12663 13.48817; 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 = 17 Starting OpenSpline(): npoints = 17 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 109 gm peak at 80 (80), valley at 65 (65) csf peak at 32, setting threshold to 64 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 82 (82), valley at 65 (65) csf peak at 33, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 39 seconds. #-------------------------------------------- #@# Skull Stripping Tue Jun 14 16:50:56 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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=5.0 skull bounding box = (47, 52, 24) --> (202, 211, 218) using (99, 105, 121) as brain centroid... mean wm in atlas = 108, using box (80,85,97) --> (118, 124,144) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 6.1 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.556 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.555550 @ (0.000, 0.000, 0.000) max log p = -4.487410 @ (4.545, -4.545, -13.636) max log p = -4.443432 @ (-6.818, -2.273, 6.818) max log p = -4.419311 @ (5.682, 3.409, -3.409) max log p = -4.419311 @ (0.000, 0.000, 0.000) max log p = -4.419311 @ (0.000, 0.000, 0.000) Found translation: (3.4, -3.4, -10.2): log p = -4.419 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.158, old_max_log_p =-4.419 (thresh=-4.4) 1.00000 0.00000 0.00000 3.40909; 0.00000 1.14215 0.47309 -73.91853; 0.00000 -0.44009 1.06246 46.27466; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.147, old_max_log_p =-4.158 (thresh=-4.2) 1.07500 0.00000 0.00000 -13.20088; 0.00000 1.22781 0.50857 -90.12550; 0.00000 -0.40708 0.98278 51.12329; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.147, old_max_log_p =-4.147 (thresh=-4.1) 1.07500 0.00000 0.00000 -13.20088; 0.00000 1.22781 0.50857 -90.12550; 0.00000 -0.40708 0.98278 51.12329; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.045, old_max_log_p =-4.147 (thresh=-4.1) 1.03367 -0.03086 -0.04498 5.64505; 0.03623 1.19280 0.45948 -85.79327; 0.03982 -0.38418 1.05616 32.20927; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.045, old_max_log_p =-4.045 (thresh=-4.0) 1.03367 -0.03086 -0.04498 5.64505; 0.03623 1.19280 0.45948 -85.79327; 0.03982 -0.38418 1.05616 32.20927; 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=-4.020, old_max_log_p =-4.045 (thresh=-4.0) 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.020, old_max_log_p =-4.020 (thresh=-4.0) 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 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 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.020 (old=-4.556) transform before final EM align: 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 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 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.03210 -0.02769 -0.05354 6.42281; 0.03618 1.19141 0.45894 -85.52612; 0.04818 -0.38352 1.05328 32.35842; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1088.321549 mri_em_register stimesec 1.296802 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 157523 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 77 mri_em_register ru_nivcsw 5815 registration took 18 minutes and 10 seconds. mri_watershed -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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=128 y=122 z=117 r=69 first estimation of the main basin volume: 1420885 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=151, y=101, z=94, 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=399979854 voxels, voxel volume =1.000 = 399979854 mmm3 = 399979.840 cm3 done. PostAnalyze...Basin Prior 14 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=126, z=110, r=8952 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 44940 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=39 , nb = -1027953758 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1044989756 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=62 , nb = 1075867356 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 1068490578 OTHER CSF_MIN=0, CSF_intensity=19, CSF_MAX=43 , nb = 1083277096 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 56, 46, 40, 79 after analyzing : 35, 46, 46, 54 RIGHT_CER before analyzing : 39, 50, 59, 89 after analyzing : 39, 56, 59, 64 LEFT_CER before analyzing : 24, 35, 55, 90 after analyzing : 24, 48, 55, 58 RIGHT_BRAIN before analyzing : 62, 49, 41, 79 after analyzing : 37, 49, 49, 56 LEFT_BRAIN before analyzing : 56, 45, 38, 79 after analyzing : 34, 45, 45, 53 OTHER before analyzing : 43, 27, 22, 31 after analyzing : 24, 27, 27, 28 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.015, std = 0.011 curvature mean = 64.368, std = 6.007 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.31, sigma = 9.55 after rotation: sse = 5.31, sigma = 9.55 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 7.02, its var is 15.25 before Erosion-Dilatation 5.27% of inacurate vertices after Erosion-Dilatation 8.81% 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 = 1379966 voxels, voxel volume = 1.000 mm3 = 1379966 mmm3 = 1379.966 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 27.749781 mri_watershed stimesec 0.525920 mri_watershed ru_maxrss 827596 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212858 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 152 mri_watershed ru_nivcsw 38 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Jun 14 17:09:37 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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=23.0 skull bounding box = (55, 67, 44) --> (191, 197, 189) using (100, 110, 117) as brain centroid... mean wm in atlas = 107, using box (83,94,99) --> (116, 125,134) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 5.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.062 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.059856 @ (0.000, 0.000, 0.000) max log p = -4.012914 @ (4.545, -4.545, -13.636) max log p = -3.952214 @ (-6.818, -2.273, -2.273) max log p = -3.941635 @ (3.409, -1.136, 1.136) max log p = -3.926034 @ (-2.841, 1.705, 0.568) max log p = -3.926034 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -6.3, -14.2): log p = -3.926 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.926 (thresh=-3.9) 1.07500 0.00000 0.00000 -11.33768; 0.00000 0.98772 0.43171 -54.25823; 0.00000 -0.38959 0.98746 49.96029; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.691, old_max_log_p =-3.692 (thresh=-3.7) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.06180 0.46409 -67.27435; 0.00000 -0.38959 0.98746 49.96029; 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=-3.506, old_max_log_p =-3.691 (thresh=-3.7) 1.05444 -0.00403 0.00413 -6.93882; 0.00239 1.11428 0.44764 -70.83475; 0.00522 -0.36775 1.03941 36.80709; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.501, old_max_log_p =-3.506 (thresh=-3.5) 1.03331 -0.02793 -0.04368 4.01456; 0.03686 1.11394 0.44643 -73.15589; 0.03972 -0.36769 1.03898 34.34509; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.497, old_max_log_p =-3.501 (thresh=-3.5) 1.03471 -0.00348 0.00495 -4.47577; 0.00301 1.11465 0.44650 -70.83851; 0.00589 -0.36658 1.03986 36.52353; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.497, old_max_log_p =-3.497 (thresh=-3.5) 1.03397 0.00852 -0.02908 -2.15049; 0.00301 1.11465 0.44650 -68.96351; 0.03974 -0.36650 1.03946 34.14227; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.469, old_max_log_p =-3.497 (thresh=-3.5) 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.469, old_max_log_p =-3.469 (thresh=-3.5) 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 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 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.469 (old=-4.062) transform before final EM align: 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 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 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1042.804469 mri_em_register stimesec 1.029843 mri_em_register ru_maxrss 600880 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159372 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 43 mri_em_register ru_nivcsw 5450 registration took 17 minutes and 24 seconds. #-------------------------------------- #@# CA Normalize Tue Jun 14 17:27:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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=23.0 skull bounding box = (55, 67, 44) --> (191, 197, 189) using (100, 110, 117) as brain centroid... mean wm in atlas = 107, using box (83,94,99) --> (116, 125,134) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 5.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34223; 0.02282 -0.36659 1.03980 36.26064; 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 (125, 69, 42) --> (190, 176, 187) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 2985 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 68, 42) --> (128, 169, 188) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 3 of 1620 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 151, 71) --> (174, 188, 118) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 301 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 151, 69) --> (126, 187, 119) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 134 (0.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 136, 100) --> (143, 195, 128) Brain_Stem: limiting intensities to 93.0 --> 132.0 0 of 420 (0.0%) samples deleted using 5460 total control points for intensity normalization... bias field = 0.950 +- 0.080 0 of 5455 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 69, 42) --> (190, 176, 187) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 2 of 3309 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 68, 42) --> (128, 169, 188) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 1814 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 151, 71) --> (174, 188, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 389 (3.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 151, 69) --> (126, 187, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 150 (1.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 136, 100) --> (143, 195, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 79 of 557 (14.2%) samples deleted using 6219 total control points for intensity normalization... bias field = 1.005 +- 0.058 4 of 6065 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 69, 42) --> (190, 176, 187) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 4 of 3299 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 68, 42) --> (128, 169, 188) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 26 of 1865 (1.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 151, 71) --> (174, 188, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 45 of 394 (11.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 151, 69) --> (126, 187, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 178 (26.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 136, 100) --> (143, 195, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 320 of 622 (51.4%) samples deleted using 6358 total control points for intensity normalization... bias field = 1.007 +- 0.044 12 of 5828 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 41 seconds. #-------------------------------------- #@# CA Reg Tue Jun 14 17:28:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_ca_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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) = 1.37 (predicted orig area = 5.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.877, neg=0, invalid=4512 0001: dt=249.065274, rms=0.792 (9.685%), neg=0, invalid=4512 0002: dt=174.428212, rms=0.769 (2.908%), neg=0, invalid=4512 0003: dt=369.920000, rms=0.752 (2.103%), neg=0, invalid=4512 0004: dt=148.994709, rms=0.744 (1.096%), neg=0, invalid=4512 0005: dt=517.888000, rms=0.737 (0.975%), neg=0, invalid=4512 0006: dt=135.281437, rms=0.731 (0.838%), neg=0, invalid=4512 0007: dt=517.888000, rms=0.726 (0.594%), neg=0, invalid=4512 0008: dt=129.472000, rms=0.723 (0.441%), neg=0, invalid=4512 0009: dt=517.888000, rms=0.720 (0.456%), neg=0, invalid=4512 0010: dt=129.472000, rms=0.718 (0.259%), neg=0, invalid=4512 0011: dt=1183.744000, rms=0.715 (0.467%), neg=0, invalid=4512 0012: dt=110.976000, rms=0.711 (0.510%), neg=0, invalid=4512 0013: dt=1775.616000, rms=0.708 (0.404%), neg=0, invalid=4512 0014: dt=129.472000, rms=0.705 (0.413%), neg=0, invalid=4512 0015: dt=129.472000, rms=0.705 (0.034%), neg=0, invalid=4512 0016: dt=129.472000, rms=0.705 (0.058%), neg=0, invalid=4512 0017: dt=129.472000, rms=0.704 (0.089%), neg=0, invalid=4512 0018: dt=129.472000, rms=0.703 (0.114%), neg=0, invalid=4512 0019: dt=129.472000, rms=0.702 (0.137%), neg=0, invalid=4512 0020: dt=129.472000, rms=0.701 (0.164%), neg=0, invalid=4512 0021: dt=129.472000, rms=0.700 (0.183%), neg=0, invalid=4512 0022: dt=129.472000, rms=0.699 (0.179%), neg=0, invalid=4512 0023: dt=129.472000, rms=0.697 (0.176%), neg=0, invalid=4512 0024: dt=129.472000, rms=0.696 (0.168%), neg=0, invalid=4512 0025: dt=129.472000, rms=0.695 (0.173%), neg=0, invalid=4512 0026: dt=129.472000, rms=0.694 (0.180%), neg=0, invalid=4512 0027: dt=129.472000, rms=0.693 (0.175%), neg=0, invalid=4512 0028: dt=129.472000, rms=0.691 (0.171%), neg=0, invalid=4512 0029: dt=129.472000, rms=0.690 (0.161%), neg=0, invalid=4512 0030: dt=129.472000, rms=0.689 (0.156%), neg=0, invalid=4512 0031: dt=129.472000, rms=0.688 (0.144%), neg=0, invalid=4512 0032: dt=129.472000, rms=0.687 (0.143%), neg=0, invalid=4512 0033: dt=129.472000, rms=0.686 (0.141%), neg=0, invalid=4512 0034: dt=129.472000, rms=0.685 (0.136%), neg=0, invalid=4512 0035: dt=129.472000, rms=0.684 (0.129%), neg=0, invalid=4512 0036: dt=129.472000, rms=0.684 (0.118%), neg=0, invalid=4512 0037: dt=129.472000, rms=0.683 (0.110%), neg=0, invalid=4512 0038: dt=1183.744000, rms=0.683 (0.043%), neg=0, invalid=4512 0039: dt=1183.744000, rms=0.683 (-3.069%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=4512 0040: dt=129.472000, rms=0.681 (0.346%), neg=0, invalid=4512 0041: dt=887.808000, rms=0.679 (0.301%), neg=0, invalid=4512 0042: dt=129.472000, rms=0.679 (0.068%), neg=0, invalid=4512 0043: dt=129.472000, rms=0.679 (0.023%), neg=0, invalid=4512 0044: dt=129.472000, rms=0.678 (0.030%), neg=0, invalid=4512 0045: dt=129.472000, rms=0.678 (0.034%), neg=0, invalid=4512 0046: dt=129.472000, rms=0.678 (0.063%), neg=0, invalid=4512 0047: dt=129.472000, rms=0.677 (0.097%), neg=0, invalid=4512 0048: dt=129.472000, rms=0.676 (0.112%), neg=0, invalid=4512 0049: dt=129.472000, rms=0.676 (0.108%), neg=0, invalid=4512 0050: dt=129.472000, rms=0.675 (0.104%), neg=0, invalid=4512 0051: dt=369.920000, rms=0.675 (0.011%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=4512 0052: dt=154.171004, rms=0.676 (1.064%), neg=0, invalid=4512 0053: dt=173.497630, rms=0.665 (1.731%), neg=0, invalid=4512 0054: dt=48.991150, rms=0.660 (0.612%), neg=0, invalid=4512 0055: dt=331.776000, rms=0.656 (0.728%), neg=0, invalid=4512 0056: dt=72.222821, rms=0.649 (1.002%), neg=0, invalid=4512 0057: dt=76.255319, rms=0.647 (0.319%), neg=0, invalid=4512 0058: dt=72.489796, rms=0.646 (0.180%), neg=0, invalid=4512 0059: dt=72.489796, rms=0.644 (0.247%), neg=0, invalid=4512 0060: dt=72.489796, rms=0.642 (0.339%), neg=0, invalid=4512 0061: dt=72.489796, rms=0.639 (0.441%), neg=0, invalid=4512 0062: dt=72.489796, rms=0.636 (0.479%), neg=0, invalid=4512 0063: dt=72.489796, rms=0.632 (0.583%), neg=0, invalid=4512 0064: dt=72.489796, rms=0.629 (0.490%), neg=0, invalid=4512 0065: dt=72.489796, rms=0.626 (0.471%), neg=0, invalid=4512 0066: dt=72.489796, rms=0.624 (0.388%), neg=0, invalid=4512 0067: dt=72.489796, rms=0.621 (0.404%), neg=0, invalid=4512 0068: dt=72.489796, rms=0.621 (0.044%), neg=0, invalid=4512 0069: dt=72.489796, rms=0.621 (0.051%), neg=0, invalid=4512 0070: dt=72.489796, rms=0.621 (0.045%), neg=0, invalid=4512 0071: dt=497.664000, rms=0.620 (0.092%), neg=0, invalid=4512 0072: dt=36.288000, rms=0.620 (0.066%), neg=0, invalid=4512 0073: dt=36.288000, rms=0.619 (0.027%), neg=0, invalid=4512 0074: dt=36.288000, rms=0.619 (0.033%), neg=0, invalid=4512 0075: dt=36.288000, rms=0.619 (0.044%), neg=0, invalid=4512 0076: dt=36.288000, rms=0.619 (0.065%), neg=0, invalid=4512 0077: dt=36.288000, rms=0.618 (0.068%), neg=0, invalid=4512 0078: dt=36.288000, rms=0.618 (0.058%), neg=0, invalid=4512 0079: dt=36.288000, rms=0.617 (0.051%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=4512 0080: dt=145.152000, rms=0.615 (0.627%), neg=0, invalid=4512 0081: dt=36.288000, rms=0.615 (0.052%), neg=0, invalid=4512 0082: dt=36.288000, rms=0.614 (0.022%), neg=0, invalid=4512 0083: dt=36.288000, rms=0.614 (0.042%), neg=0, invalid=4512 0084: dt=36.288000, rms=0.614 (0.052%), neg=0, invalid=4512 0085: dt=36.288000, rms=0.613 (0.071%), neg=0, invalid=4512 0086: dt=36.288000, rms=0.613 (0.091%), neg=0, invalid=4512 0087: dt=36.288000, rms=0.612 (0.102%), neg=0, invalid=4512 0088: dt=36.288000, rms=0.612 (0.108%), neg=0, invalid=4512 0089: dt=36.288000, rms=0.611 (0.102%), neg=0, invalid=4512 0090: dt=36.288000, rms=0.610 (0.091%), neg=0, invalid=4512 0091: dt=103.680000, rms=0.610 (0.010%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.638, neg=0, invalid=4512 0092: dt=0.700000, rms=0.636 (0.190%), neg=0, invalid=4512 0093: dt=0.700000, rms=0.636 (0.000%), neg=0, invalid=4512 0094: dt=0.700000, rms=0.636 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=4512 0095: dt=0.700000, rms=0.636 (0.189%), neg=0, invalid=4512 0096: dt=0.500000, rms=0.636 (0.000%), neg=0, invalid=4512 0097: dt=0.500000, rms=0.636 (-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=0.714, neg=0, invalid=4512 0098: dt=5.836991, rms=0.692 (3.033%), neg=0, invalid=4512 0099: dt=2.304000, rms=0.692 (0.070%), neg=0, invalid=4512 0100: dt=2.304000, rms=0.692 (-0.031%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.693, neg=0, invalid=4512 0101: dt=0.576000, rms=0.692 (0.141%), neg=0, invalid=4512 0102: dt=0.063000, rms=0.692 (0.001%), neg=0, invalid=4512 0103: dt=0.063000, rms=0.692 (0.000%), neg=0, invalid=4512 0104: dt=0.063000, rms=0.692 (-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=0.769, neg=0, invalid=4512 0105: dt=1.024000, rms=0.766 (0.435%), neg=0, invalid=4512 0106: dt=1.909774, rms=0.761 (0.605%), neg=0, invalid=4512 0107: dt=1.280000, rms=0.760 (0.133%), neg=0, invalid=4512 0108: dt=1.280000, rms=0.758 (0.240%), neg=0, invalid=4512 0109: dt=1.280000, rms=0.758 (0.014%), neg=0, invalid=4512 0110: dt=1.280000, rms=0.758 (-0.408%), neg=0, invalid=4512 0111: dt=0.000000, rms=0.758 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.759, neg=0, invalid=4512 0112: dt=1.024000, rms=0.757 (0.200%), neg=0, invalid=4512 0113: dt=1.280000, rms=0.757 (0.038%), neg=0, invalid=4512 0114: dt=1.280000, rms=0.757 (-0.010%), 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=0.707, neg=0, invalid=4512 0115: dt=0.876136, rms=0.689 (2.577%), neg=0, invalid=4512 0116: dt=0.096000, rms=0.687 (0.180%), neg=0, invalid=4512 0117: dt=0.096000, rms=0.687 (-0.077%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=4512 0118: dt=0.028000, rms=0.687 (0.150%), neg=0, invalid=4512 0119: dt=0.020000, rms=0.687 (0.004%), neg=0, invalid=4512 0120: dt=0.020000, rms=0.687 (-0.005%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12858 (33) Left_Lateral_Ventricle (4): linear fit = 1.62 x + 0.0 (1975 voxels, overlap=0.266) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1975 voxels, peak = 32), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.12673 (31) Right_Lateral_Ventricle (43): linear fit = 1.89 x + 0.0 (1522 voxels, overlap=0.098) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1522 voxels, peak = 30), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09804 (103) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (711 voxels, overlap=0.337) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (711 voxels, peak = 105), gca=105.1 gca peak = 0.20183 (93) mri peak = 0.10118 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (762 voxels, overlap=0.952) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (762 voxels, peak = 98), gca=98.1 gca peak = 0.21683 (55) mri peak = 0.05383 (83) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (764 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.38 x + 0.0 (764 voxels, peak = 76), gca=75.6 gca peak = 0.30730 (58) mri peak = 0.09363 (72) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (712 voxels, overlap=0.143) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (712 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.08409 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52099 voxels, overlap=0.937) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52099 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.10794 (106) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55456 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (55456 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03225 (75) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (19962 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (19962 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.03506 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (21834 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (21834 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.12872 (80) Right_Caudate (50): linear fit = 1.18 x + 0.0 (711 voxels, overlap=0.034) Right_Caudate (50): linear fit = 1.18 x + 0.0 (711 voxels, peak = 79), gca=79.4 gca peak = 0.15243 (71) mri peak = 0.08705 (84) Left_Caudate (11): linear fit = 1.17 x + 0.0 (656 voxels, overlap=0.040) Left_Caudate (11): linear fit = 1.17 x + 0.0 (656 voxels, peak = 83), gca=83.4 gca peak = 0.13336 (57) mri peak = 0.03550 (67) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (20251 voxels, overlap=0.033) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (20251 voxels, peak = 72), gca=72.1 gca peak = 0.13252 (56) mri peak = 0.03587 (65) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (24897 voxels, overlap=0.036) Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (24897 voxels, peak = 66), gca=66.4 gca peak = 0.18181 (84) mri peak = 0.06912 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (8594 voxels, overlap=0.110) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (8594 voxels, peak = 92), gca=92.0 gca peak = 0.20573 (83) mri peak = 0.05007 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7157 voxels, overlap=0.457) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (7157 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.08698 (64) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (223 voxels, overlap=0.986) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (223 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.07507 (63) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (239 voxels, overlap=0.599) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (239 voxels, peak = 62), gca=62.4 gca peak = 0.14181 (85) mri peak = 0.05560 (86) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4330 voxels, overlap=0.980) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4330 voxels, peak = 85), gca=84.6 gca peak = 0.11978 (83) mri peak = 0.07438 (80) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3307 voxels, overlap=0.929) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3307 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.05714 (91) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2016 voxels, overlap=0.390) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2016 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.06849 (91) Right_Putamen (51): linear fit = 1.14 x + 0.0 (1883 voxels, overlap=0.048) Right_Putamen (51): linear fit = 1.14 x + 0.0 (1883 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.08069 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10197 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10197 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.08617 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1209 voxels, overlap=0.230) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1209 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.11222 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1213 voxels, overlap=0.163) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1213 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.08162 (36) gca peak = 0.15061 (21) mri peak = 0.06734 (28) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (433 voxels, overlap=0.315) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (433 voxels, peak = 33), gca=33.3 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 Fourth_Ventricle = 0.15061 (21) 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 1.25 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Right_Pallidum too bright - rescaling by 0.969 (from 1.095) to 101.9 (was 105.1) 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=0.740, neg=0, invalid=4512 0121: dt=111.336982, rms=0.705 (4.632%), neg=0, invalid=4512 0122: dt=369.920000, rms=0.695 (1.466%), neg=0, invalid=4512 0123: dt=369.920000, rms=0.689 (0.848%), neg=0, invalid=4512 0124: dt=129.472000, rms=0.686 (0.376%), neg=0, invalid=4512 0125: dt=1183.744000, rms=0.682 (0.693%), neg=0, invalid=4512 0126: dt=129.472000, rms=0.678 (0.489%), neg=0, invalid=4512 0127: dt=443.904000, rms=0.676 (0.379%), neg=0, invalid=4512 0128: dt=110.976000, rms=0.675 (0.114%), neg=0, invalid=4512 0129: dt=517.888000, rms=0.673 (0.251%), neg=0, invalid=4512 0130: dt=129.472000, rms=0.673 (0.117%), neg=0, invalid=4512 0131: dt=517.888000, rms=0.671 (0.205%), neg=0, invalid=4512 0132: dt=110.976000, rms=0.670 (0.140%), neg=0, invalid=4512 0133: dt=517.888000, rms=0.669 (0.144%), neg=0, invalid=4512 0134: dt=110.976000, rms=0.668 (0.131%), neg=0, invalid=4512 0135: dt=517.888000, rms=0.667 (0.150%), neg=0, invalid=4512 0136: dt=110.976000, rms=0.667 (0.110%), neg=0, invalid=4512 0137: dt=517.888000, rms=0.666 (0.123%), neg=0, invalid=4512 0138: dt=110.976000, rms=0.665 (0.106%), neg=0, invalid=4512 0139: dt=517.888000, rms=0.664 (0.126%), neg=0, invalid=4512 0140: dt=110.976000, rms=0.664 (0.088%), neg=0, invalid=4512 0141: dt=517.888000, rms=0.663 (0.117%), neg=0, invalid=4512 0142: dt=110.976000, rms=0.662 (0.076%), neg=0, invalid=4512 0143: dt=517.888000, rms=0.662 (0.115%), neg=0, invalid=4512 0144: dt=110.976000, rms=0.661 (0.067%), neg=0, invalid=4512 0145: dt=517.888000, rms=0.660 (0.112%), neg=0, invalid=4512 0146: dt=110.976000, rms=0.660 (0.056%), neg=0, invalid=4512 0147: dt=517.888000, rms=0.659 (0.109%), neg=0, invalid=4512 0148: dt=110.976000, rms=0.659 (0.050%), neg=0, invalid=4512 0149: dt=110.976000, rms=0.659 (0.032%), neg=0, invalid=4512 0150: dt=110.976000, rms=0.658 (0.051%), neg=0, invalid=4512 0151: dt=110.976000, rms=0.658 (0.072%), neg=0, invalid=4512 0152: dt=110.976000, rms=0.657 (0.087%), neg=0, invalid=4512 0153: dt=110.976000, rms=0.657 (0.100%), neg=0, invalid=4512 0154: dt=110.976000, rms=0.656 (0.113%), neg=0, invalid=4512 0155: dt=110.976000, rms=0.655 (0.118%), neg=0, invalid=4512 0156: dt=110.976000, rms=0.654 (0.124%), neg=0, invalid=4512 0157: dt=110.976000, rms=0.654 (0.124%), neg=0, invalid=4512 0158: dt=110.976000, rms=0.653 (0.123%), neg=0, invalid=4512 0159: dt=110.976000, rms=0.652 (0.125%), neg=0, invalid=4512 0160: dt=110.976000, rms=0.651 (0.124%), neg=0, invalid=4512 0161: dt=110.976000, rms=0.650 (0.121%), neg=0, invalid=4512 0162: dt=110.976000, rms=0.650 (0.120%), neg=0, invalid=4512 0163: dt=110.976000, rms=0.649 (0.117%), neg=0, invalid=4512 0164: dt=110.976000, rms=0.648 (0.111%), neg=0, invalid=4512 0165: dt=110.976000, rms=0.647 (0.107%), neg=0, invalid=4512 0166: dt=110.976000, rms=0.647 (0.101%), neg=0, invalid=4512 0167: dt=110.976000, rms=0.646 (0.093%), neg=0, invalid=4512 0168: dt=110.976000, rms=0.646 (0.089%), neg=0, invalid=4512 0169: dt=110.976000, rms=0.645 (0.087%), neg=0, invalid=4512 0170: dt=110.976000, rms=0.645 (0.081%), neg=0, invalid=4512 0171: dt=110.976000, rms=0.644 (0.075%), neg=0, invalid=4512 0172: dt=110.976000, rms=0.644 (0.070%), neg=0, invalid=4512 0173: dt=110.976000, rms=0.643 (0.069%), neg=0, invalid=4512 0174: dt=110.976000, rms=0.643 (0.066%), neg=0, invalid=4512 0175: dt=110.976000, rms=0.642 (0.064%), neg=0, invalid=4512 0176: dt=110.976000, rms=0.642 (0.060%), neg=0, invalid=4512 0177: dt=110.976000, rms=0.642 (0.059%), neg=0, invalid=4512 0178: dt=110.976000, rms=0.641 (0.057%), neg=0, invalid=4512 0179: dt=110.976000, rms=0.641 (0.054%), neg=0, invalid=4512 0180: dt=110.976000, rms=0.641 (0.051%), neg=0, invalid=4512 0181: dt=110.976000, rms=0.640 (0.052%), neg=0, invalid=4512 0182: dt=110.976000, rms=0.640 (0.051%), neg=0, invalid=4512 0183: dt=110.976000, rms=0.640 (0.052%), neg=0, invalid=4512 0184: dt=110.976000, rms=0.639 (0.052%), neg=0, invalid=4512 0185: dt=110.976000, rms=0.639 (0.051%), neg=0, invalid=4512 0186: dt=110.976000, rms=0.639 (0.051%), neg=0, invalid=4512 0187: dt=110.976000, rms=0.638 (0.049%), neg=0, invalid=4512 0188: dt=110.976000, rms=0.638 (0.049%), neg=0, invalid=4512 0189: dt=110.976000, rms=0.638 (0.049%), neg=0, invalid=4512 0190: dt=110.976000, rms=0.637 (0.049%), neg=0, invalid=4512 0191: dt=110.976000, rms=0.637 (0.048%), neg=0, invalid=4512 0192: dt=110.976000, rms=0.637 (0.047%), neg=0, invalid=4512 0193: dt=110.976000, rms=0.636 (0.046%), neg=0, invalid=4512 0194: dt=110.976000, rms=0.636 (0.045%), neg=0, invalid=4512 0195: dt=110.976000, rms=0.636 (0.044%), neg=0, invalid=4512 0196: dt=110.976000, rms=0.636 (0.043%), neg=0, invalid=4512 0197: dt=110.976000, rms=0.635 (0.041%), neg=0, invalid=4512 0198: dt=110.976000, rms=0.635 (0.041%), neg=0, invalid=4512 0199: dt=110.976000, rms=0.635 (0.038%), neg=0, invalid=4512 0200: dt=110.976000, rms=0.635 (0.037%), neg=0, invalid=4512 0201: dt=110.976000, rms=0.634 (0.037%), neg=0, invalid=4512 0202: dt=110.976000, rms=0.634 (0.037%), neg=0, invalid=4512 0203: dt=110.976000, rms=0.634 (0.036%), neg=0, invalid=4512 0204: dt=110.976000, rms=0.634 (0.036%), neg=0, invalid=4512 0205: dt=110.976000, rms=0.633 (0.035%), neg=0, invalid=4512 0206: dt=110.976000, rms=0.633 (0.034%), neg=0, invalid=4512 0207: dt=110.976000, rms=0.633 (0.033%), neg=0, invalid=4512 0208: dt=110.976000, rms=0.633 (0.032%), neg=0, invalid=4512 0209: dt=110.976000, rms=0.633 (0.033%), neg=0, invalid=4512 0210: dt=110.976000, rms=0.632 (0.032%), neg=0, invalid=4512 0211: dt=110.976000, rms=0.632 (0.031%), neg=0, invalid=4512 0212: dt=110.976000, rms=0.632 (0.031%), neg=0, invalid=4512 0213: dt=110.976000, rms=0.632 (0.031%), neg=0, invalid=4512 0214: dt=110.976000, rms=0.632 (0.030%), neg=0, invalid=4512 0215: dt=110.976000, rms=0.631 (0.030%), neg=0, invalid=4512 0216: dt=110.976000, rms=0.631 (0.029%), neg=0, invalid=4512 0217: dt=110.976000, rms=0.631 (0.029%), neg=0, invalid=4512 0218: dt=110.976000, rms=0.631 (0.028%), neg=0, invalid=4512 0219: dt=110.976000, rms=0.631 (0.027%), neg=0, invalid=4512 0220: dt=110.976000, rms=0.631 (0.027%), neg=0, invalid=4512 0221: dt=110.976000, rms=0.630 (0.028%), neg=0, invalid=4512 0222: dt=110.976000, rms=0.630 (0.027%), neg=0, invalid=4512 0223: dt=110.976000, rms=0.630 (0.026%), neg=0, invalid=4512 0224: dt=110.976000, rms=0.630 (0.025%), neg=0, invalid=4512 0225: dt=110.976000, rms=0.630 (0.025%), neg=0, invalid=4512 0226: dt=110.976000, rms=0.630 (0.025%), neg=0, invalid=4512 0227: dt=110.976000, rms=0.629 (0.024%), neg=0, invalid=4512 0228: dt=28409.856000, rms=0.627 (0.344%), neg=0, invalid=4512 0229: dt=110.976000, rms=0.626 (0.137%), neg=0, invalid=4512 0230: dt=129.472000, rms=0.626 (0.016%), neg=0, invalid=4512 0231: dt=129.472000, rms=0.626 (0.008%), neg=0, invalid=4512 0232: dt=129.472000, rms=0.626 (0.011%), neg=0, invalid=4512 0233: dt=129.472000, rms=0.626 (0.014%), neg=0, invalid=4512 0234: dt=129.472000, rms=0.626 (0.015%), neg=0, invalid=4512 0235: dt=129.472000, rms=0.626 (0.013%), neg=0, invalid=4512 0236: dt=129.472000, rms=0.626 (0.012%), neg=0, invalid=4512 0237: dt=129.472000, rms=0.626 (0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=4512 0238: dt=129.472000, rms=0.626 (0.296%), neg=0, invalid=4512 0239: dt=517.888000, rms=0.625 (0.120%), neg=0, invalid=4512 0240: dt=369.920000, rms=0.625 (0.040%), neg=0, invalid=4512 0241: dt=369.920000, rms=0.624 (0.054%), neg=0, invalid=4512 0242: dt=369.920000, rms=0.624 (0.022%), neg=0, invalid=4512 0243: dt=369.920000, rms=0.623 (0.124%), neg=0, invalid=4512 0244: dt=369.920000, rms=0.623 (0.070%), neg=0, invalid=4512 0245: dt=369.920000, rms=0.623 (0.002%), neg=0, invalid=4512 0246: dt=369.920000, rms=0.622 (0.104%), neg=0, invalid=4512 0247: dt=369.920000, rms=0.622 (0.026%), neg=0, invalid=4512 0248: dt=369.920000, rms=0.622 (0.051%), neg=0, invalid=4512 0249: dt=369.920000, rms=0.621 (0.046%), neg=0, invalid=4512 0250: dt=369.920000, rms=0.621 (0.000%), neg=0, invalid=4512 0251: dt=369.920000, rms=0.621 (0.072%), neg=0, invalid=4512 0252: dt=369.920000, rms=0.621 (-0.012%), neg=0, invalid=4512 0253: dt=0.000000, rms=0.621 (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=0.625, neg=0, invalid=4512 0254: dt=124.416000, rms=0.619 (0.972%), neg=0, invalid=4512 0255: dt=331.776000, rms=0.611 (1.320%), neg=0, invalid=4512 0256: dt=31.104000, rms=0.608 (0.462%), neg=0, invalid=4512 0257: dt=1.620000, rms=0.608 (0.011%), neg=0, invalid=4512 0258: dt=0.101250, rms=0.608 (0.000%), neg=0, invalid=4512 0259: dt=0.003164, rms=0.608 (0.000%), neg=0, invalid=4512 0260: dt=0.001582, rms=0.608 (0.000%), neg=0, invalid=4512 0261: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=4512 0262: dt=145.152000, rms=0.603 (0.995%), neg=0, invalid=4512 0263: dt=144.662722, rms=0.600 (0.545%), neg=0, invalid=4512 0264: dt=65.276353, rms=0.598 (0.295%), neg=0, invalid=4512 0265: dt=414.720000, rms=0.594 (0.674%), neg=0, invalid=4512 0266: dt=70.808511, rms=0.591 (0.502%), neg=0, invalid=4512 0267: dt=103.680000, rms=0.590 (0.231%), neg=0, invalid=4512 0268: dt=64.864865, rms=0.589 (0.131%), neg=0, invalid=4512 0269: dt=331.776000, rms=0.587 (0.392%), neg=0, invalid=4512 0270: dt=67.555556, rms=0.585 (0.254%), neg=0, invalid=4512 0271: dt=124.416000, rms=0.584 (0.177%), neg=0, invalid=4512 0272: dt=36.288000, rms=0.584 (0.088%), neg=0, invalid=4512 0273: dt=414.720000, rms=0.582 (0.311%), neg=0, invalid=4512 0274: dt=36.288000, rms=0.580 (0.255%), neg=0, invalid=4512 0275: dt=103.680000, rms=0.580 (0.098%), neg=0, invalid=4512 0276: dt=103.680000, rms=0.579 (0.134%), neg=0, invalid=4512 0277: dt=62.208000, rms=0.579 (0.082%), neg=0, invalid=4512 0278: dt=248.832000, rms=0.578 (0.168%), neg=0, invalid=4512 0279: dt=66.083721, rms=0.577 (0.159%), neg=0, invalid=4512 0280: dt=36.288000, rms=0.576 (0.037%), neg=0, invalid=4512 0281: dt=36.288000, rms=0.576 (0.035%), neg=0, invalid=4512 0282: dt=36.288000, rms=0.576 (0.069%), neg=0, invalid=4512 0283: dt=36.288000, rms=0.575 (0.092%), neg=0, invalid=4512 0284: dt=36.288000, rms=0.575 (0.115%), neg=0, invalid=4512 0285: dt=36.288000, rms=0.574 (0.129%), neg=0, invalid=4512 0286: dt=36.288000, rms=0.573 (0.148%), neg=0, invalid=4512 0287: dt=36.288000, rms=0.572 (0.167%), neg=0, invalid=4512 0288: dt=36.288000, rms=0.571 (0.174%), neg=0, invalid=4512 0289: dt=36.288000, rms=0.570 (0.180%), neg=0, invalid=4512 0290: dt=36.288000, rms=0.569 (0.180%), neg=0, invalid=4512 0291: dt=36.288000, rms=0.568 (0.179%), neg=0, invalid=4512 0292: dt=36.288000, rms=0.567 (0.180%), neg=0, invalid=4512 0293: dt=36.288000, rms=0.566 (0.177%), neg=0, invalid=4512 0294: dt=36.288000, rms=0.565 (0.174%), neg=0, invalid=4512 0295: dt=36.288000, rms=0.564 (0.164%), neg=0, invalid=4512 0296: dt=36.288000, rms=0.563 (0.154%), neg=0, invalid=4512 0297: dt=36.288000, rms=0.562 (0.146%), neg=0, invalid=4512 0298: dt=36.288000, rms=0.562 (0.142%), neg=0, invalid=4512 0299: dt=36.288000, rms=0.561 (0.138%), neg=0, invalid=4512 0300: dt=36.288000, rms=0.560 (0.136%), neg=0, invalid=4512 0301: dt=1.134000, rms=0.560 (-0.000%), neg=0, invalid=4512 0302: dt=0.567000, rms=0.560 (0.000%), neg=0, invalid=4512 0303: dt=0.567000, rms=0.560 (0.000%), neg=0, invalid=4512 0304: dt=0.405000, rms=0.560 (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=0.570, neg=0, invalid=4512 0305: dt=0.000684, rms=0.568 (0.208%), neg=0, invalid=4512 0306: dt=0.000488, rms=0.568 (0.000%), neg=0, invalid=4512 0307: dt=0.000015, rms=0.568 (0.000%), neg=0, invalid=4512 0308: dt=0.000008, rms=0.568 (0.000%), neg=0, invalid=4512 0309: dt=0.000004, rms=0.568 (0.000%), neg=0, invalid=4512 0310: dt=0.000000, rms=0.568 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=4512 0311: dt=0.000000, rms=0.568 (0.208%), neg=0, invalid=4512 0312: dt=0.000000, rms=0.568 (0.000%), neg=0, invalid=4512 0313: dt=0.000002, rms=0.568 (0.000%), neg=0, invalid=4512 0314: dt=0.000000, rms=0.568 (-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=0.596, neg=0, invalid=4512 0315: dt=0.000000, rms=0.595 (0.190%), neg=0, invalid=4512 0316: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=4512 0317: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=4512 0318: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.596, neg=0, invalid=4512 0319: dt=0.000000, rms=0.595 (0.190%), neg=0, invalid=4512 0320: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=4512 0321: dt=0.000000, rms=0.595 (0.000%), neg=0, invalid=4512 0322: dt=0.000000, rms=0.595 (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=0.649, neg=0, invalid=4512 0323: dt=1.536000, rms=0.632 (2.514%), neg=0, invalid=4512 0324: dt=0.112000, rms=0.631 (0.121%), neg=0, invalid=4512 0325: dt=0.112000, rms=0.631 (0.115%), neg=0, invalid=4512 0326: dt=0.024000, rms=0.631 (0.024%), neg=0, invalid=4512 0327: dt=0.001500, rms=0.631 (0.002%), neg=0, invalid=4512 0328: dt=0.000750, rms=0.631 (0.000%), neg=0, invalid=4512 0329: dt=0.000375, rms=0.631 (0.001%), neg=0, invalid=4512 0330: dt=0.000188, rms=0.631 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.632, neg=0, invalid=4512 0331: dt=0.000240, rms=0.631 (0.150%), neg=0, invalid=4512 0332: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=4512 0333: dt=0.000024, rms=0.631 (0.000%), neg=0, invalid=4512 0334: dt=0.000012, rms=0.631 (0.000%), neg=0, invalid=4512 0335: dt=0.000003, rms=0.631 (0.000%), 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=0.547, neg=0, invalid=4512 0336: dt=0.448000, rms=0.533 (2.542%), neg=0, invalid=4512 0337: dt=0.197917, rms=0.532 (0.327%), neg=0, invalid=4512 0338: dt=0.320000, rms=0.529 (0.428%), neg=0, invalid=4512 0339: dt=0.112000, rms=0.529 (0.107%), neg=0, invalid=4512 0340: dt=0.320000, rms=0.527 (0.273%), neg=0, invalid=4512 0341: dt=0.112000, rms=0.527 (0.074%), neg=0, invalid=4512 0342: dt=0.320000, rms=0.526 (0.187%), neg=0, invalid=4512 0343: dt=0.112000, rms=0.526 (0.050%), neg=0, invalid=4512 0344: dt=0.112000, rms=0.525 (0.049%), neg=0, invalid=4512 0345: dt=0.112000, rms=0.525 (0.087%), neg=0, invalid=4512 0346: dt=0.112000, rms=0.524 (0.114%), neg=0, invalid=4512 0347: dt=0.112000, rms=0.524 (0.131%), neg=0, invalid=4512 0348: dt=0.112000, rms=0.523 (0.139%), neg=0, invalid=4512 0349: dt=0.112000, rms=0.522 (0.135%), neg=0, invalid=4512 0350: dt=0.112000, rms=0.522 (0.124%), neg=0, invalid=4512 0351: dt=0.112000, rms=0.521 (0.107%), neg=0, invalid=4512 0352: dt=0.112000, rms=0.520 (0.088%), neg=0, invalid=4512 0353: dt=0.112000, rms=0.520 (0.065%), neg=0, invalid=4512 0354: dt=0.112000, rms=0.520 (0.044%), neg=0, invalid=4512 0355: dt=0.112000, rms=0.520 (0.025%), neg=0, invalid=4512 0356: dt=0.112000, rms=0.520 (0.009%), neg=0, invalid=4512 0357: dt=0.112000, rms=0.520 (-0.000%), neg=0, invalid=4512 0358: dt=0.000000, rms=0.520 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=4512 0359: dt=0.205357, rms=0.518 (0.522%), neg=0, invalid=4512 0360: dt=0.112000, rms=0.517 (0.120%), neg=0, invalid=4512 0361: dt=0.112000, rms=0.517 (0.092%), neg=0, invalid=4512 0362: dt=0.112000, rms=0.516 (0.072%), neg=0, invalid=4512 0363: dt=0.112000, rms=0.516 (0.056%), neg=0, invalid=4512 0364: dt=0.112000, rms=0.516 (0.045%), neg=0, invalid=4512 0365: dt=0.112000, rms=0.516 (0.031%), neg=0, invalid=4512 0366: dt=0.112000, rms=0.515 (0.055%), neg=0, invalid=4512 0367: dt=0.112000, rms=0.515 (0.060%), neg=0, invalid=4512 0368: dt=0.112000, rms=0.515 (0.045%), neg=0, invalid=4512 0369: dt=0.112000, rms=0.515 (0.018%), neg=0, invalid=4512 0370: dt=0.112000, rms=0.515 (-0.014%), neg=0, invalid=4512 0371: dt=0.000000, rms=0.515 (0.000%), 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=0.513, neg=0, invalid=4512 0372: dt=32.368000, rms=0.512 (0.172%), neg=0, invalid=4512 0373: dt=0.001264, rms=0.512 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=4512 0374: dt=129.472000, rms=0.512 (0.174%), neg=0, invalid=4512 0375: dt=295.936000, rms=0.512 (0.027%), neg=0, invalid=4512 0376: dt=295.936000, rms=0.512 (-0.337%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=4512 0377: dt=20.736000, rms=0.512 (0.178%), neg=0, invalid=4512 0378: dt=20.736000, rms=0.512 (0.011%), neg=0, invalid=4512 0379: dt=20.736000, rms=0.512 (0.003%), neg=0, invalid=4512 0380: dt=20.736000, rms=0.512 (-0.010%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=4512 0381: dt=124.416000, rms=0.511 (0.364%), neg=0, invalid=4512 0382: dt=64.000000, rms=0.510 (0.128%), neg=0, invalid=4512 0383: dt=64.000000, rms=0.510 (-0.080%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=4512 iter 0, gcam->neg = 190 after 18 iterations, nbhd size=1, neg = 0 0384: dt=60.511278, rms=0.503 (1.510%), neg=0, invalid=4512 iter 0, gcam->neg = 239 after 30 iterations, nbhd size=1, neg = 0 0385: dt=44.800000, rms=0.498 (1.142%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=0, neg = 0 0386: dt=11.200000, rms=0.497 (0.171%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=0, neg = 0 0387: dt=11.200000, rms=0.496 (0.159%), neg=0, invalid=4512 iter 0, gcam->neg = 20 after 19 iterations, nbhd size=1, neg = 0 0388: dt=11.200000, rms=0.495 (0.169%), neg=0, invalid=4512 iter 0, gcam->neg = 44 after 19 iterations, nbhd size=1, neg = 0 0389: dt=11.200000, rms=0.494 (0.252%), neg=0, invalid=4512 iter 0, gcam->neg = 41 after 18 iterations, nbhd size=1, neg = 0 0390: dt=11.200000, rms=0.492 (0.370%), neg=0, invalid=4512 iter 0, gcam->neg = 84 after 21 iterations, nbhd size=1, neg = 0 0391: dt=11.200000, rms=0.490 (0.368%), neg=0, invalid=4512 iter 0, gcam->neg = 106 after 13 iterations, nbhd size=0, neg = 0 0392: dt=11.200000, rms=0.489 (0.310%), neg=0, invalid=4512 iter 0, gcam->neg = 120 after 16 iterations, nbhd size=1, neg = 0 0393: dt=11.200000, rms=0.487 (0.284%), neg=0, invalid=4512 iter 0, gcam->neg = 104 after 16 iterations, nbhd size=1, neg = 0 0394: dt=11.200000, rms=0.486 (0.271%), neg=0, invalid=4512 iter 0, gcam->neg = 181 after 20 iterations, nbhd size=1, neg = 0 0395: dt=11.200000, rms=0.485 (0.261%), neg=0, invalid=4512 iter 0, gcam->neg = 248 after 19 iterations, nbhd size=1, neg = 0 0396: dt=11.200000, rms=0.483 (0.298%), neg=0, invalid=4512 iter 0, gcam->neg = 378 after 28 iterations, nbhd size=1, neg = 0 0397: dt=11.200000, rms=0.482 (0.281%), neg=0, invalid=4512 iter 0, gcam->neg = 511 after 35 iterations, nbhd size=2, neg = 0 0398: dt=11.200000, rms=0.481 (0.221%), neg=0, invalid=4512 iter 0, gcam->neg = 213 after 23 iterations, nbhd size=1, neg = 0 0399: dt=11.200000, rms=0.480 (0.252%), neg=0, invalid=4512 iter 0, gcam->neg = 467 after 35 iterations, nbhd size=2, neg = 0 0400: dt=11.200000, rms=0.479 (0.214%), neg=0, invalid=4512 iter 0, gcam->neg = 269 after 33 iterations, nbhd size=2, neg = 0 0401: dt=11.200000, rms=0.478 (0.200%), neg=0, invalid=4512 iter 0, gcam->neg = 277 after 34 iterations, nbhd size=2, neg = 0 0402: dt=11.200000, rms=0.477 (0.148%), neg=0, invalid=4512 iter 0, gcam->neg = 189 after 31 iterations, nbhd size=2, neg = 0 0403: dt=11.200000, rms=0.476 (0.160%), neg=0, invalid=4512 iter 0, gcam->neg = 231 after 32 iterations, nbhd size=1, neg = 0 0404: dt=11.200000, rms=0.476 (0.109%), neg=0, invalid=4512 iter 0, gcam->neg = 340 after 18 iterations, nbhd size=1, neg = 0 0405: dt=11.200000, rms=0.475 (0.034%), neg=0, invalid=4512 iter 0, gcam->neg = 49 after 10 iterations, nbhd size=0, neg = 0 0406: dt=11.200000, rms=0.475 (0.040%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0407: dt=8.000000, rms=0.475 (-0.012%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=4512 iter 0, gcam->neg = 153 after 22 iterations, nbhd size=1, neg = 0 0408: dt=44.800000, rms=0.473 (0.746%), neg=0, invalid=4512 iter 0, gcam->neg = 42 after 8 iterations, nbhd size=0, neg = 0 0409: dt=25.600000, rms=0.472 (0.069%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 13 iterations, nbhd size=1, neg = 0 0410: dt=25.600000, rms=0.472 (0.149%), neg=0, invalid=4512 iter 0, gcam->neg = 36 after 24 iterations, nbhd size=1, neg = 0 0411: dt=25.600000, rms=0.471 (0.131%), neg=0, invalid=4512 iter 0, gcam->neg = 74 after 17 iterations, nbhd size=0, neg = 0 0412: dt=25.600000, rms=0.471 (0.054%), neg=0, invalid=4512 iter 0, gcam->neg = 123 after 20 iterations, nbhd size=0, neg = 0 0413: dt=25.600000, rms=0.471 (0.004%), neg=0, invalid=4512 iter 0, gcam->neg = 70 after 7 iterations, nbhd size=0, neg = 0 0414: dt=44.800000, rms=0.470 (0.099%), neg=0, invalid=4512 iter 0, gcam->neg = 25 after 7 iterations, nbhd size=0, neg = 0 0415: dt=25.600000, rms=0.470 (0.058%), neg=0, invalid=4512 iter 0, gcam->neg = 23 after 9 iterations, nbhd size=0, neg = 0 0416: dt=25.600000, rms=0.470 (0.040%), neg=0, invalid=4512 iter 0, gcam->neg = 92 after 12 iterations, nbhd size=0, neg = 0 0417: dt=25.600000, rms=0.469 (0.123%), neg=0, invalid=4512 iter 0, gcam->neg = 177 after 14 iterations, nbhd size=0, neg = 0 0418: dt=25.600000, rms=0.469 (0.105%), neg=0, invalid=4512 iter 0, gcam->neg = 244 after 42 iterations, nbhd size=2, neg = 0 0419: dt=25.600000, rms=0.469 (0.020%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=4512 0420: dt=0.252000, rms=0.478 (0.186%), neg=0, invalid=4512 0421: dt=0.216000, rms=0.478 (0.005%), neg=0, invalid=4512 0422: dt=0.216000, rms=0.478 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0423: dt=2.068966, rms=0.478 (0.210%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0424: dt=1.008000, rms=0.478 (0.005%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=1.008000, rms=0.478 (0.002%), neg=0, invalid=4512 0426: dt=1.008000, rms=0.478 (-0.016%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0427: dt=1.024000, rms=0.494 (0.346%), neg=0, invalid=4512 0428: dt=0.256000, rms=0.494 (0.006%), neg=0, invalid=4512 0429: dt=0.256000, rms=0.494 (-0.007%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=4512 0430: dt=1.280000, rms=0.493 (0.347%), neg=0, invalid=4512 0431: dt=0.448000, rms=0.493 (0.024%), neg=0, invalid=4512 0432: dt=0.448000, rms=0.493 (0.008%), neg=0, invalid=4512 0433: dt=0.448000, rms=0.493 (-0.026%), 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=0.479, neg=0, invalid=4512 iter 0, gcam->neg = 1565 after 20 iterations, nbhd size=1, neg = 0 0434: dt=1.909974, rms=0.450 (6.154%), neg=0, invalid=4512 0435: dt=0.005000, rms=0.450 (0.003%), neg=0, invalid=4512 0436: dt=0.005000, rms=0.450 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=4512 0437: dt=0.080000, rms=0.449 (0.276%), neg=0, invalid=4512 0438: dt=0.000000, rms=0.449 (0.001%), neg=0, invalid=4512 0439: dt=0.050000, rms=0.449 (-0.019%), 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=0.438, neg=0, invalid=4512 0440: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=4512 0441: dt=73.984000, rms=0.438 (0.011%), neg=0, invalid=4512 0442: dt=92.480000, rms=0.438 (0.002%), neg=0, invalid=4512 0443: dt=92.480000, rms=0.438 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=4512 0444: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=4512 0445: dt=103.680000, rms=0.438 (0.047%), neg=0, invalid=4512 0446: dt=82.944000, rms=0.438 (0.011%), neg=0, invalid=4512 0447: dt=82.944000, rms=0.438 (0.012%), neg=0, invalid=4512 0448: dt=82.944000, rms=0.437 (0.010%), neg=0, invalid=4512 0449: dt=82.944000, rms=0.437 (0.009%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=4512 iter 0, gcam->neg = 21 after 4 iterations, nbhd size=0, neg = 0 0450: dt=32.000000, rms=0.437 (0.337%), neg=0, invalid=4512 iter 0, gcam->neg = 191 after 24 iterations, nbhd size=1, neg = 0 0451: dt=91.428571, rms=0.436 (0.227%), neg=0, invalid=4512 iter 0, gcam->neg = 484 after 41 iterations, nbhd size=2, neg = 0 0452: dt=91.428571, rms=0.436 (-0.469%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=4512 iter 0, gcam->neg = 233 after 29 iterations, nbhd size=1, neg = 0 0453: dt=56.979592, rms=0.431 (0.987%), neg=0, invalid=4512 iter 0, gcam->neg = 110 after 26 iterations, nbhd size=1, neg = 0 0454: dt=44.800000, rms=0.430 (0.329%), neg=0, invalid=4512 iter 0, gcam->neg = 100 after 35 iterations, nbhd size=2, neg = 0 0455: dt=32.000000, rms=0.429 (0.085%), neg=0, invalid=4512 iter 0, gcam->neg = 20 after 13 iterations, nbhd size=1, neg = 0 0456: dt=32.000000, rms=0.428 (0.258%), neg=0, invalid=4512 iter 0, gcam->neg = 114 after 21 iterations, nbhd size=1, neg = 0 0457: dt=32.000000, rms=0.427 (0.360%), neg=0, invalid=4512 iter 0, gcam->neg = 319 after 23 iterations, nbhd size=1, neg = 0 0458: dt=32.000000, rms=0.426 (0.277%), neg=0, invalid=4512 iter 0, gcam->neg = 659 after 41 iterations, nbhd size=2, neg = 0 0459: dt=32.000000, rms=0.426 (-0.075%), neg=0, invalid=4512 0460: dt=0.000000, rms=0.426 (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=0.429, neg=0, invalid=4512 iter 0, gcam->neg = 30 after 7 iterations, nbhd size=0, neg = 0 0461: dt=3.529412, rms=0.429 (0.049%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=0, neg = 0 0462: dt=1.008000, rms=0.429 (0.005%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0463: dt=1.008000, rms=0.429 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=4512 iter 0, gcam->neg = 102 after 22 iterations, nbhd size=1, neg = 0 0464: dt=13.750000, rms=0.428 (0.235%), neg=0, invalid=4512 iter 0, gcam->neg = 186 after 29 iterations, nbhd size=1, neg = 0 0465: dt=10.666667, rms=0.427 (0.179%), neg=0, invalid=4512 iter 0, gcam->neg = 237 after 40 iterations, nbhd size=3, neg = 0 0466: dt=10.666667, rms=0.427 (-0.241%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=4512 0467: dt=0.000050, rms=0.434 (0.000%), neg=0, invalid=4512 0468: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=4512 0469: dt=0.000000, rms=0.434 (0.000%), 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=0.423, neg=0, invalid=4512 iter 0, gcam->neg = 991 after 19 iterations, nbhd size=1, neg = 0 0470: dt=0.642222, rms=0.416 (1.717%), neg=0, invalid=4512 0471: dt=0.080000, rms=0.416 (0.024%), neg=0, invalid=4512 0472: dt=0.080000, rms=0.416 (0.010%), neg=0, invalid=4512 0473: dt=0.080000, rms=0.416 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=4512 iter 0, gcam->neg = 256 after 5 iterations, nbhd size=0, neg = 0 0474: dt=0.452532, rms=0.413 (0.625%), neg=0, invalid=4512 iter 0, gcam->neg = 23 after 1 iterations, nbhd size=0, neg = 0 0475: dt=0.256000, rms=0.412 (0.106%), neg=0, invalid=4512 iter 0, gcam->neg = 15 after 1 iterations, nbhd size=0, neg = 0 0476: dt=0.256000, rms=0.412 (0.131%), neg=0, invalid=4512 iter 0, gcam->neg = 46 after 2 iterations, nbhd size=0, neg = 0 0477: dt=0.256000, rms=0.411 (0.144%), neg=0, invalid=4512 iter 0, gcam->neg = 70 after 5 iterations, nbhd size=0, neg = 0 0478: dt=0.256000, rms=0.411 (0.107%), neg=0, invalid=4512 iter 0, gcam->neg = 150 after 18 iterations, nbhd size=1, neg = 0 0479: dt=0.256000, rms=0.411 (0.065%), neg=0, invalid=4512 0480: dt=0.112000, rms=0.411 (0.027%), neg=0, invalid=4512 0481: dt=0.112000, rms=0.411 (0.009%), neg=0, invalid=4512 0482: dt=0.112000, rms=0.410 (0.003%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0483: dt=0.112000, rms=0.410 (-0.006%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 5 hours, 51 minutes and 8 seconds. mri_ca_register utimesec 20183.513639 mri_ca_register stimesec 19.355057 mri_ca_register ru_maxrss 1289168 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5167894 mri_ca_register ru_majflt 12086 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 750624 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 14255 mri_ca_register ru_nivcsw 85988 FSRUNTIME@ mri_ca_register 5.8523 hours 1 threads #-------------------------------------- #@# SubCort Seg Tue Jun 14 23:19:51 EDT 2016 mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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-0-102 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/AD18/mri mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 5.82 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 = 0.13577 (31) Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (8324 voxels, overlap=0.106) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (8324 voxels, peak = 31), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.14401 (31) Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (8986 voxels, overlap=0.108) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8986 voxels, peak = 28), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.19460 (104) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (365 voxels, overlap=0.277) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (365 voxels, peak = 103), gca=103.1 gca peak = 0.16930 (96) mri peak = 0.17730 (103) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (280 voxels, overlap=0.362) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (280 voxels, peak = 102), gca=102.2 gca peak = 0.24553 (55) mri peak = 0.07510 (67) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (709 voxels, overlap=0.064) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (709 voxels, peak = 66), gca=66.3 gca peak = 0.30264 (59) mri peak = 0.06944 (72) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (952 voxels, overlap=0.749) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (952 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.09283 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (28431 voxels, overlap=0.737) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (28431 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.12245 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (28909 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (28909 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04363 (75) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23479 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (23479 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04357 (77) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (19880 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (19880 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.08183 (84) Right_Caudate (50): linear fit = 1.24 x + 0.0 (1049 voxels, overlap=0.026) Right_Caudate (50): linear fit = 1.24 x + 0.0 (1049 voxels, peak = 82), gca=81.5 gca peak = 0.15280 (69) mri peak = 0.08724 (82) Left_Caudate (11): linear fit = 1.15 x + 0.0 (781 voxels, overlap=0.217) Left_Caudate (11): linear fit = 1.15 x + 0.0 (781 voxels, peak = 80), gca=79.7 gca peak = 0.13902 (56) mri peak = 0.06090 (68) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (24531 voxels, overlap=0.076) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (24531 voxels, peak = 70), gca=69.7 gca peak = 0.14777 (55) mri peak = 0.06300 (68) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (23580 voxels, overlap=0.148) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (23580 voxels, peak = 67), gca=67.4 gca peak = 0.16765 (84) mri peak = 0.15444 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (4136 voxels, overlap=0.087) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (4136 voxels, peak = 92), gca=92.0 gca peak = 0.18739 (84) mri peak = 0.11765 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5922 voxels, overlap=0.139) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (5922 voxels, peak = 93), gca=92.8 gca peak = 0.29869 (57) mri peak = 0.12191 (74) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (204 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (204 voxels, peak = 72), gca=71.5 gca peak = 0.33601 (57) mri peak = 0.09442 (77) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (258 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (258 voxels, peak = 76), gca=75.5 gca peak = 0.11131 (90) mri peak = 0.06457 (88) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2703 voxels, overlap=0.992) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (2703 voxels, peak = 88), gca=87.8 gca peak = 0.11793 (83) mri peak = 0.06744 (88) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (2623 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (2623 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.10236 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1010 voxels, overlap=0.355) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1010 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.09236 (89) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1128 voxels, overlap=0.176) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1128 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.07014 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (10799 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (10799 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.09133 (100) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1151 voxels, overlap=0.084) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1151 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.09894 (99) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1141 voxels, overlap=0.179) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1141 voxels, peak = 98), gca=97.9 gca peak = 0.14975 (24) mri peak = 0.13004 (25) Third_Ventricle (14): linear fit = 1.05 x + 0.0 (382 voxels, overlap=0.821) Third_Ventricle (14): linear fit = 1.05 x + 0.0 (382 voxels, peak = 25), gca=25.3 gca peak = 0.19357 (14) mri peak = 0.10380 (26) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (390 voxels, overlap=0.354) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (390 voxels, peak = 22), gca=21.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) 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 1.28 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.35 x + 0.0 Left_Pallidum too bright - rescaling by 0.997 (from 1.065) to 101.9 (was 102.2) Right_Pallidum too bright - rescaling by 0.989 (from 1.085) to 101.9 (was 103.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.13577 (31) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8324 voxels, overlap=0.741) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (8324 voxels, peak = 32), gca=32.4 gca peak = 0.13981 (19) mri peak = 0.14401 (31) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8986 voxels, overlap=0.313) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8986 voxels, peak = 29), gca=28.5 gca peak = 0.21610 (101) mri peak = 0.19460 (104) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (365 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (365 voxels, peak = 102), gca=101.5 gca peak = 0.15995 (100) mri peak = 0.17730 (103) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (280 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (280 voxels, peak = 100), gca=100.5 gca peak = 0.26666 (67) mri peak = 0.07510 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (709 voxels, overlap=0.979) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (709 voxels, peak = 67), gca=67.0 gca peak = 0.28516 (69) mri peak = 0.06944 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (952 voxels, overlap=1.014) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (952 voxels, peak = 69), gca=69.0 gca peak = 0.07785 (104) mri peak = 0.09283 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28431 voxels, overlap=0.799) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28431 voxels, peak = 105), gca=104.5 gca peak = 0.07820 (106) mri peak = 0.12245 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28909 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28909 voxels, peak = 106), gca=106.0 gca peak = 0.07274 (78) mri peak = 0.04363 (75) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23479 voxels, overlap=0.947) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23479 voxels, peak = 77), gca=76.8 gca peak = 0.09074 (75) mri peak = 0.04357 (77) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19880 voxels, overlap=0.939) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19880 voxels, peak = 75), gca=75.0 gca peak = 0.22966 (81) mri peak = 0.08183 (84) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1049 voxels, overlap=1.003) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1049 voxels, peak = 79), gca=79.0 gca peak = 0.14387 (79) mri peak = 0.08724 (82) Left_Caudate (11): linear fit = 1.01 x + 0.0 (781 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.01 x + 0.0 (781 voxels, peak = 80), gca=80.2 gca peak = 0.11552 (70) mri peak = 0.06090 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (24531 voxels, overlap=0.975) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (24531 voxels, peak = 69), gca=69.0 gca peak = 0.12399 (67) mri peak = 0.06300 (68) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23580 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23580 voxels, peak = 66), gca=66.0 gca peak = 0.15182 (92) mri peak = 0.15444 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4136 voxels, overlap=0.879) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4136 voxels, peak = 92), gca=92.0 gca peak = 0.16614 (93) mri peak = 0.11765 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5922 voxels, overlap=0.912) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5922 voxels, peak = 93), gca=92.5 gca peak = 0.28392 (73) mri peak = 0.12191 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (204 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (204 voxels, peak = 73), gca=73.0 gca peak = 0.30280 (75) mri peak = 0.09442 (77) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (258 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (258 voxels, peak = 76), gca=76.1 gca peak = 0.11390 (86) mri peak = 0.06457 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2703 voxels, overlap=0.965) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2703 voxels, peak = 86), gca=86.0 gca peak = 0.11628 (85) mri peak = 0.06744 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2623 voxels, overlap=0.991) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2623 voxels, peak = 85), gca=85.0 gca peak = 0.07894 (84) mri peak = 0.10236 (89) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1010 voxels, overlap=0.837) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1010 voxels, peak = 85), gca=85.3 gca peak = 0.08197 (88) mri peak = 0.09236 (89) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1128 voxels, overlap=0.788) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1128 voxels, peak = 90), gca=90.2 gca peak = 0.07190 (90) mri peak = 0.07014 (88) Brain_Stem (16): linear fit = 1.01 x + 0.0 (10799 voxels, overlap=0.846) Brain_Stem (16): linear fit = 1.01 x + 0.0 (10799 voxels, peak = 91), gca=91.3 gca peak = 0.10164 (96) mri peak = 0.09133 (100) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1151 voxels, overlap=0.797) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1151 voxels, peak = 96), gca=96.5 gca peak = 0.15461 (96) mri peak = 0.09894 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1141 voxels, overlap=0.879) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1141 voxels, peak = 96), gca=96.0 gca peak = 0.16720 (27) mri peak = 0.13004 (25) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (382 voxels, overlap=0.926) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (382 voxels, peak = 25), gca=25.2 gca peak = 0.17375 (20) mri peak = 0.10380 (26) Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (390 voxels, overlap=0.811) Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (390 voxels, peak = 24), gca=23.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.17076 (49) gca peak Left_Accumbens_area = 0.61316 (72) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.24202 (28) gca peak Right_Accumbens_area = 0.29898 (80) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14506 (37) gca peak Fifth_Ventricle = 0.51669 (42) gca peak WM_hypointensities = 0.07770 (78) gca peak non_WM_hypointensities = 0.09187 (44) gca peak Optic_Chiasm = 0.68943 (75) 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 1.16 x + 0.0 Right_Pallidum too bright - rescaling by 1.006 (from 1.005) to 102.1 (was 101.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 48773 voxels changed in iteration 0 of unlikely voxel relabeling 74 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 49661 gm and wm labels changed (%36 to gray, %64 to white out of all changed labels) 198 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 63458 changed. image ll: -2.093, PF=0.500 pass 2: 16046 changed. image ll: -2.092, PF=0.500 pass 3: 5091 changed. pass 4: 2051 changed. 38455 voxels changed in iteration 0 of unlikely voxel relabeling 224 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5373 voxels changed in iteration 0 of unlikely voxel relabeling 39 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4677 voxels changed in iteration 0 of unlikely voxel relabeling 38 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4492 voxels changed in iteration 0 of unlikely voxel relabeling 43 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 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 4113.215696 mri_ca_label stimesec 11.368271 mri_ca_label ru_maxrss 2089124 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 675511 mri_ca_label ru_majflt 810 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 51672 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 1061 mri_ca_label ru_nivcsw 63602 auto-labeling took 68 minutes and 48 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/transforms/cc_up.lta AD18 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/AD18/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/norm.mgz 26100 voxels in left wm, 44393 in right wm, xrange [120, 130] searching rotation angles z=[-8 6], y=[-10 4] searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 global minimum found at slice 125.4, rotations (-2.51, -0.98) final transformation (x=125.4, yr=-2.511, zr=-0.983): 0.99889 0.01715 -0.04381 5.18325; -0.01714 0.99985 0.00075 22.09101; 0.04382 0.00000 0.99904 24.59939; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 131] in xformed coordinates best xformed slice 127 cc center is found at 127 108 98 eigenvectors: 0.00351 -0.00852 0.99996; -0.16351 -0.98651 -0.00783; 0.98653 -0.16348 -0.00485; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Wed Jun 15 00:29:35 EDT 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jun 15 00:29:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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... 884 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 109 gm peak at 84 (84), valley at 58 (58) csf peak at 33, setting threshold to 67 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 109 gm peak at 83 (83), valley at 59 (59) csf peak at 33, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 0 seconds. #-------------------------------------------- #@# Mask BFS Wed Jun 15 00:33:37 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1355261 voxels in mask (pct= 8.08) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jun 15 00:33:39 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 (102.0): 102.7 +- 5.4 [79.0 --> 125.0] GM (72.0) : 69.2 +- 13.4 [30.0 --> 95.0] setting bottom of white matter range to 82.6 setting top of gray matter range to 96.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4625 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2373 filled 1925 bright non-wm voxels segmented. 2499 diagonally connected voxels added... white matter segmentation took 2.0 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 0.90 minutes reading wm segmentation from wm.seg.mgz... 973 voxels added to wm to prevent paths from MTL structures to cortex 5829 additional wm voxels added 0 additional wm voxels added SEG EDIT: 97856 voxels turned on, 41391 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 26 found - 26 modified | TOTAL: 26 pass 2 (xy+): 0 found - 26 modified | TOTAL: 26 pass 1 (xy-): 27 found - 27 modified | TOTAL: 53 pass 2 (xy-): 0 found - 27 modified | TOTAL: 53 pass 1 (yz+): 36 found - 36 modified | TOTAL: 89 pass 2 (yz+): 0 found - 36 modified | TOTAL: 89 pass 1 (yz-): 36 found - 36 modified | TOTAL: 125 pass 2 (yz-): 0 found - 36 modified | TOTAL: 125 pass 1 (xz+): 29 found - 29 modified | TOTAL: 154 pass 2 (xz+): 0 found - 29 modified | TOTAL: 154 pass 1 (xz-): 74 found - 74 modified | TOTAL: 228 pass 2 (xz-): 0 found - 74 modified | TOTAL: 228 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 10 found - 10 modified | TOTAL: 16 pass 2 (+++): 0 found - 10 modified | TOTAL: 16 pass 1 (+++): 4 found - 4 modified | TOTAL: 20 pass 2 (+++): 0 found - 4 modified | TOTAL: 20 pass 1 (+++): 7 found - 7 modified | TOTAL: 27 pass 2 (+++): 0 found - 7 modified | TOTAL: 27 Iteration Number : 1 pass 1 (++): 39 found - 39 modified | TOTAL: 39 pass 2 (++): 0 found - 39 modified | TOTAL: 39 pass 1 (+-): 48 found - 48 modified | TOTAL: 87 pass 2 (+-): 0 found - 48 modified | TOTAL: 87 pass 1 (--): 25 found - 25 modified | TOTAL: 112 pass 2 (--): 0 found - 25 modified | TOTAL: 112 pass 1 (-+): 31 found - 31 modified | TOTAL: 143 pass 2 (-+): 0 found - 31 modified | TOTAL: 143 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 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 = 416 (out of 506927: 0.082063) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jun 15 00:36:37 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34222; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03569 0.00253 -0.01208 -3.45224; 0.00302 1.11727 0.44755 -70.34222; 0.02282 -0.36659 1.03980 36.26064; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1131 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (125, 112, 91), TAL = (3.0, -37.0, 16.0) talairach voxel to voxel transform 0.96530 0.00131 0.01065 3.03858; 0.00515 0.78429 -0.33751 67.42484; -0.01937 0.27648 0.84250 -11.16844; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 112, 91) --> (3.0, -37.0, 16.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, -37.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -37.00, 16.00) SRC: (107.44, 125.10, 94.39) search lh wm seed point around talairach space (-15.00, -37.00, 16.00), SRC: (142.19, 125.29, 93.69) 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 Jun 15 00:37:25 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 0 found - 0 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 245711: 0.004070) 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: 1613 vertices, 1767 faces slice 60: 8577 vertices, 8879 faces slice 70: 19336 vertices, 19712 faces slice 80: 30290 vertices, 30641 faces slice 90: 40142 vertices, 40488 faces slice 100: 49484 vertices, 49855 faces slice 110: 58832 vertices, 59175 faces slice 120: 67830 vertices, 68176 faces slice 130: 76677 vertices, 77007 faces slice 140: 85192 vertices, 85465 faces slice 150: 92422 vertices, 92676 faces slice 160: 98644 vertices, 98841 faces slice 170: 102870 vertices, 103026 faces slice 180: 105868 vertices, 105963 faces slice 190: 106594 vertices, 106626 faces slice 200: 106594 vertices, 106626 faces slice 210: 106594 vertices, 106626 faces slice 220: 106594 vertices, 106626 faces slice 230: 106594 vertices, 106626 faces slice 240: 106594 vertices, 106626 faces slice 250: 106594 vertices, 106626 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... 106594 voxel in cpt #1: X=-32 [v=106594,e=319878,f=213252] located at (-24.499258, -22.592276, 7.455560) For the whole surface: X=-32 [v=106594,e=319878,f=213252] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Jun 15 00:45:02 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 3 found - 3 modified | TOTAL: 4 pass 2 (yz-): 0 found - 3 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 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 = 5 (out of 244069: 0.002049) 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: 744 vertices, 844 faces slice 60: 5884 vertices, 6127 faces slice 70: 15809 vertices, 16165 faces slice 80: 27414 vertices, 27778 faces slice 90: 37153 vertices, 37475 faces slice 100: 46318 vertices, 46675 faces slice 110: 56135 vertices, 56490 faces slice 120: 65377 vertices, 65737 faces slice 130: 74070 vertices, 74420 faces slice 140: 82940 vertices, 83267 faces slice 150: 90732 vertices, 91041 faces slice 160: 97379 vertices, 97646 faces slice 170: 102156 vertices, 102375 faces slice 180: 105944 vertices, 106126 faces slice 190: 107447 vertices, 107541 faces slice 200: 107474 vertices, 107554 faces slice 210: 107474 vertices, 107554 faces slice 220: 107474 vertices, 107554 faces slice 230: 107474 vertices, 107554 faces slice 240: 107474 vertices, 107554 faces slice 250: 107474 vertices, 107554 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... 107474 voxel in cpt #1: X=-80 [v=107474,e=322662,f=215108] located at (29.583546, -19.141281, 8.658625) For the whole surface: X=-80 [v=107474,e=322662,f=215108] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jun 15 00:45:11 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 Wed Jun 15 00:45:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 Wed Jun 15 00:45:23 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.0 mm, total surface area = 56039 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 54.357736 mris_inflate stimesec 0.107983 mris_inflate ru_maxrss 138116 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 18588 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 95 mris_inflate ru_nivcsw 81 #-------------------------------------------- #@# Inflation1 rh Wed Jun 15 00:46:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.2 mm, total surface area = 56577 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.060 (target=0.015) step 030: RMS=0.055 (target=0.015) step 035: RMS=0.052 (target=0.015) step 040: RMS=0.048 (target=0.015) step 045: RMS=0.046 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.045 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 41.989616 mris_inflate stimesec 0.061990 mris_inflate ru_maxrss 139292 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 18374 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 30 mris_inflate ru_nivcsw 167 #-------------------------------------------- #@# QSphere lh Wed Jun 15 00:47:00 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 1.12 +- 0.61 (0.00-->6.42) (max @ vno 46156 --> 47074) face area 0.04 +- 0.05 (-0.11-->0.96) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.389... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.445, avgs=0 005/300: dt: 0.9000, rms radial error=174.188, avgs=0 010/300: dt: 0.9000, rms radial error=173.636, avgs=0 015/300: dt: 0.9000, rms radial error=172.912, avgs=0 020/300: dt: 0.9000, rms radial error=172.087, avgs=0 025/300: dt: 0.9000, rms radial error=171.203, avgs=0 030/300: dt: 0.9000, rms radial error=170.287, avgs=0 035/300: dt: 0.9000, rms radial error=169.353, avgs=0 040/300: dt: 0.9000, rms radial error=168.411, avgs=0 045/300: dt: 0.9000, rms radial error=167.466, avgs=0 050/300: dt: 0.9000, rms radial error=166.520, avgs=0 055/300: dt: 0.9000, rms radial error=165.576, avgs=0 060/300: dt: 0.9000, rms radial error=164.636, avgs=0 065/300: dt: 0.9000, rms radial error=163.703, avgs=0 070/300: dt: 0.9000, rms radial error=162.783, avgs=0 075/300: dt: 0.9000, rms radial error=161.868, avgs=0 080/300: dt: 0.9000, rms radial error=160.957, avgs=0 085/300: dt: 0.9000, rms radial error=160.050, avgs=0 090/300: dt: 0.9000, rms radial error=159.149, avgs=0 095/300: dt: 0.9000, rms radial error=158.252, avgs=0 100/300: dt: 0.9000, rms radial error=157.359, avgs=0 105/300: dt: 0.9000, rms radial error=156.472, avgs=0 110/300: dt: 0.9000, rms radial error=155.589, avgs=0 115/300: dt: 0.9000, rms radial error=154.711, avgs=0 120/300: dt: 0.9000, rms radial error=153.838, avgs=0 125/300: dt: 0.9000, rms radial error=152.970, avgs=0 130/300: dt: 0.9000, rms radial error=152.107, avgs=0 135/300: dt: 0.9000, rms radial error=151.249, avgs=0 140/300: dt: 0.9000, rms radial error=150.396, avgs=0 145/300: dt: 0.9000, rms radial error=149.547, avgs=0 150/300: dt: 0.9000, rms radial error=148.703, avgs=0 155/300: dt: 0.9000, rms radial error=147.863, avgs=0 160/300: dt: 0.9000, rms radial error=147.028, avgs=0 165/300: dt: 0.9000, rms radial error=146.197, avgs=0 170/300: dt: 0.9000, rms radial error=145.372, avgs=0 175/300: dt: 0.9000, rms radial error=144.551, avgs=0 180/300: dt: 0.9000, rms radial error=143.737, avgs=0 185/300: dt: 0.9000, rms radial error=142.927, avgs=0 190/300: dt: 0.9000, rms radial error=142.122, avgs=0 195/300: dt: 0.9000, rms radial error=141.321, avgs=0 200/300: dt: 0.9000, rms radial error=140.525, avgs=0 205/300: dt: 0.9000, rms radial error=139.733, avgs=0 210/300: dt: 0.9000, rms radial error=138.945, avgs=0 215/300: dt: 0.9000, rms radial error=138.162, avgs=0 220/300: dt: 0.9000, rms radial error=137.382, avgs=0 225/300: dt: 0.9000, rms radial error=136.608, avgs=0 230/300: dt: 0.9000, rms radial error=135.838, avgs=0 235/300: dt: 0.9000, rms radial error=135.071, avgs=0 240/300: dt: 0.9000, rms radial error=134.310, avgs=0 245/300: dt: 0.9000, rms radial error=133.552, avgs=0 250/300: dt: 0.9000, rms radial error=132.799, avgs=0 255/300: dt: 0.9000, rms radial error=132.050, avgs=0 260/300: dt: 0.9000, rms radial error=131.305, avgs=0 265/300: dt: 0.9000, rms radial error=130.564, avgs=0 270/300: dt: 0.9000, rms radial error=129.828, avgs=0 275/300: dt: 0.9000, rms radial error=129.095, avgs=0 280/300: dt: 0.9000, rms radial error=128.367, avgs=0 285/300: dt: 0.9000, rms radial error=127.643, avgs=0 290/300: dt: 0.9000, rms radial error=126.923, avgs=0 295/300: dt: 0.9000, rms radial error=126.207, avgs=0 300/300: dt: 0.9000, rms radial error=125.495, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11408.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 2 (K=40.0), pass 1, starting sse = 1601.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00062 epoch 3 (K=160.0), pass 1, starting sse = 125.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/12 = 0.01102 epoch 4 (K=640.0), pass 1, starting sse = 7.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/14 = 0.01120 final distance error %22.60 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 288.861086 mris_sphere stimesec 0.076988 mris_sphere ru_maxrss 138296 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 18638 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 80 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 100 mris_sphere ru_nivcsw 403 FSRUNTIME@ mris_sphere 0.0803 hours 1 threads #-------------------------------------------- #@# QSphere rh Wed Jun 15 00:51:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 1.12 +- 0.62 (0.00-->7.72) (max @ vno 51109 --> 52017) face area 0.04 +- 0.04 (-0.47-->0.89) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.385... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.673, avgs=0 005/300: dt: 0.9000, rms radial error=174.418, avgs=0 010/300: dt: 0.9000, rms radial error=173.870, avgs=0 015/300: dt: 0.9000, rms radial error=173.150, avgs=0 020/300: dt: 0.9000, rms radial error=172.329, avgs=0 025/300: dt: 0.9000, rms radial error=171.449, avgs=0 030/300: dt: 0.9000, rms radial error=170.536, avgs=0 035/300: dt: 0.9000, rms radial error=169.606, avgs=0 040/300: dt: 0.9000, rms radial error=168.669, avgs=0 045/300: dt: 0.9000, rms radial error=167.728, avgs=0 050/300: dt: 0.9000, rms radial error=166.787, avgs=0 055/300: dt: 0.9000, rms radial error=165.847, avgs=0 060/300: dt: 0.9000, rms radial error=164.910, avgs=0 065/300: dt: 0.9000, rms radial error=163.977, avgs=0 070/300: dt: 0.9000, rms radial error=163.049, avgs=0 075/300: dt: 0.9000, rms radial error=162.134, avgs=0 080/300: dt: 0.9000, rms radial error=161.224, avgs=0 085/300: dt: 0.9000, rms radial error=160.318, avgs=0 090/300: dt: 0.9000, rms radial error=159.418, avgs=0 095/300: dt: 0.9000, rms radial error=158.522, avgs=0 100/300: dt: 0.9000, rms radial error=157.630, avgs=0 105/300: dt: 0.9000, rms radial error=156.743, avgs=0 110/300: dt: 0.9000, rms radial error=155.861, avgs=0 115/300: dt: 0.9000, rms radial error=154.984, avgs=0 120/300: dt: 0.9000, rms radial error=154.111, avgs=0 125/300: dt: 0.9000, rms radial error=153.242, avgs=0 130/300: dt: 0.9000, rms radial error=152.379, avgs=0 135/300: dt: 0.9000, rms radial error=151.519, avgs=0 140/300: dt: 0.9000, rms radial error=150.664, avgs=0 145/300: dt: 0.9000, rms radial error=149.814, avgs=0 150/300: dt: 0.9000, rms radial error=148.969, avgs=0 155/300: dt: 0.9000, rms radial error=148.128, avgs=0 160/300: dt: 0.9000, rms radial error=147.292, avgs=0 165/300: dt: 0.9000, rms radial error=146.461, avgs=0 170/300: dt: 0.9000, rms radial error=145.634, avgs=0 175/300: dt: 0.9000, rms radial error=144.812, avgs=0 180/300: dt: 0.9000, rms radial error=143.995, avgs=0 185/300: dt: 0.9000, rms radial error=143.182, avgs=0 190/300: dt: 0.9000, rms radial error=142.374, avgs=0 195/300: dt: 0.9000, rms radial error=141.570, avgs=0 200/300: dt: 0.9000, rms radial error=140.771, avgs=0 205/300: dt: 0.9000, rms radial error=139.976, avgs=0 210/300: dt: 0.9000, rms radial error=139.185, avgs=0 215/300: dt: 0.9000, rms radial error=138.399, avgs=0 220/300: dt: 0.9000, rms radial error=137.618, avgs=0 225/300: dt: 0.9000, rms radial error=136.841, avgs=0 230/300: dt: 0.9000, rms radial error=136.068, avgs=0 235/300: dt: 0.9000, rms radial error=135.300, avgs=0 240/300: dt: 0.9000, rms radial error=134.537, avgs=0 245/300: dt: 0.9000, rms radial error=133.777, avgs=0 250/300: dt: 0.9000, rms radial error=133.022, avgs=0 255/300: dt: 0.9000, rms radial error=132.271, avgs=0 260/300: dt: 0.9000, rms radial error=131.524, avgs=0 265/300: dt: 0.9000, rms radial error=130.782, avgs=0 270/300: dt: 0.9000, rms radial error=130.043, avgs=0 275/300: dt: 0.9000, rms radial error=129.309, avgs=0 280/300: dt: 0.9000, rms radial error=128.578, avgs=0 285/300: dt: 0.9000, rms radial error=127.852, avgs=0 290/300: dt: 0.9000, rms radial error=127.130, avgs=0 295/300: dt: 0.9000, rms radial error=126.412, avgs=0 300/300: dt: 0.9000, rms radial error=125.698, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11543.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 1649.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00057 epoch 3 (K=160.0), pass 1, starting sse = 147.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00647 epoch 4 (K=640.0), pass 1, starting sse = 13.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00664 final distance error %23.74 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 298.279654 mris_sphere stimesec 0.061990 mris_sphere ru_maxrss 139480 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 18417 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 31 mris_sphere ru_nivcsw 1852 FSRUNTIME@ mris_sphere 0.0829 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Wed Jun 15 00:56:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Jun 15 00:56:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Jun 15 00:56:48 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD18 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=-32 (nv=106594, nf=213252, ne=319878, g=17) 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... 2980 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 27 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.5114 (-4.2557) -vertex loglikelihood: -5.9068 (-2.9534) -normal dot loglikelihood: -3.6023 (-3.6023) -quad curv loglikelihood: -6.5929 (-3.2965) Total Loglikelihood : -24.6135 CORRECTING DEFECT 0 (vertices=706, convex hull=202) After retessellation of defect 0, euler #=-24 (104918,314223,209281) : difference with theory (-24) = 0 CORRECTING DEFECT 1 (vertices=45, convex hull=78) After retessellation of defect 1, euler #=-23 (104927,314280,209330) : difference with theory (-23) = 0 CORRECTING DEFECT 2 (vertices=28, convex hull=55) After retessellation of defect 2, euler #=-22 (104938,314333,209373) : difference with theory (-22) = 0 CORRECTING DEFECT 3 (vertices=56, convex hull=87) After retessellation of defect 3, euler #=-21 (104969,314460,209470) : difference with theory (-21) = 0 CORRECTING DEFECT 4 (vertices=89, convex hull=110) After retessellation of defect 4, euler #=-20 (104998,314592,209574) : difference with theory (-20) = 0 CORRECTING DEFECT 5 (vertices=48, convex hull=87) After retessellation of defect 5, euler #=-19 (105009,314662,209634) : difference with theory (-19) = 0 CORRECTING DEFECT 6 (vertices=11, convex hull=23) After retessellation of defect 6, euler #=-18 (105011,314675,209646) : difference with theory (-18) = 0 CORRECTING DEFECT 7 (vertices=29, convex hull=25) After retessellation of defect 7, euler #=-17 (105015,314694,209662) : difference with theory (-17) = 0 CORRECTING DEFECT 8 (vertices=5, convex hull=13) After retessellation of defect 8, euler #=-16 (105016,314700,209668) : difference with theory (-16) = 0 CORRECTING DEFECT 9 (vertices=7, convex hull=21) After retessellation of defect 9, euler #=-15 (105018,314712,209679) : difference with theory (-15) = 0 CORRECTING DEFECT 10 (vertices=10, convex hull=21) After retessellation of defect 10, euler #=-14 (105020,314723,209689) : difference with theory (-14) = 0 CORRECTING DEFECT 11 (vertices=31, convex hull=19) After retessellation of defect 11, euler #=-13 (105023,314736,209700) : difference with theory (-13) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=26) After retessellation of defect 12, euler #=-12 (105029,314760,209719) : difference with theory (-12) = 0 CORRECTING DEFECT 13 (vertices=88, convex hull=98) After retessellation of defect 13, euler #=-11 (105067,314917,209839) : difference with theory (-11) = 0 CORRECTING DEFECT 14 (vertices=20, convex hull=68) After retessellation of defect 14, euler #=-10 (105076,314967,209881) : difference with theory (-10) = 0 CORRECTING DEFECT 15 (vertices=31, convex hull=61) After retessellation of defect 15, euler #=-9 (105094,315047,209944) : difference with theory (-9) = 0 CORRECTING DEFECT 16 (vertices=45, convex hull=26) After retessellation of defect 16, euler #=-8 (105102,315080,209970) : difference with theory (-8) = 0 CORRECTING DEFECT 17 (vertices=10, convex hull=24) After retessellation of defect 17, euler #=-7 (105104,315093,209982) : difference with theory (-7) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=29) After retessellation of defect 18, euler #=-6 (105107,315110,209997) : difference with theory (-6) = 0 CORRECTING DEFECT 19 (vertices=38, convex hull=86) After retessellation of defect 19, euler #=-5 (105126,315202,210071) : difference with theory (-5) = 0 CORRECTING DEFECT 20 (vertices=45, convex hull=51) After retessellation of defect 20, euler #=-4 (105143,315272,210125) : difference with theory (-4) = 0 CORRECTING DEFECT 21 (vertices=42, convex hull=26) After retessellation of defect 21, euler #=-3 (105152,315308,210153) : difference with theory (-3) = 0 CORRECTING DEFECT 22 (vertices=125, convex hull=130) After retessellation of defect 22, euler #=-2 (105177,315444,210265) : difference with theory (-2) = 0 CORRECTING DEFECT 23 (vertices=132, convex hull=62) After retessellation of defect 23, euler #=-1 (105187,315502,210314) : difference with theory (-1) = 0 CORRECTING DEFECT 24 (vertices=29, convex hull=64) After retessellation of defect 24, euler #=0 (105201,315568,210367) : difference with theory (0) = 0 CORRECTING DEFECT 25 (vertices=49, convex hull=31) After retessellation of defect 25, euler #=1 (105210,315607,210398) : difference with theory (1) = 0 CORRECTING DEFECT 26 (vertices=17, convex hull=51) After retessellation of defect 26, euler #=2 (105219,315651,210434) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->6.78) (max @ vno 24819 --> 24861) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->6.78) (max @ vno 24819 --> 24861) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 116 mutations (37.3%), 195 crossovers (62.7%), 141 vertices were eliminated building final representation... 1375 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=105219, nf=210434, ne=315651, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 20.4 minutes 0 defective edges removing intersecting faces 000: 141 intersecting 001: 7 intersecting mris_fix_topology utimesec 1222.701121 mris_fix_topology stimesec 0.317951 mris_fix_topology ru_maxrss 338576 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 52942 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 135 mris_fix_topology ru_nivcsw 2224 FSRUNTIME@ mris_fix_topology lh 0.3398 hours 1 threads #@# Fix Topology rh Wed Jun 15 01:17:12 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD18 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=-80 (nv=107474, nf=215108, ne=322662, g=41) 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 12 iterations marking ambiguous vertices... 6944 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 0 -merging segment 14 into 17 42 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6850 (-4.3425) -vertex loglikelihood: -5.9484 (-2.9742) -normal dot loglikelihood: -3.6616 (-3.6616) -quad curv loglikelihood: -6.5496 (-3.2748) Total Loglikelihood : -24.8446 CORRECTING DEFECT 0 (vertices=1962, convex hull=356) XL defect detected... After retessellation of defect 0, euler #=-37 (103430,309175,205708) : difference with theory (-39) = -2 CORRECTING DEFECT 1 (vertices=5, convex hull=21) After retessellation of defect 1, euler #=-36 (103431,309184,205717) : difference with theory (-38) = -2 CORRECTING DEFECT 2 (vertices=11, convex hull=33) After retessellation of defect 2, euler #=-35 (103432,309198,205731) : difference with theory (-37) = -2 CORRECTING DEFECT 3 (vertices=6, convex hull=21) After retessellation of defect 3, euler #=-34 (103432,309204,205738) : difference with theory (-36) = -2 CORRECTING DEFECT 4 (vertices=6, convex hull=32) After retessellation of defect 4, euler #=-33 (103434,309219,205752) : difference with theory (-35) = -2 CORRECTING DEFECT 5 (vertices=43, convex hull=65) After retessellation of defect 5, euler #=-32 (103454,309306,205820) : difference with theory (-34) = -2 CORRECTING DEFECT 6 (vertices=136, convex hull=131) After retessellation of defect 6, euler #=-31 (103528,309589,206030) : difference with theory (-33) = -2 CORRECTING DEFECT 7 (vertices=54, convex hull=76) After retessellation of defect 7, euler #=-30 (103551,309691,206110) : difference with theory (-32) = -2 CORRECTING DEFECT 8 (vertices=10, convex hull=29) After retessellation of defect 8, euler #=-29 (103552,309704,206123) : difference with theory (-31) = -2 CORRECTING DEFECT 9 (vertices=19, convex hull=54) After retessellation of defect 9, euler #=-28 (103565,309764,206171) : difference with theory (-30) = -2 CORRECTING DEFECT 10 (vertices=47, convex hull=74) After retessellation of defect 10, euler #=-27 (103574,309822,206221) : difference with theory (-29) = -2 CORRECTING DEFECT 11 (vertices=8, convex hull=21) After retessellation of defect 11, euler #=-26 (103576,309839,206237) : difference with theory (-28) = -2 CORRECTING DEFECT 12 (vertices=49, convex hull=75) After retessellation of defect 12, euler #=-25 (103604,309952,206323) : difference with theory (-27) = -2 CORRECTING DEFECT 13 (vertices=39, convex hull=58) After retessellation of defect 13, euler #=-24 (103614,310004,206366) : difference with theory (-26) = -2 CORRECTING DEFECT 14 (vertices=60, convex hull=75) After retessellation of defect 14, euler #=-23 (103639,310113,206451) : difference with theory (-25) = -2 CORRECTING DEFECT 15 (vertices=119, convex hull=195) After retessellation of defect 15, euler #=-21 (103648,310233,206564) : difference with theory (-24) = -3 CORRECTING DEFECT 16 (vertices=21, convex hull=48) After retessellation of defect 16, euler #=-20 (103659,310284,206605) : difference with theory (-23) = -3 CORRECTING DEFECT 17 (vertices=41, convex hull=68) After retessellation of defect 17, euler #=-19 (103677,310365,206669) : difference with theory (-22) = -3 CORRECTING DEFECT 18 (vertices=6, convex hull=18) After retessellation of defect 18, euler #=-18 (103678,310373,206677) : difference with theory (-21) = -3 CORRECTING DEFECT 19 (vertices=17, convex hull=61) After retessellation of defect 19, euler #=-17 (103687,310421,206717) : difference with theory (-20) = -3 CORRECTING DEFECT 20 (vertices=33, convex hull=60) After retessellation of defect 20, euler #=-16 (103703,310495,206776) : difference with theory (-19) = -3 CORRECTING DEFECT 21 (vertices=181, convex hull=164) After retessellation of defect 21, euler #=-15 (103757,310734,206962) : difference with theory (-18) = -3 CORRECTING DEFECT 22 (vertices=6, convex hull=15) After retessellation of defect 22, euler #=-14 (103758,310742,206970) : difference with theory (-17) = -3 CORRECTING DEFECT 23 (vertices=299, convex hull=201) After retessellation of defect 23, euler #=-15 (103817,311032,207200) : difference with theory (-16) = -1 CORRECTING DEFECT 24 (vertices=23, convex hull=51) After retessellation of defect 24, euler #=-14 (103829,311085,207242) : difference with theory (-15) = -1 CORRECTING DEFECT 25 (vertices=87, convex hull=94) After retessellation of defect 25, euler #=-13 (103845,311175,207317) : difference with theory (-14) = -1 CORRECTING DEFECT 26 (vertices=79, convex hull=57) After retessellation of defect 26, euler #=-12 (103854,311226,207360) : difference with theory (-13) = -1 CORRECTING DEFECT 27 (vertices=47, convex hull=59) After retessellation of defect 27, euler #=-11 (103882,311333,207440) : difference with theory (-12) = -1 CORRECTING DEFECT 28 (vertices=17, convex hull=40) After retessellation of defect 28, euler #=-10 (103891,311375,207474) : difference with theory (-11) = -1 CORRECTING DEFECT 29 (vertices=72, convex hull=110) After retessellation of defect 29, euler #=-9 (103931,311542,207602) : difference with theory (-10) = -1 CORRECTING DEFECT 30 (vertices=164, convex hull=76) After retessellation of defect 30, euler #=-9 (103964,311678,207705) : difference with theory (-9) = 0 CORRECTING DEFECT 31 (vertices=19, convex hull=25) After retessellation of defect 31, euler #=-8 (103966,311693,207719) : difference with theory (-8) = 0 CORRECTING DEFECT 32 (vertices=89, convex hull=62) After retessellation of defect 32, euler #=-7 (103982,311769,207780) : difference with theory (-7) = 0 CORRECTING DEFECT 33 (vertices=9, convex hull=16) After retessellation of defect 33, euler #=-6 (103982,311774,207786) : difference with theory (-6) = 0 CORRECTING DEFECT 34 (vertices=6, convex hull=32) After retessellation of defect 34, euler #=-5 (103983,311785,207797) : difference with theory (-5) = 0 CORRECTING DEFECT 35 (vertices=30, convex hull=60) After retessellation of defect 35, euler #=-4 (103992,311835,207839) : difference with theory (-4) = 0 CORRECTING DEFECT 36 (vertices=12, convex hull=14) After retessellation of defect 36, euler #=-3 (103993,311840,207844) : difference with theory (-3) = 0 CORRECTING DEFECT 37 (vertices=89, convex hull=115) After retessellation of defect 37, euler #=-2 (104028,311992,207962) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=29, convex hull=74) After retessellation of defect 38, euler #=-1 (104044,312069,208024) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=29, convex hull=52) After retessellation of defect 39, euler #=0 (104054,312119,208065) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=32, convex hull=80) After retessellation of defect 40, euler #=1 (104071,312197,208127) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=50, convex hull=26) After retessellation of defect 41, euler #=2 (104078,312228,208152) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.05-->7.34) (max @ vno 100023 --> 102243) 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 (0.05-->7.34) (max @ vno 100023 --> 102243) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 175 mutations (36.3%), 307 crossovers (63.7%), 846 vertices were eliminated building final representation... 3396 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=104078, nf=208152, ne=312228, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 33.0 minutes 0 defective edges removing intersecting faces 000: 294 intersecting 001: 11 intersecting mris_fix_topology utimesec 1978.587209 mris_fix_topology stimesec 0.367944 mris_fix_topology ru_maxrss 357292 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 49681 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 86 mris_fix_topology ru_nivcsw 2622 FSRUNTIME@ mris_fix_topology rh 0.5498 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 105219 - 315651 + 210434 = 2 --> 0 holes F =2V-4: 210434 = 210438-4 (0) 2E=3F: 631302 = 631302 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 104078 - 312228 + 208152 = 2 --> 0 holes F =2V-4: 208152 = 208156-4 (0) 2E=3F: 624456 = 624456 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 24 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 26 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jun 15 01:50:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD18 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/AD18/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... 11835 bright wm thresholded. 2057 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.orig... computing class statistics... border white: 208945 voxels (1.25%) border gray 222051 voxels (1.32%) WM (96.0): 97.0 +- 6.7 [70.0 --> 110.0] GM (79.0) : 76.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 105.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 53.3 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.32) (max @ vno 23793 --> 24861) face area 0.28 +- 0.12 (0.00-->2.10) mean absolute distance = 0.89 +- 1.10 3351 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=99+-4.3, GM=77+-7.0 mean inside = 92.9, mean outside = 80.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=85.2, 616 (616) missing vertices, mean dist 0.2 [1.0 (%37.0)->0.9 (%63.0))] %42 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.10-->3.31) (max @ vno 23793 --> 24861) face area 0.28 +- 0.13 (0.00-->1.94) mean absolute distance = 0.52 +- 0.94 4154 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1662803.4, rms=7.899 001: dt: 0.5000, sse=1023127.1, rms=5.564 (29.561%) 002: dt: 0.5000, sse=714122.6, rms=3.933 (29.314%) 003: dt: 0.5000, sse=578634.4, rms=2.919 (25.771%) 004: dt: 0.5000, sse=521568.5, rms=2.384 (18.340%) 005: dt: 0.5000, sse=500863.9, rms=2.143 (10.093%) 006: dt: 0.5000, sse=494375.0, rms=2.052 (4.251%) rms = 2.01, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=492909.2, rms=2.014 (1.876%) 008: dt: 0.2500, sse=456039.7, rms=1.391 (30.920%) 009: dt: 0.2500, sse=452280.7, rms=1.304 (6.263%) rms = 1.29, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=450668.9, rms=1.291 (0.986%) rms = 1.28, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=449849.4, rms=1.278 (1.015%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=86.5, 460 (390) missing vertices, mean dist -0.3 [0.7 (%55.2)->0.3 (%44.8))] %46 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->3.64) (max @ vno 92800 --> 105154) face area 0.35 +- 0.16 (0.00-->2.63) mean absolute distance = 0.48 +- 0.62 3604 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=724755.3, rms=3.227 012: dt: 0.5000, sse=622404.4, rms=2.115 (34.446%) 013: dt: 0.5000, sse=582155.9, rms=1.713 (19.004%) 014: dt: 0.5000, sse=575618.9, rms=1.610 (6.007%) rms = 1.59, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=576948.2, rms=1.587 (1.434%) 016: dt: 0.2500, sse=553907.6, rms=1.229 (22.564%) rms = 1.18, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=547017.7, rms=1.184 (3.692%) rms = 1.17, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=543476.2, rms=1.168 (1.300%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.7, 421 (334) missing vertices, mean dist -0.3 [0.6 (%62.9)->0.3 (%37.1))] %63 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->3.64) (max @ vno 74614 --> 73739) face area 0.34 +- 0.16 (0.00-->2.70) mean absolute distance = 0.38 +- 0.46 3003 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=724310.1, rms=3.329 019: dt: 0.5000, sse=602155.9, rms=1.874 (43.699%) 020: dt: 0.5000, sse=557044.3, rms=1.459 (22.148%) rms = 1.43, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=553199.9, rms=1.427 (2.222%) 022: dt: 0.2500, sse=551429.8, rms=1.131 (20.699%) rms = 1.10, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=533110.9, rms=1.098 (2.964%) rms = 1.09, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=535412.8, rms=1.090 (0.665%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.9, 387 (282) missing vertices, mean dist -0.1 [0.5 (%58.3)->0.3 (%41.7))] %74 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/AD18/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=582000.5, rms=2.021 025: dt: 0.5000, sse=548707.3, rms=1.098 (45.653%) rms = 1.23, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=514982.6, rms=0.958 (12.814%) rms = 0.92, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=534786.6, rms=0.918 (4.116%) rms = 0.90, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=528112.9, rms=0.900 (1.964%) positioning took 0.4 minutes generating cortex label... 12 non-cortical segments detected only using segment with 7552 vertices erasing segment 1 (vno[0] = 57109) erasing segment 2 (vno[0] = 71328) erasing segment 3 (vno[0] = 78995) erasing segment 4 (vno[0] = 80433) erasing segment 5 (vno[0] = 82011) erasing segment 6 (vno[0] = 82044) erasing segment 7 (vno[0] = 82080) erasing segment 8 (vno[0] = 83602) erasing segment 9 (vno[0] = 85137) erasing segment 10 (vno[0] = 89542) erasing segment 11 (vno[0] = 90569) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/lh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->3.79) (max @ vno 73739 --> 74614) face area 0.33 +- 0.16 (0.00-->2.52) refinement took 3.9 minutes #-------------------------------------------- #@# Make White Surf rh Wed Jun 15 01:54:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD18 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/AD18/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... 11835 bright wm thresholded. 2057 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.orig... computing class statistics... border white: 208945 voxels (1.25%) border gray 222051 voxels (1.32%) WM (96.0): 97.0 +- 6.7 [70.0 --> 110.0] GM (79.0) : 76.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.2 (was 70) setting MAX_BORDER_WHITE to 105.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 54.3 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.68) (max @ vno 102243 --> 103996) face area 0.28 +- 0.13 (0.00-->2.37) mean absolute distance = 0.88 +- 1.11 3402 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=99+-4.3, GM=78+-7.8 mean inside = 92.9, mean outside = 80.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=85.7, 455 (455) missing vertices, mean dist 0.1 [1.0 (%38.6)->0.8 (%61.4))] %36 local maxima, %57 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->4.07) (max @ vno 50435 --> 45593) face area 0.28 +- 0.13 (0.00-->2.15) mean absolute distance = 0.50 +- 0.92 4293 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1676869.1, rms=7.958 001: dt: 0.5000, sse=984563.9, rms=5.450 (31.516%) 002: dt: 0.5000, sse=680031.2, rms=3.766 (30.903%) 003: dt: 0.5000, sse=558259.6, rms=2.811 (25.338%) 004: dt: 0.5000, sse=514124.5, rms=2.355 (16.231%) 005: dt: 0.5000, sse=500515.8, rms=2.171 (7.819%) 006: dt: 0.5000, sse=502120.9, rms=2.104 (3.094%) rms = 2.08, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=498315.8, rms=2.076 (1.305%) 008: dt: 0.2500, sse=457411.5, rms=1.467 (29.357%) 009: dt: 0.2500, sse=451472.3, rms=1.383 (5.700%) rms = 1.37, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=451064.7, rms=1.368 (1.122%) rms = 1.35, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=450678.9, rms=1.354 (0.993%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=87.1, 334 (245) missing vertices, mean dist -0.3 [0.7 (%56.2)->0.3 (%43.8))] %43 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->4.30) (max @ vno 50435 --> 45593) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.44 +- 0.61 3151 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=699837.6, rms=3.124 012: dt: 0.5000, sse=596012.3, rms=2.064 (33.912%) 013: dt: 0.5000, sse=578516.8, rms=1.725 (16.429%) 014: dt: 0.5000, sse=564007.6, rms=1.648 (4.480%) rms = 1.64, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=559886.8, rms=1.644 (0.247%) 016: dt: 0.2500, sse=543303.1, rms=1.287 (21.727%) rms = 1.24, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=556231.2, rms=1.240 (3.659%) rms = 1.22, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=542537.2, rms=1.224 (1.255%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.0, 313 (225) missing vertices, mean dist -0.3 [0.6 (%62.0)->0.3 (%38.0))] %60 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.06-->4.41) (max @ vno 50435 --> 45593) face area 0.34 +- 0.16 (0.00-->3.39) mean absolute distance = 0.36 +- 0.46 2748 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=693877.4, rms=3.107 019: dt: 0.5000, sse=579080.8, rms=1.792 (42.329%) 020: dt: 0.5000, sse=552973.9, rms=1.477 (17.588%) rms = 1.47, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=544737.6, rms=1.472 (0.327%) 022: dt: 0.2500, sse=547172.4, rms=1.174 (20.244%) rms = 1.14, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=526636.1, rms=1.137 (3.144%) rms = 1.13, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=528403.9, rms=1.126 (0.982%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=90.2, 315 (220) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))] %71 local maxima, %22 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/AD18/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=568531.9, rms=1.942 025: dt: 0.5000, sse=517765.2, rms=1.117 (42.463%) rms = 1.27, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=510402.1, rms=0.978 (12.476%) rms = 0.94, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=516020.3, rms=0.943 (3.544%) rms = 0.93, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=519346.0, rms=0.927 (1.732%) positioning took 0.4 minutes generating cortex label... 10 non-cortical segments detected only using segment with 8021 vertices erasing segment 1 (vno[0] = 60247) erasing segment 2 (vno[0] = 69579) erasing segment 3 (vno[0] = 77087) erasing segment 4 (vno[0] = 77603) erasing segment 5 (vno[0] = 78323) erasing segment 6 (vno[0] = 79402) erasing segment 7 (vno[0] = 79913) erasing segment 8 (vno[0] = 79934) erasing segment 9 (vno[0] = 85327) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/rh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.area vertex spacing 0.89 +- 0.26 (0.04-->4.48) (max @ vno 45593 --> 50435) face area 0.33 +- 0.16 (0.00-->3.49) refinement took 3.7 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jun 15 01:57:59 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 01:58:05 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 01:58:10 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.1 mm, total surface area = 63098 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 45.842030 mris_inflate stimesec 0.058991 mris_inflate ru_maxrss 136404 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 18792 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 39 mris_inflate ru_nivcsw 67 #-------------------------------------------- #@# Inflation2 rh Wed Jun 15 01:58:56 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.2 mm, total surface area = 62600 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 49.099535 mris_inflate stimesec 0.072988 mris_inflate ru_maxrss 135012 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 17928 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 64 #-------------------------------------------- #@# Curv .H and .K lh Wed Jun 15 01:59:46 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf mris_curvature -w lh.white total integrated curvature = 7.906*4pi (99.355) --> -7 handles ICI = 148.7, FI = 1239.0, variation=20529.365 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 127 vertices thresholded to be in k1 ~ [-2.78 0.61], k2 ~ [-0.11 0.48] total integrated curvature = 0.520*4pi (6.536) --> 0 handles ICI = 1.3, FI = 7.5, variation=132.026 79 vertices thresholded to be in [-0.18 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 89 vertices thresholded to be in [-0.83 0.30] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.029 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Jun 15 02:00:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf mris_curvature -w rh.white total integrated curvature = 7.308*4pi (91.840) --> -6 handles ICI = 153.3, FI = 1254.0, variation=20905.990 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 101 vertices thresholded to be in k1 ~ [-2.62 0.62], k2 ~ [-0.20 0.15] total integrated curvature = 0.458*4pi (5.750) --> 1 handles ICI = 1.3, FI = 8.0, variation=138.713 102 vertices thresholded to be in [-0.04 0.11] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 86 vertices thresholded to be in [-0.88 0.27] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.019, std = 0.031 done. #----------------------------------------- #@# Curvature Stats lh Wed Jun 15 02:02:09 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm AD18 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 [ AD18/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 [ 198 ] Gb_filter = 0 WARN: S lookup min: -0.300559 WARN: S explicit min: 0.000000 vertex = 234 #----------------------------------------- #@# Curvature Stats rh Wed Jun 15 02:02:13 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm AD18 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 [ AD18/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 [ 207 ] Gb_filter = 0 WARN: S lookup min: -0.206308 WARN: S explicit min: 0.000000 vertex = 191 #-------------------------------------------- #@# Sphere lh Wed Jun 15 02:02:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 0.364... 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 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.70 pass 1: epoch 2 of 3 starting distance error %18.71 unfolding complete - removing small folds... starting distance error %18.67 removing remaining folds... final distance error %18.70 MRISunfold() return, current seed 1234 -01: dt=0.0000, 81 negative triangles 191: dt=0.9900, 81 negative triangles 192: dt=0.9900, 22 negative triangles 193: dt=0.9900, 5 negative triangles 194: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.80 hours mris_sphere utimesec 2879.685221 mris_sphere stimesec 0.542917 mris_sphere ru_maxrss 186768 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 31739 mris_sphere ru_majflt 13 mris_sphere ru_nswap 0 mris_sphere ru_inblock 824 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 57 mris_sphere ru_nivcsw 5647 FSRUNTIME@ mris_sphere 0.8003 hours 1 threads #-------------------------------------------- #@# Sphere rh Wed Jun 15 02:50:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 0.366... 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 %18.98 pass 1: epoch 2 of 3 starting distance error %19.00 unfolding complete - removing small folds... starting distance error %18.95 removing remaining folds... final distance error %18.97 MRISunfold() return, current seed 1234 -01: dt=0.0000, 114 negative triangles 239: dt=0.9900, 114 negative triangles 240: dt=0.9900, 54 negative triangles 241: dt=0.9900, 41 negative triangles 242: dt=0.9900, 30 negative triangles 243: dt=0.9900, 26 negative triangles 244: dt=0.9900, 31 negative triangles 245: dt=0.9900, 24 negative triangles 246: dt=0.9900, 26 negative triangles 247: dt=0.9900, 28 negative triangles 248: dt=0.9900, 24 negative triangles 249: dt=0.9900, 30 negative triangles 250: dt=0.9900, 24 negative triangles 251: dt=0.9900, 20 negative triangles 252: dt=0.9900, 26 negative triangles 253: dt=0.9900, 22 negative triangles 254: dt=0.9900, 20 negative triangles 255: dt=0.9900, 18 negative triangles 256: dt=0.9900, 18 negative triangles 257: dt=0.9900, 15 negative triangles 258: dt=0.9900, 16 negative triangles 259: dt=0.9900, 13 negative triangles 260: dt=0.9900, 13 negative triangles 261: dt=0.9900, 13 negative triangles 262: dt=0.9900, 8 negative triangles 263: dt=0.9900, 17 negative triangles 264: dt=0.9900, 11 negative triangles 265: dt=0.9900, 10 negative triangles 266: dt=0.9900, 9 negative triangles 267: dt=0.9900, 14 negative triangles 268: dt=0.9900, 11 negative triangles 269: dt=0.9900, 6 negative triangles 270: dt=0.9900, 13 negative triangles 271: dt=0.9900, 6 negative triangles 272: dt=0.9900, 3 negative triangles 273: dt=0.9900, 4 negative triangles 274: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.87 hours mris_sphere utimesec 3113.328702 mris_sphere stimesec 0.840872 mris_sphere ru_maxrss 184596 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 31179 mris_sphere ru_majflt 18 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1016 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 60 mris_sphere ru_nivcsw 14854 FSRUNTIME@ mris_sphere 0.8654 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Wed Jun 15 03:42:14 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 5.196 curvature mean = 0.033, std = 0.818 curvature mean = 0.018, std = 0.884 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 236649.4, tmin=1.1042 d=32.00 min @ (0.00, 0.00, 8.00) sse = 155827.5, tmin=2.2306 d=4.00 min @ (1.00, 0.00, -1.00) sse = 154722.5, tmin=5.6102 d=2.00 min @ (0.00, 0.50, 0.50) sse = 154192.6, tmin=6.7545 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 154127.2, tmin=7.9011 d=0.50 min @ (0.12, 0.00, -0.12) sse = 154104.0, tmin=9.0551 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 9.06 min curvature mean = 0.014, std = 0.853 curvature mean = 0.005, std = 0.958 curvature mean = 0.012, std = 0.866 curvature mean = 0.001, std = 0.984 curvature mean = 0.012, std = 0.869 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.030, std = 0.270 curvature mean = 0.039, std = 0.248 curvature mean = 0.054, std = 0.406 curvature mean = 0.036, std = 0.308 curvature mean = 0.028, std = 0.599 curvature mean = 0.035, std = 0.335 curvature mean = 0.014, std = 0.736 curvature mean = 0.034, std = 0.347 curvature mean = 0.005, std = 0.831 MRISregister() return, current seed 0 -01: dt=0.0000, 29 negative triangles 099: dt=0.9900, 29 negative triangles 100: dt=0.9405, 43 negative triangles expanding nbhd size to 1 101: dt=0.9900, 36 negative triangles 102: dt=0.9900, 34 negative triangles 103: dt=0.9900, 27 negative triangles 104: dt=0.9900, 28 negative triangles 105: dt=0.9900, 24 negative triangles 106: dt=0.9900, 24 negative triangles 107: dt=0.9900, 29 negative triangles 108: dt=0.9900, 21 negative triangles 109: dt=0.9900, 20 negative triangles 110: dt=0.9900, 19 negative triangles 111: dt=0.9900, 21 negative triangles 112: dt=0.9900, 16 negative triangles 113: dt=0.9900, 12 negative triangles 114: dt=0.9900, 12 negative triangles 115: dt=0.9900, 13 negative triangles 116: dt=0.9900, 10 negative triangles 117: dt=0.9900, 10 negative triangles 118: dt=0.9900, 9 negative triangles 119: dt=0.9900, 9 negative triangles 120: dt=0.9900, 5 negative triangles 121: dt=0.9900, 4 negative triangles 122: dt=0.9900, 4 negative triangles 123: dt=0.9900, 3 negative triangles 124: dt=0.9900, 2 negative triangles 125: dt=0.9900, 4 negative triangles 126: dt=0.9900, 1 negative triangles 127: dt=0.9900, 3 negative triangles 128: dt=0.9900, 1 negative triangles 129: dt=0.9900, 1 negative triangles 130: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.09 hours mris_register utimesec 3927.577917 mris_register stimesec 0.681896 mris_register ru_maxrss 185588 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 26724 mris_register ru_majflt 142 mris_register ru_nswap 0 mris_register ru_inblock 9384 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 279 mris_register ru_nivcsw 4876 FSRUNTIME@ mris_register 1.0916 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Wed Jun 15 04:47:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 5.126 curvature mean = 0.035, std = 0.817 curvature mean = 0.019, std = 0.885 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 221291.2, tmin=1.1226 d=32.00 min @ (8.00, 8.00, 8.00) sse = 177103.1, tmin=2.2791 d=16.00 min @ (0.00, -4.00, -4.00) sse = 157415.7, tmin=3.4004 d=8.00 min @ (-2.00, 0.00, 2.00) sse = 151440.5, tmin=4.5475 d=4.00 min @ (1.00, 0.00, 0.00) sse = 149403.1, tmin=5.6537 d=2.00 min @ (0.00, 0.00, -0.50) sse = 149188.0, tmin=6.7989 d=1.00 min @ (0.00, 0.25, 0.25) sse = 149033.6, tmin=7.9781 d=0.50 min @ (0.00, 0.00, -0.12) sse = 149010.5, tmin=9.1626 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 9.16 min curvature mean = 0.016, std = 0.853 curvature mean = 0.006, std = 0.959 curvature mean = 0.014, std = 0.865 curvature mean = 0.002, std = 0.984 curvature mean = 0.013, std = 0.869 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.035, std = 0.298 curvature mean = 0.035, std = 0.246 curvature mean = 0.059, std = 0.378 curvature mean = 0.031, std = 0.307 curvature mean = 0.036, std = 0.549 curvature mean = 0.029, std = 0.335 curvature mean = 0.021, std = 0.679 curvature mean = 0.028, std = 0.347 curvature mean = 0.008, std = 0.779 MRISregister() return, current seed 0 -01: dt=0.0000, 36 negative triangles 101: dt=0.9900, 36 negative triangles expanding nbhd size to 1 102: dt=0.9900, 48 negative triangles 103: dt=0.9900, 32 negative triangles 104: dt=0.9900, 34 negative triangles 105: dt=0.9900, 34 negative triangles 106: dt=0.9900, 29 negative triangles 107: dt=0.9900, 29 negative triangles 108: dt=0.9900, 22 negative triangles 109: dt=0.9900, 22 negative triangles 110: dt=0.9900, 17 negative triangles 111: dt=0.9900, 18 negative triangles 112: dt=0.9900, 16 negative triangles 113: dt=0.9900, 14 negative triangles 114: dt=0.9900, 13 negative triangles 115: dt=0.9900, 9 negative triangles 116: dt=0.9900, 7 negative triangles 117: dt=0.9900, 8 negative triangles 118: dt=0.9900, 8 negative triangles 119: dt=0.9900, 3 negative triangles 120: dt=0.9900, 5 negative triangles 121: dt=0.9900, 2 negative triangles 122: dt=0.9900, 4 negative triangles 123: dt=0.9900, 1 negative triangles 124: dt=0.9900, 2 negative triangles 125: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.11 hours mris_register utimesec 4000.407845 mris_register stimesec 0.967852 mris_register ru_maxrss 185660 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 25536 mris_register ru_majflt 16 mris_register ru_nswap 0 mris_register ru_inblock 1056 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 133 mris_register ru_nivcsw 5855 FSRUNTIME@ mris_register 1.1118 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Wed Jun 15 05:54:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 05:54:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 05:54:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 05:54:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 05:54:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 676 labels changed using aseg relabeling using gibbs priors... 000: 2370 changed, 105219 examined... 001: 525 changed, 10373 examined... 002: 101 changed, 3036 examined... 003: 32 changed, 587 examined... 004: 8 changed, 191 examined... 005: 6 changed, 47 examined... 006: 1 changed, 28 examined... 007: 0 changed, 7 examined... 178 labels changed using aseg 000: 74 total segments, 32 labels (69 vertices) changed 001: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1376 vertices marked for relabeling... 1376 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Wed Jun 15 05:54:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 990 labels changed using aseg relabeling using gibbs priors... 000: 2213 changed, 104078 examined... 001: 514 changed, 9575 examined... 002: 119 changed, 2914 examined... 003: 26 changed, 743 examined... 004: 14 changed, 172 examined... 005: 5 changed, 101 examined... 006: 3 changed, 36 examined... 007: 1 changed, 20 examined... 008: 0 changed, 7 examined... 217 labels changed using aseg 000: 74 total segments, 25 labels (158 vertices) changed 001: 50 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1287 vertices marked for relabeling... 1287 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Jun 15 05:55:03 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD18 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/AD18/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... 11835 bright wm thresholded. 2057 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.orig... computing class statistics... border white: 208945 voxels (1.25%) border gray 222051 voxels (1.32%) WM (96.0): 97.0 +- 6.7 [70.0 --> 110.0] GM (79.0) : 76.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 105.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 53.3 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-4.3, GM=77+-7.0 mean inside = 92.9, mean outside = 80.5 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=62.5, 284 (284) missing vertices, mean dist 1.9 [2.0 (%0.1)->2.7 (%99.9))] %22 local maxima, %47 large gradients and %25 min vals, 121 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=16068523.0, rms=28.023 001: dt: 0.0500, sse=14742269.0, rms=26.803 (4.351%) 002: dt: 0.0500, sse=13819012.0, rms=25.920 (3.294%) 003: dt: 0.0500, sse=13094291.0, rms=25.206 (2.757%) 004: dt: 0.0500, sse=12488648.0, rms=24.592 (2.433%) 005: dt: 0.0500, sse=11961422.0, rms=24.046 (2.223%) 006: dt: 0.0500, sse=11489574.0, rms=23.546 (2.080%) 007: dt: 0.0500, sse=11058410.0, rms=23.079 (1.981%) 008: dt: 0.0500, sse=10658444.0, rms=22.638 (1.913%) 009: dt: 0.0500, sse=10282753.0, rms=22.215 (1.867%) 010: dt: 0.0500, sse=9927152.0, rms=21.807 (1.835%) positioning took 0.8 minutes mean border=62.3, 140 (109) missing vertices, mean dist 1.5 [1.1 (%0.1)->2.1 (%99.9))] %23 local maxima, %47 large gradients and %25 min vals, 119 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=10613163.0, rms=22.569 011: dt: 0.0500, sse=10272120.0, rms=22.185 (1.701%) 012: dt: 0.0500, sse=9946158.0, rms=21.812 (1.683%) 013: dt: 0.0500, sse=9633441.0, rms=21.448 (1.670%) 014: dt: 0.0500, sse=9333176.0, rms=21.092 (1.659%) 015: dt: 0.0500, sse=9044251.0, rms=20.744 (1.651%) 016: dt: 0.0500, sse=8766118.0, rms=20.403 (1.643%) 017: dt: 0.0500, sse=8498100.0, rms=20.069 (1.637%) 018: dt: 0.0500, sse=8240717.0, rms=19.743 (1.625%) 019: dt: 0.0500, sse=7992999.5, rms=19.424 (1.616%) 020: dt: 0.0500, sse=7754619.5, rms=19.112 (1.607%) positioning took 0.8 minutes mean border=62.1, 124 (77) missing vertices, mean dist 1.3 [0.2 (%1.1)->1.8 (%98.9))] %23 local maxima, %47 large gradients and %24 min vals, 123 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=7878053.5, rms=19.274 021: dt: 0.0500, sse=7639707.0, rms=18.960 (1.632%) 022: dt: 0.0500, sse=7410725.5, rms=18.653 (1.620%) 023: dt: 0.0500, sse=7188512.5, rms=18.350 (1.625%) 024: dt: 0.0500, sse=6975869.0, rms=18.055 (1.607%) 025: dt: 0.0500, sse=6772194.5, rms=17.768 (1.590%) 026: dt: 0.0500, sse=6577075.0, rms=17.488 (1.573%) 027: dt: 0.0500, sse=6388699.5, rms=17.214 (1.568%) 028: dt: 0.0500, sse=6204298.0, rms=16.941 (1.585%) 029: dt: 0.0500, sse=6024293.0, rms=16.671 (1.597%) 030: dt: 0.0500, sse=5848701.5, rms=16.402 (1.610%) positioning took 0.8 minutes mean border=62.0, 161 (64) missing vertices, mean dist 1.1 [0.1 (%10.9)->1.6 (%89.1))] %23 local maxima, %47 large gradients and %24 min vals, 112 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=5929310.0, rms=16.522 031: dt: 0.5000, sse=4654338.0, rms=14.444 (12.574%) 032: dt: 0.5000, sse=3664922.0, rms=12.592 (12.824%) 033: dt: 0.5000, sse=2870373.2, rms=10.884 (13.568%) 034: dt: 0.5000, sse=2280388.8, rms=9.408 (13.558%) 035: dt: 0.5000, sse=1858341.5, rms=8.195 (12.891%) 036: dt: 0.5000, sse=1578237.8, rms=7.272 (11.270%) 037: dt: 0.5000, sse=1375339.5, rms=6.527 (10.238%) 038: dt: 0.5000, sse=1245645.2, rms=5.995 (8.161%) 039: dt: 0.5000, sse=1151548.0, rms=5.584 (6.855%) 040: dt: 0.5000, sse=1093047.2, rms=5.303 (5.026%) 041: dt: 0.5000, sse=1048686.5, rms=5.088 (4.045%) 042: dt: 0.5000, sse=1024978.2, rms=4.961 (2.504%) 043: dt: 0.5000, sse=1004519.5, rms=4.858 (2.081%) 044: dt: 0.5000, sse=993921.4, rms=4.797 (1.262%) 045: dt: 0.5000, sse=981783.4, rms=4.735 (1.275%) rms = 4.70, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=977009.7, rms=4.704 (0.668%) 047: dt: 0.2500, sse=874906.7, rms=4.056 (13.777%) 048: dt: 0.2500, sse=849494.6, rms=3.889 (4.100%) rms = 3.88, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=847958.6, rms=3.876 (0.358%) 050: dt: 0.1250, sse=837111.8, rms=3.798 (2.003%) rms = 3.79, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=835982.6, rms=3.790 (0.208%) positioning took 1.8 minutes mean border=60.7, 1245 (16) missing vertices, mean dist 0.2 [0.2 (%45.2)->0.5 (%54.8))] %37 local maxima, %36 large gradients and %21 min vals, 115 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=1049503.4, rms=4.405 052: dt: 0.5000, sse=952196.6, rms=3.823 (13.228%) rms = 3.79, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=941919.4, rms=3.790 (0.864%) 054: dt: 0.2500, sse=833368.5, rms=2.891 (23.711%) 055: dt: 0.2500, sse=809465.4, rms=2.668 (7.720%) 056: dt: 0.2500, sse=802493.6, rms=2.599 (2.590%) rms = 2.56, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=798744.9, rms=2.564 (1.344%) 058: dt: 0.1250, sse=787600.0, rms=2.440 (4.826%) rms = 2.42, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=785669.6, rms=2.421 (0.782%) positioning took 0.7 minutes mean border=60.0, 1406 (11) missing vertices, mean dist 0.1 [0.1 (%51.7)->0.4 (%48.3))] %46 local maxima, %27 large gradients and %20 min vals, 116 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=826431.1, rms=2.865 rms = 3.10, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=796173.9, rms=2.581 (9.902%) 061: dt: 0.2500, sse=783097.6, rms=2.458 (4.782%) rms = 2.41, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=777700.9, rms=2.411 (1.891%) 063: dt: 0.1250, sse=771863.9, rms=2.343 (2.837%) rms = 2.33, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=770001.9, rms=2.326 (0.719%) positioning took 0.5 minutes mean border=59.4, 2306 (8) missing vertices, mean dist 0.1 [0.1 (%51.4)->0.3 (%48.6))] %51 local maxima, %22 large gradients and %19 min vals, 118 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/AD18/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=789804.7, rms=2.511 rms = 2.79, time step reduction 1 of 3 to 0.250... 065: dt: 0.2500, sse=774653.1, rms=2.350 (6.407%) 066: dt: 0.2500, sse=767186.6, rms=2.281 (2.961%) rms = 2.25, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=763853.6, rms=2.255 (1.145%) 068: dt: 0.1250, sse=758972.0, rms=2.195 (2.645%) rms = 2.18, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=757234.9, rms=2.179 (0.730%) positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.area.pial vertex spacing 0.99 +- 0.41 (0.02-->6.87) (max @ vno 48803 --> 49777) face area 0.39 +- 0.29 (0.00-->5.79) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 105219 vertices processed 25000 of 105219 vertices processed 50000 of 105219 vertices processed 75000 of 105219 vertices processed 100000 of 105219 vertices processed 0 of 105219 vertices processed 25000 of 105219 vertices processed 50000 of 105219 vertices processed 75000 of 105219 vertices processed 100000 of 105219 vertices processed thickness calculation complete, 210:685 truncations. 26877 vertices at 0 distance 74676 vertices at 1 distance 61332 vertices at 2 distance 24246 vertices at 3 distance 8010 vertices at 4 distance 2408 vertices at 5 distance 757 vertices at 6 distance 247 vertices at 7 distance 126 vertices at 8 distance 65 vertices at 9 distance 31 vertices at 10 distance 27 vertices at 11 distance 12 vertices at 12 distance 9 vertices at 13 distance 10 vertices at 14 distance 7 vertices at 15 distance 15 vertices at 16 distance 18 vertices at 17 distance 10 vertices at 18 distance 3 vertices at 19 distance 2 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.thickness positioning took 8.1 minutes #-------------------------------------------- #@# Make Pial Surf rh Wed Jun 15 06:03:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD18 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/AD18/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... 11835 bright wm thresholded. 2057 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.orig... computing class statistics... border white: 208945 voxels (1.25%) border gray 222051 voxels (1.32%) WM (96.0): 97.0 +- 6.7 [70.0 --> 110.0] GM (79.0) : 76.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.2 (was 70) setting MAX_BORDER_WHITE to 105.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 54.3 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99+-4.3, GM=78+-7.8 mean inside = 92.9, mean outside = 80.2 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 4 with 2 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=63.1, 305 (305) missing vertices, mean dist 2.0 [1.3 (%0.0)->2.6 (%100.0))] %25 local maxima, %48 large gradients and %21 min vals, 126 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=15556595.0, rms=27.794 001: dt: 0.0500, sse=14247272.0, rms=26.559 (4.442%) 002: dt: 0.0500, sse=13333427.0, rms=25.662 (3.377%) 003: dt: 0.0500, sse=12615166.0, rms=24.934 (2.836%) 004: dt: 0.0500, sse=12014470.0, rms=24.309 (2.508%) 005: dt: 0.0500, sse=11490569.0, rms=23.750 (2.300%) 006: dt: 0.0500, sse=11021266.0, rms=23.238 (2.157%) 007: dt: 0.0500, sse=10591377.0, rms=22.758 (2.063%) 008: dt: 0.0500, sse=10192650.0, rms=22.305 (1.994%) 009: dt: 0.0500, sse=9818515.0, rms=21.870 (1.948%) 010: dt: 0.0500, sse=9464355.0, rms=21.451 (1.918%) positioning took 0.8 minutes mean border=62.9, 163 (147) missing vertices, mean dist 1.6 [0.3 (%0.1)->2.0 (%99.9))] %26 local maxima, %48 large gradients and %20 min vals, 105 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=10168550.0, rms=22.262 011: dt: 0.0500, sse=9829853.0, rms=21.868 (1.766%) 012: dt: 0.0500, sse=9506561.0, rms=21.486 (1.747%) 013: dt: 0.0500, sse=9197218.0, rms=21.114 (1.732%) 014: dt: 0.0500, sse=8901110.0, rms=20.752 (1.717%) 015: dt: 0.0500, sse=8617341.0, rms=20.398 (1.703%) 016: dt: 0.0500, sse=8345692.0, rms=20.054 (1.688%) 017: dt: 0.0500, sse=8085409.0, rms=19.718 (1.673%) 018: dt: 0.0500, sse=7836784.0, rms=19.392 (1.653%) 019: dt: 0.0500, sse=7598489.5, rms=19.075 (1.639%) 020: dt: 0.0500, sse=7370161.0, rms=18.765 (1.623%) positioning took 0.8 minutes mean border=62.6, 153 (113) missing vertices, mean dist 1.3 [0.1 (%1.3)->1.7 (%98.7))] %26 local maxima, %48 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=7496029.5, rms=18.937 021: dt: 0.0500, sse=7266287.0, rms=18.623 (1.657%) 022: dt: 0.0500, sse=7047062.0, rms=18.318 (1.635%) 023: dt: 0.0500, sse=6834627.0, rms=18.018 (1.638%) 024: dt: 0.0500, sse=6633016.5, rms=17.729 (1.606%) 025: dt: 0.0500, sse=6441315.5, rms=17.449 (1.578%) 026: dt: 0.0500, sse=6258449.0, rms=17.178 (1.554%) 027: dt: 0.0500, sse=6082212.0, rms=16.912 (1.546%) 028: dt: 0.0500, sse=5909911.0, rms=16.649 (1.559%) 029: dt: 0.0500, sse=5741933.0, rms=16.387 (1.569%) 030: dt: 0.0500, sse=5578199.5, rms=16.129 (1.579%) positioning took 0.8 minutes mean border=62.5, 178 (98) missing vertices, mean dist 1.1 [0.1 (%12.9)->1.6 (%87.1))] %26 local maxima, %49 large gradients and %19 min vals, 101 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=5662552.0, rms=16.257 031: dt: 0.5000, sse=4479961.5, rms=14.271 (12.218%) 032: dt: 0.5000, sse=3580413.8, rms=12.544 (12.102%) 033: dt: 0.5000, sse=2874242.5, rms=11.006 (12.262%) 034: dt: 0.5000, sse=2346768.2, rms=9.689 (11.966%) 035: dt: 0.5000, sse=1960177.4, rms=8.601 (11.230%) 036: dt: 0.5000, sse=1681977.4, rms=7.715 (10.299%) 037: dt: 0.5000, sse=1477314.8, rms=6.997 (9.302%) 038: dt: 0.5000, sse=1339437.6, rms=6.460 (7.675%) 039: dt: 0.5000, sse=1239600.9, rms=6.050 (6.351%) 040: dt: 0.5000, sse=1173629.8, rms=5.752 (4.925%) 041: dt: 0.5000, sse=1120854.4, rms=5.512 (4.170%) 042: dt: 0.5000, sse=1084070.1, rms=5.329 (3.317%) 043: dt: 0.5000, sse=1052239.4, rms=5.175 (2.905%) 044: dt: 0.5000, sse=1030539.9, rms=5.058 (2.248%) 045: dt: 0.5000, sse=1010416.0, rms=4.958 (1.980%) 046: dt: 0.5000, sse=1000040.0, rms=4.897 (1.231%) 047: dt: 0.5000, sse=986994.4, rms=4.833 (1.307%) rms = 4.80, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=982539.1, rms=4.802 (0.638%) 049: dt: 0.2500, sse=873397.1, rms=4.118 (14.256%) 050: dt: 0.2500, sse=849613.4, rms=3.961 (3.810%) rms = 3.95, time step reduction 2 of 3 to 0.125... 051: dt: 0.2500, sse=848614.9, rms=3.950 (0.273%) 052: dt: 0.1250, sse=834907.9, rms=3.853 (2.462%) rms = 3.85, time step reduction 3 of 3 to 0.062... 053: dt: 0.1250, sse=834069.1, rms=3.846 (0.161%) positioning took 2.0 minutes mean border=61.0, 1197 (20) missing vertices, mean dist 0.2 [0.2 (%43.0)->0.5 (%57.0))] %42 local maxima, %35 large gradients and %16 min vals, 86 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=1102703.0, rms=4.742 054: dt: 0.5000, sse=993951.6, rms=4.127 (12.959%) 055: dt: 0.5000, sse=970875.5, rms=4.016 (2.691%) rms = 4.02, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=867353.6, rms=3.226 (19.677%) 057: dt: 0.2500, sse=829560.8, rms=2.884 (10.598%) 058: dt: 0.2500, sse=818385.5, rms=2.778 (3.692%) 059: dt: 0.2500, sse=811693.7, rms=2.718 (2.157%) rms = 2.69, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=808119.7, rms=2.687 (1.130%) 061: dt: 0.1250, sse=792386.7, rms=2.521 (6.166%) rms = 2.50, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=789829.8, rms=2.496 (1.001%) positioning took 0.8 minutes mean border=60.3, 1241 (6) missing vertices, mean dist 0.1 [0.2 (%49.1)->0.4 (%50.9))] %52 local maxima, %26 large gradients and %15 min vals, 76 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=836943.7, rms=2.972 rms = 3.23, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=802251.6, rms=2.652 (10.765%) 064: dt: 0.2500, sse=786847.3, rms=2.506 (5.517%) 065: dt: 0.2500, sse=780248.2, rms=2.448 (2.278%) rms = 2.42, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=777118.9, rms=2.423 (1.037%) 067: dt: 0.1250, sse=770778.2, rms=2.349 (3.068%) rms = 2.33, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=768924.6, rms=2.332 (0.711%) positioning took 0.5 minutes mean border=59.6, 2124 (4) missing vertices, mean dist 0.1 [0.2 (%49.7)->0.3 (%50.3))] %56 local maxima, %21 large gradients and %15 min vals, 104 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/AD18/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=787797.3, rms=2.510 rms = 2.82, time step reduction 1 of 3 to 0.250... 069: dt: 0.2500, sse=771828.4, rms=2.337 (6.900%) 070: dt: 0.2500, sse=764077.6, rms=2.264 (3.143%) rms = 2.23, time step reduction 2 of 3 to 0.125... 071: dt: 0.2500, sse=760793.3, rms=2.235 (1.278%) 072: dt: 0.1250, sse=755687.2, rms=2.171 (2.848%) rms = 2.15, time step reduction 3 of 3 to 0.062... 073: dt: 0.1250, sse=753751.8, rms=2.153 (0.808%) positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.area.pial vertex spacing 0.99 +- 0.41 (0.01-->7.03) (max @ vno 74651 --> 74618) face area 0.40 +- 0.30 (0.00-->6.80) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 104078 vertices processed 25000 of 104078 vertices processed 50000 of 104078 vertices processed 75000 of 104078 vertices processed 100000 of 104078 vertices processed 0 of 104078 vertices processed 25000 of 104078 vertices processed 50000 of 104078 vertices processed 75000 of 104078 vertices processed 100000 of 104078 vertices processed thickness calculation complete, 245:893 truncations. 29076 vertices at 0 distance 69958 vertices at 1 distance 58323 vertices at 2 distance 25389 vertices at 3 distance 8533 vertices at 4 distance 2751 vertices at 5 distance 891 vertices at 6 distance 336 vertices at 7 distance 117 vertices at 8 distance 70 vertices at 9 distance 56 vertices at 10 distance 23 vertices at 11 distance 33 vertices at 12 distance 21 vertices at 13 distance 19 vertices at 14 distance 14 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 5 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/AD18/surf/rh.thickness positioning took 8.2 minutes #-------------------------------------------- #@# Surf Volume lh Wed Jun 15 06:11:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 lh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/lh.cortex.label Total face volume 169008 Total vertex volume 165970 (mask=0) #@# AD18 lh 165970 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Wed Jun 15 06:11:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 rh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/rh.cortex.label Total face volume 167237 Total vertex volume 164086 (mask=0) #@# AD18 rh 164086 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Wed Jun 15 06:11:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 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 = 51 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Wed Jun 15 06:17:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 1179 778 1735 2.353 0.485 0.123 0.031 10 1.4 bankssts 529 353 815 2.710 0.618 0.124 0.023 6 0.5 caudalanteriorcingulate 2476 1708 4585 2.477 0.476 0.129 0.031 27 3.2 caudalmiddlefrontal 1995 1310 2340 1.867 0.488 0.156 0.033 33 2.9 cuneus 523 325 1069 2.243 0.813 0.125 0.057 9 1.0 entorhinal 3824 2533 7132 2.444 0.680 0.137 0.040 49 6.7 fusiform 4066 2744 7318 2.412 0.618 0.140 0.037 51 6.0 inferiorparietal 4220 2813 9345 2.784 0.748 0.140 0.045 60 7.4 inferiortemporal 858 544 1402 2.377 0.662 0.110 0.027 9 0.9 isthmuscingulate 5885 3851 9434 2.268 0.591 0.151 0.041 81 10.1 lateraloccipital 3010 1975 5177 2.393 0.691 0.131 0.037 36 4.8 lateralorbitofrontal 3646 2418 4797 1.954 0.587 0.152 0.049 61 7.6 lingual 2370 1584 4075 2.390 0.676 0.136 0.045 38 4.1 medialorbitofrontal 3478 2397 6408 2.402 0.621 0.136 0.035 42 5.2 middletemporal 795 538 1565 2.542 0.788 0.097 0.019 5 0.6 parahippocampal 1788 1179 3142 2.388 0.536 0.125 0.031 18 2.3 paracentral 1773 1140 2914 2.302 0.426 0.124 0.038 33 2.6 parsopercularis 759 536 1581 2.336 0.506 0.156 0.045 10 1.4 parsorbitalis 1414 954 2390 2.257 0.520 0.130 0.034 15 1.8 parstriangularis 1542 1041 1250 1.383 0.365 0.132 0.033 16 2.0 pericalcarine 5419 3473 7619 1.928 0.554 0.116 0.024 50 5.6 postcentral 614 404 943 2.717 0.843 0.146 0.044 9 1.0 posteriorcingulate 6750 4302 10460 2.263 0.576 0.112 0.026 54 7.8 precentral 3757 2576 5950 2.227 0.539 0.141 0.036 50 5.4 precuneus 933 600 2051 2.854 1.157 0.131 0.036 14 1.4 rostralanteriorcingulate 5375 3621 10286 2.365 0.645 0.142 0.041 73 8.7 rostralmiddlefrontal 8311 5609 16935 2.623 0.580 0.127 0.031 85 10.8 superiorfrontal 6586 4329 9584 2.048 0.517 0.130 0.030 78 8.1 superiorparietal 4899 3097 8255 2.357 0.571 0.116 0.033 46 6.8 superiortemporal 4197 2800 6996 2.299 0.561 0.135 0.033 50 5.7 supramarginal 369 264 1326 3.112 0.488 0.181 0.077 8 1.3 frontalpole 550 379 1965 3.007 0.860 0.141 0.052 10 1.1 temporalpole 604 355 725 2.028 0.372 0.123 0.029 6 0.7 transversetemporal 2821 1847 4399 2.549 0.843 0.118 0.041 26 4.4 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 AD18 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 1179 692 1735 2.353 0.485 0.127 0.038 26 2.1 bankssts 529 332 815 2.710 0.618 0.090 0.018 7 0.3 caudalanteriorcingulate 2476 1937 4585 2.477 0.476 0.136 0.029 33 3.1 caudalmiddlefrontal 1995 1366 2340 1.867 0.488 0.126 0.030 44 2.5 cuneus 523 578 1069 2.243 0.813 0.187 0.051 6 1.4 entorhinal 3824 3178 7132 2.444 0.680 0.150 0.038 66 7.0 fusiform 4066 3269 7318 2.412 0.618 0.142 0.031 47 6.1 inferiorparietal 4220 3669 9345 2.784 0.748 0.146 0.035 71 7.1 inferiortemporal 858 636 1402 2.377 0.662 0.122 0.029 7 1.1 isthmuscingulate 5885 4602 9434 2.268 0.591 0.138 0.033 121 9.2 lateraloccipital 3010 2298 5177 2.393 0.691 0.130 0.032 35 3.9 lateralorbitofrontal 3646 2762 4797 1.954 0.587 0.133 0.039 63 6.4 lingual 2370 1848 4075 2.390 0.676 0.151 0.041 67 4.3 medialorbitofrontal 3478 2872 6408 2.402 0.621 0.135 0.028 46 4.5 middletemporal 795 735 1565 2.542 0.788 0.141 0.030 8 1.1 parahippocampal 1788 1469 3142 2.388 0.536 0.123 0.025 19 2.0 paracentral 1773 1402 2914 2.302 0.426 0.128 0.024 20 1.8 parsopercularis 759 787 1581 2.336 0.506 0.173 0.034 8 1.2 parsorbitalis 1414 1089 2390 2.257 0.520 0.142 0.031 16 1.9 parstriangularis 1542 881 1250 1.383 0.365 0.111 0.028 21 1.9 pericalcarine 5419 4396 7619 1.928 0.554 0.124 0.021 42 5.1 postcentral 614 377 943 2.717 0.843 0.141 0.055 24 1.2 posteriorcingulate 6750 4898 10460 2.263 0.576 0.103 0.018 54 5.3 precentral 3757 2741 5950 2.227 0.539 0.129 0.028 54 4.5 precuneus 933 836 2051 2.854 1.157 0.144 0.026 10 1.0 rostralanteriorcingulate 5375 4810 10286 2.365 0.645 0.165 0.037 83 8.9 rostralmiddlefrontal 8311 7056 16935 2.623 0.580 0.141 0.029 98 10.5 superiorfrontal 6586 4955 9584 2.048 0.517 0.125 0.038 142 7.2 superiorparietal 4899 3834 8255 2.357 0.571 0.123 0.026 44 5.7 superiortemporal 4197 3232 6996 2.299 0.561 0.133 0.028 52 5.0 supramarginal 369 547 1326 3.112 0.488 0.237 0.044 4 0.8 frontalpole 550 840 1965 3.007 0.860 0.227 0.037 6 1.1 temporalpole 604 391 725 2.028 0.372 0.095 0.021 5 0.4 transversetemporal 2821 1570 4399 2.549 0.843 0.105 0.028 34 3.0 insula #----------------------------------------- #@# Parcellation Stats rh Wed Jun 15 06:18:09 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 862 597 1330 2.247 0.346 0.097 0.021 5 0.7 bankssts 858 587 1566 2.696 0.854 0.159 0.037 17 1.4 caudalanteriorcingulate 2213 1520 4388 2.543 0.544 0.135 0.040 27 4.1 caudalmiddlefrontal 2167 1452 2589 1.750 0.482 0.154 0.036 36 3.2 cuneus 386 290 984 2.316 1.065 0.147 0.058 5 1.0 entorhinal 3382 2267 6040 2.357 0.685 0.143 0.048 58 6.5 fusiform 5429 3556 9821 2.582 0.551 0.140 0.041 73 8.7 inferiorparietal 3600 2410 7696 2.549 0.699 0.143 0.049 55 7.1 inferiortemporal 992 617 1388 2.188 0.685 0.130 0.036 16 1.5 isthmuscingulate 6176 4174 10973 2.426 0.631 0.151 0.045 82 11.7 lateraloccipital 3037 1899 5157 2.404 0.628 0.134 0.047 50 5.7 lateralorbitofrontal 3340 2234 4340 1.914 0.537 0.146 0.042 44 6.1 lingual 2258 1485 4142 2.394 0.787 0.127 0.043 31 3.6 medialorbitofrontal 3477 2341 7138 2.572 0.661 0.134 0.042 45 6.1 middletemporal 718 521 1464 2.511 0.734 0.102 0.021 5 0.5 parahippocampal 1800 1195 2749 2.133 0.577 0.124 0.030 17 2.2 paracentral 1262 858 2309 2.434 0.511 0.118 0.027 11 1.4 parsopercularis 957 626 1859 2.356 0.599 0.145 0.042 13 1.9 parsorbitalis 1595 1040 2957 2.463 0.583 0.130 0.036 17 2.3 parstriangularis 1687 1214 1604 1.425 0.332 0.137 0.028 20 1.9 pericalcarine 5099 3315 6660 1.830 0.585 0.111 0.026 49 5.5 postcentral 724 483 1140 2.644 0.536 0.140 0.043 9 1.2 posteriorcingulate 6309 4107 9278 2.128 0.595 0.112 0.027 52 7.3 precentral 4112 2734 6403 2.276 0.585 0.129 0.031 45 5.0 precuneus 833 563 1738 2.468 0.862 0.134 0.029 11 1.0 rostralanteriorcingulate 5933 4013 12217 2.390 0.769 0.143 0.044 91 10.7 rostralmiddlefrontal 7832 5189 15185 2.529 0.608 0.126 0.034 87 10.5 superiorfrontal 5915 3978 9500 2.251 0.619 0.145 0.037 85 8.8 superiorparietal 4422 2838 6850 2.158 0.583 0.111 0.032 44 5.9 superiortemporal 4009 2649 6182 2.170 0.493 0.120 0.032 43 5.3 supramarginal 368 238 1051 2.775 0.707 0.172 0.078 11 1.1 frontalpole 557 379 2182 2.996 0.916 0.148 0.050 9 1.4 temporalpole 545 304 630 1.919 0.318 0.108 0.029 5 0.6 transversetemporal 2797 1817 4575 2.583 0.872 0.112 0.039 26 4.4 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 AD18 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 862 571 1330 2.247 0.346 0.092 0.019 8 0.7 bankssts 858 648 1566 2.696 0.854 0.180 0.081 72 4.1 caudalanteriorcingulate 2213 1865 4388 2.543 0.544 0.134 0.029 24 3.0 caudalmiddlefrontal 2167 1646 2589 1.750 0.482 0.128 0.028 42 2.6 cuneus 386 493 984 2.316 1.065 0.174 0.039 3 0.6 entorhinal 3382 2805 6040 2.357 0.685 0.158 0.039 75 6.3 fusiform 5429 4077 9821 2.582 0.551 0.140 0.038 116 9.2 inferiorparietal 3600 3381 7696 2.549 0.699 0.159 0.037 81 6.1 inferiortemporal 992 725 1388 2.188 0.685 0.154 0.071 60 4.0 isthmuscingulate 6176 4905 10973 2.426 0.631 0.130 0.028 72 7.9 lateraloccipital 3037 2310 5157 2.404 0.628 0.135 0.033 48 4.6 lateralorbitofrontal 3340 2566 4340 1.914 0.537 0.140 0.046 85 5.8 lingual 2258 1909 4142 2.394 0.787 0.140 0.031 26 3.0 medialorbitofrontal 3477 3133 7138 2.572 0.661 0.145 0.029 41 4.6 middletemporal 718 677 1464 2.511 0.734 0.167 0.044 8 1.5 parahippocampal 1800 1393 2749 2.133 0.577 0.126 0.027 34 2.4 paracentral 1262 1055 2309 2.434 0.511 0.136 0.028 15 1.5 parsopercularis 957 938 1859 2.356 0.599 0.159 0.032 10 1.5 parsorbitalis 1595 1361 2957 2.463 0.583 0.135 0.030 21 2.0 parstriangularis 1687 1156 1604 1.425 0.332 0.118 0.038 25 2.6 pericalcarine 5099 3978 6660 1.830 0.585 0.111 0.019 37 4.1 postcentral 724 476 1140 2.644 0.536 0.150 0.053 27 1.4 posteriorcingulate 6309 4555 9278 2.128 0.595 0.101 0.018 51 4.6 precentral 4112 2891 6403 2.276 0.585 0.130 0.030 53 5.1 precuneus 833 778 1738 2.468 0.862 0.157 0.030 16 1.2 rostralanteriorcingulate 5933 5677 12217 2.390 0.769 0.172 0.036 82 9.1 rostralmiddlefrontal 7832 6478 15185 2.529 0.608 0.136 0.028 115 9.3 superiorfrontal 5915 4461 9500 2.251 0.619 0.132 0.027 85 7.1 superiorparietal 4422 3463 6850 2.158 0.583 0.119 0.023 36 4.3 superiortemporal 4009 2973 6182 2.170 0.493 0.115 0.024 39 3.7 supramarginal 368 489 1051 2.775 0.707 0.212 0.039 4 0.6 frontalpole 557 959 2182 2.996 0.916 0.251 0.039 6 1.2 temporalpole 545 363 630 1.919 0.318 0.093 0.018 3 0.4 transversetemporal 2797 1661 4575 2.583 0.872 0.101 0.023 32 2.6 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Jun 15 06:19:11 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 278 labels changed using aseg relabeling using gibbs priors... 000: 7173 changed, 105219 examined... 001: 1689 changed, 27959 examined... 002: 505 changed, 8799 examined... 003: 195 changed, 2871 examined... 004: 96 changed, 1178 examined... 005: 38 changed, 541 examined... 006: 28 changed, 226 examined... 007: 22 changed, 163 examined... 008: 12 changed, 122 examined... 009: 3 changed, 62 examined... 010: 4 changed, 17 examined... 011: 3 changed, 13 examined... 012: 0 changed, 7 examined... 86 labels changed using aseg 000: 230 total segments, 140 labels (1779 vertices) changed 001: 100 total segments, 10 labels (49 vertices) changed 002: 90 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 898 vertices marked for relabeling... 898 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Wed Jun 15 06:19:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 435 labels changed using aseg relabeling using gibbs priors... 000: 6968 changed, 104078 examined... 001: 1553 changed, 27233 examined... 002: 481 changed, 8340 examined... 003: 202 changed, 2748 examined... 004: 101 changed, 1175 examined... 005: 54 changed, 599 examined... 006: 29 changed, 298 examined... 007: 10 changed, 161 examined... 008: 6 changed, 61 examined... 009: 3 changed, 33 examined... 010: 3 changed, 16 examined... 011: 1 changed, 17 examined... 012: 0 changed, 7 examined... 29 labels changed using aseg 000: 212 total segments, 127 labels (1175 vertices) changed 001: 92 total segments, 7 labels (31 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 24 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 795 vertices marked for relabeling... 795 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jun 15 06:19:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 758 526 1981 2.878 0.633 0.159 0.054 12 1.9 G&S_frontomargin 1105 748 2023 2.424 0.631 0.140 0.039 13 1.6 G&S_occipital_inf 1435 941 2684 2.378 0.571 0.126 0.032 14 2.0 G&S_paracentral 1275 816 2286 2.370 0.374 0.126 0.033 16 1.6 G&S_subcentral 476 321 1667 3.051 0.691 0.148 0.053 7 1.0 G&S_transv_frontopol 1840 1237 3509 2.686 0.767 0.134 0.032 23 2.4 G&S_cingul-Ant 848 611 1378 2.603 0.514 0.110 0.017 6 0.6 G&S_cingul-Mid-Ant 933 632 1559 2.740 0.682 0.134 0.038 10 1.4 G&S_cingul-Mid-Post 268 167 491 2.577 0.341 0.139 0.036 4 0.4 G_cingul-Post-dorsal 201 130 360 2.344 0.729 0.117 0.026 2 0.2 G_cingul-Post-ventral 1832 1218 2323 1.787 0.541 0.149 0.032 27 2.6 G_cuneus 1159 735 2218 2.412 0.399 0.140 0.049 29 2.1 G_front_inf-Opercular 376 253 784 2.219 0.541 0.159 0.049 6 0.8 G_front_inf-Orbital 896 587 1764 2.387 0.516 0.138 0.043 13 1.4 G_front_inf-Triangul 3232 2167 7005 2.517 0.575 0.150 0.044 52 5.7 G_front_middle 5488 3579 11957 2.716 0.587 0.132 0.037 69 8.3 G_front_sup 490 292 760 2.499 0.571 0.117 0.057 8 0.8 G_Ins_lg&S_cent_ins 589 359 1280 2.907 0.957 0.138 0.068 8 1.7 G_insular_short 1709 1116 3566 2.559 0.548 0.161 0.047 29 3.4 G_occipital_middle 1363 854 2107 2.366 0.501 0.150 0.041 22 2.2 G_occipital_sup 1325 868 3026 2.765 0.620 0.144 0.037 20 2.0 G_oc-temp_lat-fusifor 2781 1782 3770 1.940 0.640 0.155 0.053 51 6.4 G_oc-temp_med-Lingual 1247 752 2411 2.479 0.836 0.110 0.049 16 2.4 G_oc-temp_med-Parahip 2034 1296 4041 2.429 0.677 0.145 0.049 33 4.1 G_orbital 1718 1137 3708 2.580 0.633 0.161 0.046 30 3.3 G_pariet_inf-Angular 2066 1357 4125 2.485 0.503 0.141 0.038 29 3.3 G_pariet_inf-Supramar 2765 1809 4549 2.140 0.498 0.137 0.033 40 3.9 G_parietal_sup 2028 1224 3316 2.147 0.483 0.122 0.028 22 2.4 G_postcentral 2458 1436 4554 2.476 0.586 0.112 0.029 22 3.1 G_precentral 1927 1313 3842 2.412 0.453 0.157 0.042 34 3.1 G_precuneus 762 527 1838 2.553 0.653 0.160 0.061 15 2.0 G_rectus 697 434 830 2.373 1.057 0.087 0.035 5 0.5 G_subcallosal 454 254 599 2.111 0.376 0.110 0.031 4 0.5 G_temp_sup-G_T_transv 1774 1050 3915 2.649 0.534 0.136 0.049 26 3.9 G_temp_sup-Lateral 592 395 1156 2.549 0.564 0.088 0.025 2 0.7 G_temp_sup-Plan_polar 853 535 1411 2.399 0.547 0.111 0.027 8 0.9 G_temp_sup-Plan_tempo 2530 1628 6267 2.867 0.767 0.146 0.052 45 4.8 G_temporal_inf 1997 1334 4187 2.501 0.565 0.147 0.042 29 3.7 G_temporal_middle 259 178 279 1.844 0.382 0.112 0.021 2 0.2 Lat_Fis-ant-Horizont 129 90 180 2.046 0.358 0.103 0.019 1 0.1 Lat_Fis-ant-Vertical 1002 671 1142 2.055 0.441 0.121 0.026 7 1.1 Lat_Fis-post 1864 1196 2917 2.175 0.622 0.153 0.041 27 3.2 Pole_occipital 1425 967 4552 2.995 0.835 0.144 0.051 23 3.1 Pole_temporal 1727 1188 1627 1.645 0.555 0.134 0.035 17 2.4 S_calcarine 2929 1983 3045 1.716 0.579 0.110 0.022 19 2.7 S_central 790 555 1152 2.273 0.473 0.148 0.038 9 1.2 S_cingul-Marginalis 344 261 495 2.245 0.408 0.104 0.017 2 0.2 S_circular_insula_ant 1282 879 1677 2.370 0.771 0.102 0.021 7 1.2 S_circular_insula_inf 1295 880 1455 2.116 0.450 0.118 0.026 8 1.5 S_circular_insula_sup 885 611 1309 2.285 0.574 0.110 0.025 6 0.8 S_collat_transv_ant 456 309 434 1.785 0.387 0.155 0.037 5 0.9 S_collat_transv_post 1439 963 1917 2.126 0.422 0.126 0.033 14 1.9 S_front_inf 892 595 1093 1.995 0.456 0.120 0.027 6 1.0 S_front_middle 2667 1843 4589 2.266 0.521 0.117 0.024 26 2.6 S_front_sup 207 144 301 2.560 0.496 0.135 0.026 2 0.2 S_interm_prim-Jensen 1887 1285 2116 1.830 0.558 0.109 0.021 13 1.6 S_intrapariet&P_trans 703 486 832 2.084 0.390 0.129 0.027 6 0.8 S_oc_middle&Lunatus 919 616 1179 1.968 0.475 0.129 0.032 9 1.3 S_oc_sup&transversal 436 291 502 2.059 0.472 0.153 0.035 6 0.6 S_occipital_ant 805 571 1221 2.360 0.563 0.135 0.031 7 1.1 S_oc-temp_lat 1614 1138 2228 2.071 0.562 0.131 0.029 17 2.0 S_oc-temp_med&Lingual 128 90 204 2.209 0.391 0.127 0.027 1 0.2 S_orbital_lateral 451 303 564 2.033 0.540 0.127 0.025 6 0.5 S_orbital_med-olfact 1071 749 1891 2.508 0.735 0.128 0.029 8 1.4 S_orbital-H_Shaped 1693 1107 1811 1.863 0.467 0.125 0.028 18 2.1 S_parieto_occipital 421 253 497 2.340 1.041 0.113 0.031 5 0.4 S_pericallosal 2347 1562 2802 1.901 0.449 0.122 0.026 21 2.5 S_postcentral 1285 886 1881 2.346 0.446 0.098 0.016 6 0.9 S_precentral-inf-part 1242 850 1723 2.185 0.510 0.110 0.022 8 1.1 S_precentral-sup-part 566 384 977 2.561 0.735 0.154 0.042 8 1.0 S_suborbital 563 410 828 2.259 0.551 0.121 0.020 4 0.4 S_subparietal 931 654 1276 2.547 0.656 0.133 0.031 8 1.1 S_temporal_inf 4169 2876 5769 2.167 0.489 0.120 0.029 35 4.4 S_temporal_sup 211 132 257 2.033 0.474 0.101 0.014 1 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jun 15 06:20:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 676 448 1644 2.657 0.869 0.136 0.040 10 1.0 G&S_frontomargin 1017 695 2347 2.859 0.709 0.146 0.039 12 1.8 G&S_occipital_inf 1244 798 2140 2.220 0.677 0.123 0.028 15 1.3 G&S_paracentral 1285 812 2228 2.380 0.549 0.131 0.040 15 2.1 G&S_subcentral 888 585 2499 2.803 0.851 0.154 0.064 21 2.5 G&S_transv_frontopol 2240 1558 4112 2.470 0.636 0.127 0.025 24 2.3 G&S_cingul-Ant 1102 802 1967 2.503 0.626 0.134 0.031 12 1.5 G&S_cingul-Mid-Ant 948 632 1468 2.495 0.541 0.138 0.038 11 1.3 G&S_cingul-Mid-Post 242 160 454 2.716 0.308 0.147 0.040 4 0.4 G_cingul-Post-dorsal 259 169 423 2.082 0.626 0.125 0.029 3 0.3 G_cingul-Post-ventral 2031 1382 2506 1.731 0.483 0.160 0.037 37 2.9 G_cuneus 913 583 2007 2.613 0.480 0.129 0.033 11 1.4 G_front_inf-Opercular 268 179 453 2.137 0.518 0.171 0.046 4 0.6 G_front_inf-Orbital 837 522 1897 2.639 0.615 0.139 0.043 12 1.5 G_front_inf-Triangul 3416 2234 8023 2.640 0.659 0.166 0.061 76 9.0 G_front_middle 5080 3239 10868 2.653 0.587 0.132 0.040 67 8.3 G_front_sup 426 248 763 2.939 0.660 0.118 0.064 8 0.9 G_Ins_lg&S_cent_ins 649 374 1419 3.143 0.989 0.127 0.057 7 1.6 G_insular_short 1696 1088 3764 2.668 0.576 0.152 0.049 28 3.5 G_occipital_middle 1220 782 1998 2.341 0.573 0.154 0.042 20 2.1 G_occipital_sup 1447 921 2745 2.465 0.657 0.143 0.046 22 2.7 G_oc-temp_lat-fusifor 2168 1385 3138 1.999 0.577 0.141 0.039 27 3.5 G_oc-temp_med-Lingual 981 665 2191 2.513 0.909 0.130 0.054 17 2.2 G_oc-temp_med-Parahip 2170 1312 4783 2.633 0.677 0.144 0.061 46 5.4 G_orbital 2393 1536 4606 2.553 0.471 0.153 0.048 42 4.5 G_pariet_inf-Angular 1853 1199 3165 2.189 0.497 0.118 0.034 21 2.8 G_pariet_inf-Supramar 1824 1234 3509 2.409 0.635 0.155 0.041 31 3.1 G_parietal_sup 1874 1101 2735 2.009 0.499 0.122 0.029 24 2.2 G_postcentral 2288 1332 4017 2.358 0.528 0.118 0.032 24 3.2 G_precentral 1819 1198 3523 2.511 0.618 0.154 0.042 32 3.0 G_precuneus 621 411 1561 2.498 0.664 0.149 0.051 13 1.3 G_rectus 394 259 495 2.144 1.068 0.100 0.054 3 0.7 G_subcallosal 398 193 486 2.013 0.381 0.106 0.035 5 0.5 G_temp_sup-G_T_transv 1585 939 3030 2.401 0.646 0.130 0.052 26 3.4 G_temp_sup-Lateral 558 362 1036 2.346 0.457 0.081 0.019 2 0.4 G_temp_sup-Plan_polar 684 462 1046 2.036 0.507 0.092 0.018 3 0.5 G_temp_sup-Plan_tempo 1993 1279 4638 2.613 0.707 0.152 0.064 38 4.8 G_temporal_inf 2123 1409 4948 2.668 0.617 0.147 0.056 36 4.9 G_temporal_middle 300 189 350 2.179 0.409 0.111 0.030 2 0.3 Lat_Fis-ant-Horizont 179 129 272 2.366 0.603 0.114 0.023 1 0.2 Lat_Fis-ant-Vertical 1469 1021 1826 2.058 0.686 0.119 0.028 10 1.9 Lat_Fis-post 3079 2063 4885 2.219 0.658 0.160 0.051 45 6.7 Pole_occipital 1415 971 4850 3.057 0.756 0.167 0.060 32 4.0 Pole_temporal 1701 1233 1635 1.577 0.470 0.131 0.030 18 2.1 S_calcarine 2900 2087 2752 1.479 0.415 0.091 0.015 12 1.9 S_central 927 629 1343 2.185 0.522 0.145 0.039 11 1.6 S_cingul-Marginalis 314 234 489 2.331 0.432 0.103 0.020 1 0.3 S_circular_insula_ant 1203 816 1384 1.998 0.548 0.082 0.019 5 1.0 S_circular_insula_inf 1005 704 1398 2.350 0.510 0.110 0.028 6 1.2 S_circular_insula_sup 891 636 1272 2.079 0.557 0.107 0.023 5 0.8 S_collat_transv_ant 427 286 428 1.935 0.455 0.138 0.040 5 0.8 S_collat_transv_post 1210 849 1667 2.126 0.443 0.127 0.029 10 1.4 S_front_inf 1450 1015 2251 2.009 0.576 0.117 0.027 10 1.6 S_front_middle 1768 1250 2903 2.185 0.591 0.112 0.023 13 1.5 S_front_sup 381 262 455 2.179 0.332 0.120 0.022 3 0.4 S_interm_prim-Jensen 2222 1510 2983 2.141 0.530 0.132 0.034 25 2.8 S_intrapariet&P_trans 684 476 965 2.441 0.466 0.119 0.025 5 0.5 S_oc_middle&Lunatus 1033 721 1359 2.189 0.614 0.109 0.020 7 0.8 S_oc_sup&transversal 550 354 759 2.374 0.505 0.145 0.040 6 1.0 S_occipital_ant 765 552 1354 2.337 0.551 0.140 0.031 9 0.9 S_oc-temp_lat 1345 1014 1771 1.993 0.572 0.124 0.027 11 1.5 S_oc-temp_med&Lingual 272 183 355 1.981 0.467 0.134 0.027 2 0.4 S_orbital_lateral 593 380 643 1.799 0.415 0.121 0.025 5 0.5 S_orbital_med-olfact 999 674 1739 2.458 0.599 0.124 0.030 9 1.3 S_orbital-H_Shaped 1902 1226 2170 1.899 0.522 0.107 0.021 13 1.7 S_parieto_occipital 847 485 714 2.173 1.007 0.135 0.034 17 1.1 S_pericallosal 1796 1273 2311 1.816 0.523 0.142 0.037 25 2.9 S_postcentral 1102 763 1655 2.287 0.404 0.106 0.024 6 1.1 S_precentral-inf-part 1292 898 1533 2.071 0.478 0.109 0.020 8 1.1 S_precentral-sup-part 198 131 372 2.797 0.714 0.111 0.030 1 0.2 S_suborbital 747 517 1188 2.465 0.428 0.138 0.034 7 1.2 S_subparietal 758 530 1161 2.410 0.753 0.124 0.023 5 0.8 S_temporal_inf 4150 2827 6083 2.305 0.542 0.110 0.024 29 3.9 S_temporal_sup 167 115 179 2.041 0.342 0.149 0.029 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Jun 15 06:21:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 944 labels changed using aseg relabeling using gibbs priors... 000: 1572 changed, 105219 examined... 001: 410 changed, 7442 examined... 002: 110 changed, 2327 examined... 003: 57 changed, 647 examined... 004: 34 changed, 322 examined... 005: 32 changed, 197 examined... 006: 19 changed, 155 examined... 007: 12 changed, 108 examined... 008: 14 changed, 75 examined... 009: 14 changed, 76 examined... 010: 14 changed, 68 examined... 011: 8 changed, 61 examined... 012: 4 changed, 44 examined... 013: 2 changed, 27 examined... 014: 2 changed, 11 examined... 015: 4 changed, 15 examined... 016: 7 changed, 24 examined... 017: 11 changed, 36 examined... 018: 6 changed, 47 examined... 019: 7 changed, 28 examined... 020: 4 changed, 38 examined... 021: 4 changed, 25 examined... 022: 3 changed, 25 examined... 023: 3 changed, 17 examined... 024: 3 changed, 17 examined... 025: 2 changed, 14 examined... 026: 1 changed, 10 examined... 027: 2 changed, 9 examined... 028: 4 changed, 11 examined... 029: 3 changed, 20 examined... 030: 2 changed, 14 examined... 031: 3 changed, 13 examined... 032: 1 changed, 10 examined... 033: 1 changed, 7 examined... 034: 2 changed, 7 examined... 035: 4 changed, 10 examined... 036: 3 changed, 18 examined... 037: 3 changed, 18 examined... 038: 2 changed, 17 examined... 039: 0 changed, 10 examined... 391 labels changed using aseg 000: 49 total segments, 16 labels (124 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 455 vertices marked for relabeling... 455 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Wed Jun 15 06:21:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD18 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... 1436 labels changed using aseg relabeling using gibbs priors... 000: 1601 changed, 104078 examined... 001: 384 changed, 7511 examined... 002: 124 changed, 2164 examined... 003: 55 changed, 728 examined... 004: 25 changed, 331 examined... 005: 19 changed, 154 examined... 006: 13 changed, 101 examined... 007: 12 changed, 73 examined... 008: 6 changed, 55 examined... 009: 11 changed, 45 examined... 010: 8 changed, 52 examined... 011: 5 changed, 49 examined... 012: 3 changed, 26 examined... 013: 4 changed, 23 examined... 014: 5 changed, 24 examined... 015: 4 changed, 31 examined... 016: 0 changed, 16 examined... 290 labels changed using aseg 000: 54 total segments, 21 labels (319 vertices) changed 001: 34 total segments, 1 labels (6 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 347 vertices marked for relabeling... 347 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jun 15 06:21:32 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 1106 761 1948 2.749 0.515 0.130 0.023 12 1.0 caudalanteriorcingulate 2705 1867 4964 2.456 0.479 0.130 0.031 30 3.5 caudalmiddlefrontal 2572 1688 3136 1.867 0.510 0.147 0.031 38 3.5 cuneus 438 272 829 2.153 0.801 0.116 0.053 7 0.7 entorhinal 3435 2289 6104 2.409 0.644 0.137 0.039 43 5.8 fusiform 4049 2734 7238 2.410 0.629 0.141 0.037 51 6.0 inferiorparietal 4448 2945 10229 2.778 0.759 0.139 0.046 64 8.1 inferiortemporal 854 541 1405 2.388 0.657 0.111 0.028 9 0.9 isthmuscingulate 5980 3920 9587 2.285 0.582 0.153 0.042 85 10.2 lateraloccipital 3353 2197 6329 2.545 0.760 0.136 0.044 45 5.8 lateralorbitofrontal 3774 2490 4988 1.958 0.591 0.153 0.049 63 8.1 lingual 1869 1257 3591 2.443 0.691 0.148 0.052 33 3.9 medialorbitofrontal 4584 3115 8177 2.416 0.621 0.134 0.035 52 6.6 middletemporal 833 562 1637 2.558 0.777 0.098 0.020 5 0.6 parahippocampal 2147 1407 3722 2.425 0.529 0.123 0.032 21 2.7 paracentral 1692 1073 2783 2.339 0.398 0.129 0.040 33 2.7 parsopercularis 814 560 1416 2.122 0.545 0.125 0.033 8 1.1 parsorbitalis 1622 1107 2688 2.240 0.514 0.132 0.034 18 2.2 parstriangularis 1554 1053 1267 1.382 0.365 0.130 0.032 15 1.9 pericalcarine 6056 3914 8316 1.924 0.537 0.120 0.026 57 6.6 postcentral 814 531 1350 2.697 0.760 0.143 0.043 11 1.4 posteriorcingulate 6599 4201 10364 2.281 0.577 0.111 0.026 52 7.5 precentral 3708 2544 6041 2.266 0.514 0.143 0.036 51 5.3 precuneus 1232 794 2495 2.722 1.082 0.122 0.031 16 1.5 rostralanteriorcingulate 3932 2681 7479 2.311 0.604 0.146 0.042 54 6.8 rostralmiddlefrontal 8761 5895 17914 2.585 0.620 0.128 0.033 95 11.9 superiorfrontal 5280 3460 7737 2.029 0.521 0.126 0.028 61 6.3 superiorparietal 6211 3974 11388 2.434 0.628 0.120 0.035 65 9.0 superiortemporal 3851 2574 6338 2.284 0.557 0.131 0.032 43 5.1 supramarginal 605 354 723 2.042 0.392 0.124 0.028 6 0.7 transversetemporal 2437 1617 3783 2.480 0.796 0.119 0.041 23 4.0 insula #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jun 15 06:22:03 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 911 627 1662 2.696 0.837 0.159 0.037 18 1.5 caudalanteriorcingulate 2413 1657 4620 2.498 0.560 0.134 0.039 28 4.4 caudalmiddlefrontal 2648 1747 3182 1.788 0.502 0.149 0.036 41 3.9 cuneus 375 268 879 2.348 1.045 0.150 0.059 5 1.1 entorhinal 3037 2027 5177 2.331 0.652 0.139 0.045 45 5.3 fusiform 5441 3569 9848 2.584 0.552 0.140 0.040 74 8.7 inferiorparietal 3925 2632 8606 2.553 0.713 0.146 0.052 68 8.0 inferiortemporal 987 615 1380 2.185 0.680 0.131 0.036 16 1.4 isthmuscingulate 6129 4152 10813 2.416 0.633 0.151 0.045 82 11.5 lateraloccipital 3250 2033 6175 2.525 0.682 0.138 0.049 56 6.4 lateralorbitofrontal 3325 2231 4300 1.902 0.533 0.147 0.042 43 6.1 lingual 1843 1193 3537 2.428 0.795 0.134 0.046 29 3.2 medialorbitofrontal 4116 2785 8143 2.534 0.644 0.128 0.039 48 6.5 middletemporal 756 552 1546 2.496 0.737 0.101 0.021 5 0.5 parahippocampal 1853 1232 2913 2.164 0.594 0.120 0.028 16 2.1 paracentral 1418 966 2573 2.456 0.513 0.122 0.029 13 1.7 parsopercularis 817 537 1466 2.333 0.505 0.140 0.044 9 1.5 parsorbitalis 1629 1065 2946 2.412 0.593 0.134 0.037 19 2.4 parstriangularis 1681 1213 1594 1.420 0.324 0.139 0.028 21 1.9 pericalcarine 5638 3680 7335 1.846 0.584 0.116 0.028 58 6.4 postcentral 846 558 1371 2.591 0.531 0.139 0.042 11 1.3 posteriorcingulate 6003 3901 9002 2.144 0.597 0.111 0.027 50 6.9 precentral 4188 2768 6684 2.307 0.563 0.131 0.032 48 5.5 precuneus 1039 705 2050 2.422 0.889 0.125 0.027 12 1.1 rostralanteriorcingulate 4239 2848 8489 2.364 0.736 0.143 0.044 64 7.5 rostralmiddlefrontal 9735 6489 18985 2.480 0.652 0.130 0.037 121 14.4 superiorfrontal 4911 3311 8060 2.266 0.635 0.143 0.036 70 7.3 superiorparietal 5722 3721 10288 2.275 0.659 0.117 0.034 61 8.3 superiortemporal 3733 2479 5729 2.169 0.496 0.116 0.030 37 4.8 supramarginal 510 280 599 1.930 0.326 0.103 0.029 4 0.6 transversetemporal 2533 1650 4134 2.578 0.897 0.110 0.039 24 4.0 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Jun 15 06:22:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts pctsurfcon --s AD18 --lh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts/pctsurfcon.log Wed Jun 15 06:22:36 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts /usr/local/freesurfer/stable6//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-102 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/AD18/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.wm.mgh --regheader AD18 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 54048 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.wm.mgh Dim: 105219 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.gm.mgh --projfrac 0.3 --regheader AD18 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 63247 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.gm.mgh Dim: 105219 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16521/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.w-g.pct.mgh --annot AD18 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/lh.w-g.pct.mgh --annot AD18 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/lh.w-g.pct.mgh Vertex Area is 0.660424 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 06:22:41 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts pctsurfcon --s AD18 --rh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts/pctsurfcon.log Wed Jun 15 06:22:41 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/scripts /usr/local/freesurfer/stable6//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-102 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/AD18/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.wm.mgh --regheader AD18 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 52907 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.wm.mgh Dim: 104078 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.gm.mgh --projfrac 0.3 --regheader AD18 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 62647 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.gm.mgh Dim: 104078 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/tmp.pctsurfcon.16576/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.w-g.pct.mgh --annot AD18 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.w-g.pct.mgh --annot AD18 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.w-g.pct.mgh Vertex Area is 0.662987 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 06:22:46 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 5669 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 5238 voxels changed to hypointensity... 9422 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Wed Jun 15 06:23:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 mri_aparc2aseg --s AD18 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD18 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/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 = 326766 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Wed Jun 15 06:24:19 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 mri_aparc2aseg --s AD18 --volmask --aseg aseg.presurf.hypos --annot aparc.a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD18 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/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 = 326766 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed Jun 15 06:25:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 mri_aparc2aseg --s AD18 --volmask --aseg aseg.presurf.hypos --annot aparc.DKTatlas SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD18 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/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/AD18/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 = 326766 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Wed Jun 15 06:26:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Wed Jun 15 06:26:22 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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-0-102 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/AD18/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-0-102 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 06:26:22 EDT 2016 Ended at Wed Jun 15 06:26:31 EDT 2016 Apas2aseg-Run-Time-Sec 9 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Wed Jun 15 06:26:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 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 AD18 $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 AD18 sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1324996 mm^3 (det: 1.470273 ) Computing euler number orig.nofix lheno = -32, rheno = -80 orig.nofix lhholes = 17, rhholes = 41 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 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 06:30:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 mri_aparc2aseg --s AD18 --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 AD18 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/AD18/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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/AD18/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7904 vertices from left hemi Ripped 8427 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/AD18/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 = 715691 Used brute-force search on 148 voxels Fixing Parahip LH WM Found 11 clusters 0 k 2.000000 1 k 2.000000 2 k 1.000000 3 k 2.000000 4 k 1.000000 5 k 3.000000 6 k 901.000000 7 k 1.000000 8 k 2.000000 9 k 7.000000 10 k 1.000000 Fixing Parahip RH WM Found 12 clusters 0 k 4.000000 1 k 25.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 985.000000 6 k 1.000000 7 k 1.000000 8 k 2.000000 9 k 1.000000 10 k 2.000000 11 k 2.000000 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 AD18 --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 AD18 --surf-wm-vol --ctab /usr/local/freesurfer/stable6//WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-102 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1324996 mm^3 (det: 1.470273 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 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/AD18/label #-------------------------------------------- #@# BA_exvivo Labels lh Wed Jun 15 06:41:29 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8170 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 146 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4223 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6179 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6069 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4270 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 639 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14228 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4340 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3654 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 1089 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5730 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 1812 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9926 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 236 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1526 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 222 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1421 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1052 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2188 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1578 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2043 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2428 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1605 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 327 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7362 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2004 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1211 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 791 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4196 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 936 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4270 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 27 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 540 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 609 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 AD18 --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 = AD18 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/AD18/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 105219 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 547 mri_label2label: Done mris_label2annot --s AD18 --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/AD18/label cmdline mris_label2annot --s AD18 --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-0-102 machine x86_64 user fdu0 subject AD18 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/AD18/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 69905 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/lh.BA_exvivo.annot mris_label2annot --s AD18 --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/AD18/label cmdline mris_label2annot --s AD18 --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-0-102 machine x86_64 user fdu0 subject AD18 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/AD18/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 83459 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 1014 650 1198 1.679 0.530 0.102 0.021 7 0.9 BA1_exvivo 3387 2179 4857 2.020 0.487 0.125 0.028 35 3.9 BA2_exvivo 1162 747 1642 2.102 0.640 0.096 0.020 6 1.0 BA3a_exvivo 2019 1387 2544 1.864 0.617 0.129 0.029 18 2.3 BA3b_exvivo 1466 909 2585 2.415 0.528 0.130 0.035 16 2.2 BA4a_exvivo 1336 797 2315 2.401 0.634 0.118 0.029 12 1.9 BA4p_exvivo 7955 5261 14662 2.528 0.553 0.118 0.028 69 9.1 BA6_exvivo 1804 1228 3050 2.303 0.408 0.126 0.030 21 2.2 BA44_exvivo 2111 1452 3910 2.306 0.526 0.154 0.047 32 3.9 BA45_exvivo 3233 2095 3984 1.798 0.671 0.141 0.036 40 4.8 V1_exvivo 6967 4649 9685 2.067 0.603 0.158 0.044 112 13.2 V2_exvivo 1375 921 2181 2.221 0.569 0.156 0.050 20 2.9 MT_exvivo 714 453 1646 2.661 0.823 0.130 0.068 10 2.2 perirhinal_exvivo 771 524 1716 2.386 0.837 0.118 0.032 7 1.0 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 AD18 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 169008 Total vertex volume 165970 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 637 412 647 1.504 0.431 0.087 0.016 3 0.4 BA1_exvivo 1434 892 2209 2.045 0.544 0.114 0.023 15 1.4 BA2_exvivo 1015 655 1306 1.995 0.613 0.103 0.022 6 1.0 BA3a_exvivo 1223 867 1216 1.611 0.504 0.132 0.029 11 1.3 BA3b_exvivo 1472 873 2584 2.472 0.583 0.119 0.031 14 2.0 BA4a_exvivo 1058 663 1864 2.334 0.628 0.120 0.028 9 1.4 BA4p_exvivo 4609 2961 7756 2.417 0.545 0.109 0.026 35 4.7 BA6_exvivo 1178 768 1993 2.335 0.402 0.122 0.032 15 1.4 BA44_exvivo 839 580 1493 2.303 0.563 0.139 0.040 10 1.2 BA45_exvivo 3460 2235 4285 1.818 0.661 0.143 0.037 44 5.3 V1_exvivo 3630 2403 4727 2.048 0.615 0.166 0.049 69 7.7 V2_exvivo 372 262 600 2.115 0.519 0.168 0.043 5 0.8 MT_exvivo 389 227 836 2.697 0.678 0.125 0.085 6 1.6 perirhinal_exvivo 444 291 909 2.323 0.768 0.126 0.046 5 0.9 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Wed Jun 15 06:46:51 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6810 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4091 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4675 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5875 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 376 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12632 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7095 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5620 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 673 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 1373 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9389 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 269 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2201 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 810 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 887 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2731 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1733 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2283 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1404 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1522 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 241 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7200 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1050 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1223 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3664 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 593 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4030 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 335 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 786 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 AD18 --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 = AD18 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/AD18/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 104078 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 329 mri_label2label: Done mris_label2annot --s AD18 --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/AD18/label cmdline mris_label2annot --s AD18 --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-0-102 machine x86_64 user fdu0 subject AD18 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/AD18/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 72477 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/label/rh.BA_exvivo.annot mris_label2annot --s AD18 --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/AD18/label cmdline mris_label2annot --s AD18 --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-0-102 machine x86_64 user fdu0 subject AD18 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/AD18/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 85952 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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 AD18 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 627 425 933 1.943 0.581 0.109 0.021 5 0.6 BA1_exvivo 2252 1570 3203 1.905 0.534 0.134 0.034 30 3.1 BA2_exvivo 1112 736 1201 1.556 0.484 0.091 0.019 8 0.9 BA3a_exvivo 1665 976 2506 2.081 0.524 0.126 0.039 23 2.7 BA3b_exvivo 1242 909 1573 1.743 0.576 0.126 0.025 11 1.3 BA4a_exvivo 1159 825 1105 1.401 0.373 0.105 0.019 7 1.0 BA4p_exvivo 6760 4296 11374 2.355 0.602 0.114 0.030 58 8.5 BA6_exvivo 2505 1608 4348 2.447 0.494 0.119 0.032 25 3.3 BA44_exvivo 2813 1893 5263 2.402 0.581 0.136 0.040 32 4.9 BA45_exvivo 2703 1897 2771 1.551 0.432 0.139 0.031 34 3.5 V1_exvivo 6163 4060 8270 2.013 0.566 0.151 0.042 89 10.9 V2_exvivo 1787 1209 3449 2.590 0.620 0.143 0.039 21 2.9 MT_exvivo 529 338 18 2.437 1.397 0.088 0.021 2 0.5 perirhinal_exvivo 284 166 194 2.297 0.895 0.150 0.087 9 1.0 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 AD18 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 167237 Total vertex volume 164086 (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) = 1324996 mm^3 (det: 1.470273 ) lhCtxGM: 164632.622 163987.000 diff= 645.6 pctdiff= 0.392 rhCtxGM: 161902.024 161548.000 diff= 354.0 pctdiff= 0.219 lhCtxWM: 195942.948 201548.500 diff=-5605.6 pctdiff=-2.861 rhCtxWM: 192245.952 189245.500 diff= 3000.5 pctdiff= 1.561 SubCortGMVol 40064.000 SupraTentVol 813659.545 (808957.000) diff=4702.545 pctdiff=0.578 SupraTentVolNotVent 761104.545 (756402.000) diff=4702.545 pctdiff=0.618 BrainSegVol 937739.000 (933069.000) diff=4670.000 pctdiff=0.498 BrainSegVolNotVent 879212.000 (877425.545) diff=1786.455 pctdiff=0.203 BrainSegVolNotVent 879212.000 CerebellumVol 122629.000 VentChorVol 52555.000 3rd4th5thCSF 5972.000 CSFVol 1302.000, OptChiasmVol 181.000 MaskVol 1375037.000 374 246 561 1.989 0.557 0.116 0.028 4 0.5 BA1_exvivo 1320 921 1820 1.855 0.544 0.138 0.034 20 2.0 BA2_exvivo 986 659 1038 1.468 0.403 0.084 0.014 6 0.6 BA3a_exvivo 1357 787 2080 2.137 0.531 0.131 0.043 20 2.5 BA3b_exvivo 747 561 1133 1.910 0.648 0.128 0.027 7 0.9 BA4a_exvivo 980 707 885 1.350 0.317 0.102 0.016 5 0.7 BA4p_exvivo 4492 2743 7228 2.329 0.615 0.109 0.031 38 5.7 BA6_exvivo 623 378 1091 2.484 0.522 0.111 0.026 6 0.6 BA44_exvivo 689 464 1453 2.626 0.604 0.122 0.035 7 1.1 BA45_exvivo 2572 1783 2628 1.556 0.436 0.138 0.031 32 3.2 V1_exvivo 3150 2058 3965 1.882 0.540 0.144 0.042 43 5.5 V2_exvivo 288 185 568 2.619 0.457 0.166 0.056 5 0.7 MT_exvivo 324 202 6 2.812 1.422 0.082 0.018 1 0.3 perirhinal_exvivo 224 119 55 2.348 1.064 0.153 0.099 8 1.0 entorhinal_exvivo Started at Tue Jun 14 16:42:42 EDT 2016 Ended at Wed Jun 15 06:51:56 EDT 2016 #@#%# recon-all-run-time-hours 14.154 recon-all -s AD18 finished without error at Wed Jun 15 06:51:56 EDT 2016 New invocation of recon-all Wed Jul 20 15:33:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18 /usr/local/freesurfer/stable6/bin/recon-all -skullstrip -clean-bm -gcut -subjid AD18 subjid AD18 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/stable6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160714 Linux compute-0-104 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: 32877252 6045436 26831816 168 223852 2890700 -/+ buffers/cache: 2930884 29946368 Swap: 67108860 89220 67019640 pbsjob 11971132.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: stable6 $ TimeStamp: 2016/07/20-19:33:19-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:19-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: tkregister2.c,v 1.132 2016/05/04 22:17:15 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:19-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:20-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:20-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:20-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:20-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:21-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_label2label.c,v 1.48 2016/03/16 23:36:50 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:21-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:21-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:21-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_ca_register.c,v 1.96 2016/04/30 02:37:04 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:21-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_ca_label.c,v 1.113 2016/05/13 18:02:49 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:22-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:22-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:22-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:22-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:22-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:23-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:23-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:23-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:24-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:24-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:24-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:25-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:25-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:25-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:25-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:26-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:26-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:26-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:26-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:27-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.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: stable6 $ TimeStamp: 2016/07/20-19:33:27-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.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: stable6 $ TimeStamp: 2016/07/20-19:33:27-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:27-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:27-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:28-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:28-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/07/20-19:33:28-GMT BuildTimeStamp: Jul 14 2016 15:17:20 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: fdu0 Machine: compute-0-104 Platform: Linux PlatformVersion: 2.6.32-573.8.1.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 ####################################### mv -f /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri/brainmask.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/trash #-------------------------------------------- #@# Skull Stripping Wed Jul 20 15:33:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri mri_watershed -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/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=128 y=122 z=117 r=69 first estimation of the main basin volume: 1420885 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=151, y=101, z=94, 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=399562062 voxels, voxel volume =1.000 = 399562062 mmm3 = 399562.048 cm3 done. PostAnalyze...Basin Prior 14 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=126, z=110, r=8952 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 44940 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=39 , nb = -1027953758 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1044989756 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=62 , nb = 1075867356 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 1068490578 OTHER CSF_MIN=0, CSF_intensity=19, CSF_MAX=43 , nb = 1083277096 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 56, 46, 40, 79 after analyzing : 35, 46, 46, 54 RIGHT_CER before analyzing : 39, 50, 59, 89 after analyzing : 39, 56, 59, 64 LEFT_CER before analyzing : 24, 35, 55, 90 after analyzing : 24, 48, 55, 58 RIGHT_BRAIN before analyzing : 62, 49, 41, 79 after analyzing : 37, 49, 49, 56 LEFT_BRAIN before analyzing : 56, 45, 38, 79 after analyzing : 34, 45, 45, 53 OTHER before analyzing : 43, 27, 22, 31 after analyzing : 24, 27, 27, 28 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.015, std = 0.011 curvature mean = 64.368, std = 6.007 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.31, sigma = 9.55 after rotation: sse = 5.31, sigma = 9.55 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 7.02, its var is 15.25 before Erosion-Dilatation 5.27% of inacurate vertices after Erosion-Dilatation 8.81% 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 = 1379966 voxels, voxel volume = 1.000 mm3 = 1379966 mmm3 = 1379.966 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 27.729784 mri_watershed stimesec 0.475927 mri_watershed ru_maxrss 827620 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212854 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 146 mri_watershed ru_nivcsw 2843 mri_watershed done rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed. reading mask... white mean: 105.175743 threshold set to: 105.175743*0.400000=42.070297 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... mri_binarize --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD18/mri cmdline mri_binarize.bin --i brainmask.gcuts.mgz --o brainmask.gcuts.mgz --binval 999 --min 1 sysname Linux hostname compute-0-104 machine x86_64 user fdu0 input brainmask.gcuts.mgz frame 0 nErode3d 0 nErode2d 0 output brainmask.gcuts.mgz Binarizing based on threshold min 1 max +infinity binval 999 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 133851 values in range Counting number of voxels in first frame Found 133851 voxels in final mask Count: 133851 133851.000000 16777216 0.797814 mri_binarize done cp brainmask.auto.mgz brainmask.mgz Started at Wed Jul 20 15:33:18 EDT 2016 Ended at Wed Jul 20 15:34:25 EDT 2016 #@#%# recon-all-run-time-hours 0.019 recon-all -s AD18 finished without error at Wed Jul 20 15:34:25 EDT 2016