Wed Jul 6 13:11:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 /usr/local/freesurfer/stable6/bin/recon-all -all -nuintensitycor-3T -subjid AD01 -i /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD01/AD01_MR.nii subjid AD01 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-20160705 Linux compute-0-92 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 29360128 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877324 3441116 29436208 4 19956 2370588 -/+ buffers/cache: 1050572 31826752 Swap: 67108860 97580 67011280 pbsjob 11868605.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: 2016/07/06-17:11:42-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:43-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: tkregister2.c,v 1.132 2016/05/04 22:17:15 greve Exp $ User: fdu0 Machine: compute-0-92 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 1.12.0, 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: stable6 $ TimeStamp: 2016/07/06-17:11:44-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:44-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:44-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:44-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_label2label.c,v 1.48 2016/03/16 23:36:50 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_ca_register.c,v 1.96 2016/04/30 02:37:04 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:45-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_ca_label.c,v 1.113 2016/05/13 18:02:49 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:46-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:46-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:46-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:46-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:46-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:47-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:47-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:47-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:47-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:47-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:48-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:48-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:48-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:48-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:48-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:49-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:49-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:49-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:49-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:49-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:50-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:50-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:50-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:50-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:51-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:51-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: fdu0 Machine: compute-0-92 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: 2016/07/06-17:11:51-GMT BuildTimeStamp: Jul 5 2016 17:25:45 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: fdu0 Machine: compute-0-92 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 ####################################### /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD01/AD01_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/orig/001.mgz mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/MR/AD01/AD01_MR.nii /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/AD01_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/AD01/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Jul 6 13:11:56 EDT 2016 Found 1 runs /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/orig/001.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_convert /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/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/AD01/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/talairach.xfm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/orig.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jul 6 13:12:08 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/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-0-92 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 Wed Jul 6 13:12:08 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.5141 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5141/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5141/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.5141/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jul 6 13:12:12 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.5141/nu0.mnc ./tmp.mri_nu_correct.mni.5141/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5141/0/ -iterations 1000 -distance 50 [fdu0@compute-0-92:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/] [2016-07-06 13:12:12] 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.5141/0/ ./tmp.mri_nu_correct.mni.5141/nu0.mnc ./tmp.mri_nu_correct.mni.5141/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 Number of iterations: 28 CV of field change: 0.000989069 mri_convert ./tmp.mri_nu_correct.mni.5141/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.5141/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.5141/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... Wed Jul 6 13:13:21 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 Wed Jul 6 13:13:21 EDT 2016 Ended at Wed Jul 6 13:14:37 EDT 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Jul 6 13:14:39 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4617, pval=0.1049 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6/bin/extract_talairach_avi_QA.awk /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/talairach_avi.log TalAviQA: 0.97655 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Jul 6 13:14:39 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/AD01/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-0-92 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 Wed Jul 6 13:14:39 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.5866 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5866/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5866/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.5866/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jul 6 13:14:43 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.5866/nu0.mnc ./tmp.mri_nu_correct.mni.5866/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5866/0/ -iterations 1000 -distance 50 [fdu0@compute-0-92:/autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/] [2016-07-06 13:14:43] 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.5866/0/ ./tmp.mri_nu_correct.mni.5866/nu0.mnc ./tmp.mri_nu_correct.mni.5866/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 Number of iterations: 28 CV of field change: 0.000989069 mri_binarize --i ./tmp.mri_nu_correct.mni.5866/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5866/ones.mgz $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/AD01/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5866/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5866/ones.mgz sysname Linux hostname compute-0-92 machine x86_64 user fdu0 input ./tmp.mri_nu_correct.mni.5866/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5866/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.5866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5866/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.5866/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5866/input.mean.dat sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5866/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.5866/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5866/ones.mgz --i ./tmp.mri_nu_correct.mni.5866/nu1.mnc --sum ./tmp.mri_nu_correct.mni.5866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5866/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.5866/ones.mgz --i ./tmp.mri_nu_correct.mni.5866/nu1.mnc --sum ./tmp.mri_nu_correct.mni.5866/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5866/output.mean.dat sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5866/ones.mgz Loading ./tmp.mri_nu_correct.mni.5866/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.5866/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5866/nu1.mnc ./tmp.mri_nu_correct.mni.5866/nu1.mnc mul 1.01955756308003457780 Saving result to './tmp.mri_nu_correct.mni.5866/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5866/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5866/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.5866/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, 98) to ( 3, 110) Wed Jul 6 13:16:33 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Jul 6 13:16:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.06925 0.03739 0.04659 1.29732; -0.08401 1.00740 0.49779 2.87946; -0.01499 -0.53716 1.09725 15.20784; 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 = 15 Starting OpenSpline(): npoints = 15 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 90 gm peak at 62 (62), valley at 19 (19) csf peak at 16, setting threshold to 46 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 86 (86), valley at 49 (49) csf peak at 31, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 9 seconds. #-------------------------------------------- #@# Skull Stripping Wed Jul 6 13:19:45 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = (49, 41, 33) --> (212, 255, 225) using (103, 112, 129) as brain centroid... mean wm in atlas = 108, using box (83,86,105) --> (123, 138,152) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 7.6 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -4.731 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.587849 @ (-9.091, 9.091, -27.273) max log p = -4.537642 @ (4.545, -4.545, 4.545) max log p = -4.537642 @ (0.000, 0.000, 0.000) max log p = -4.529351 @ (-1.136, 1.136, 1.136) max log p = -4.519840 @ (3.977, 0.568, -3.977) max log p = -4.504059 @ (-2.557, 0.284, 0.284) Found translation: (-4.3, 6.5, -25.3): log p = -4.504 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.248, old_max_log_p =-4.504 (thresh=-4.5) 1.07500 0.00000 0.00000 -13.94662; 0.00000 1.14215 0.47309 -69.68526; 0.00000 -0.44009 1.06246 33.40150; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.223, old_max_log_p =-4.248 (thresh=-4.2) 1.06580 0.05744 -0.13868 -2.64038; 0.00000 1.22781 0.50857 -85.57472; 0.12979 -0.40360 0.97437 23.06818; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.220, old_max_log_p =-4.223 (thresh=-4.2) 1.07363 0.00427 -0.01031 -13.01685; 0.00000 1.22781 0.50857 -85.57472; -0.01043 -0.40764 0.98413 40.46393; 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=-4.134, old_max_log_p =-4.220 (thresh=-4.2) 1.03126 0.07143 -0.05455 -12.54122; -0.03439 1.29605 0.53965 -92.20695; 0.06205 -0.42173 1.01815 26.74645; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.134 (thresh=-4.1) 1.03183 0.02898 -0.07218 -4.79890; -0.00063 1.29769 0.53757 -94.70260; 0.06205 -0.42173 1.01815 28.62145; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.129 (thresh=-4.1) 1.03183 0.02898 -0.07218 -4.79890; -0.00063 1.29769 0.53757 -94.70260; 0.06205 -0.42173 1.01815 28.62145; 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=-4.096, old_max_log_p =-4.129 (thresh=-4.1) 1.03266 0.03275 -0.05117 -7.13099; -0.00945 1.30393 0.53089 -94.45788; 0.04531 -0.41297 1.02716 28.52236; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.096, old_max_log_p =-4.096 (thresh=-4.1) 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 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 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.096 (old=-4.731) transform before final EM align: 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 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 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.03266 0.03275 -0.05117 -7.13099; -0.00944 1.30240 0.53027 -94.18057; 0.04536 -0.41345 1.02837 28.42580; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1218.432770 mri_em_register stimesec 1.552763 mri_em_register ru_maxrss 609772 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157517 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 66 mri_em_register ru_nivcsw 7369 registration took 20 minutes and 20 seconds. mri_watershed -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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=130 y=117 z=122 r=85 first estimation of the main basin volume: 2658284 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=107, y=112, z=86, Imax=255 CSF=21, 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=676967720 voxels, voxel volume =1.000 = 676967720 mmm3 = 676967.744 cm3 done. PostAnalyze...Basin Prior 10 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=130,y=120, z=117, r=9364 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=69 , nb = 44670 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = -1028193570 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = -1049414910 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=74 , nb = -1085321003 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=85 , nb = 1063594842 OTHER CSF_MIN=6, CSF_intensity=28, CSF_MAX=61 , nb = 1082752914 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 69, 53, 44, 82 after analyzing : 32, 53, 53, 60 RIGHT_CER before analyzing : 16, 28, 56, 86 after analyzing : 16, 46, 56, 56 LEFT_CER before analyzing : 23, 35, 53, 82 after analyzing : 23, 47, 53, 55 RIGHT_BRAIN before analyzing : 74, 53, 42, 82 after analyzing : 40, 53, 53, 60 LEFT_BRAIN before analyzing : 85, 45, 11, 83 after analyzing : 27, 45, 45, 54 OTHER before analyzing : 61, 67, 70, 85 after analyzing : 61, 69, 70, 73 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...67 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 64.566, std = 7.407 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.32, sigma = 15.00 after rotation: sse = 7.32, sigma = 15.00 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.50, its var is 17.02 before Erosion-Dilatation 7.47% of inacurate vertices after Erosion-Dilatation 13.50% 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...48 iterations mri_strip_skull: done peeling brain Brain Size = 1417328 voxels, voxel volume = 1.000 mm3 = 1417328 mmm3 = 1417.328 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 29.141569 mri_watershed stimesec 0.487925 mri_watershed ru_maxrss 835244 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 214765 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 92 mri_watershed ru_nivcsw 42 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Jul 6 13:40:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_em_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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=21.0 skull bounding box = (63, 57, 47) --> (197, 191, 199) using (108, 102, 123) as brain centroid... mean wm in atlas = 107, using box (92,86,104) --> (124, 118,141) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 5.5 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.348 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.140411 @ (-9.091, 9.091, -27.273) max log p = -3.996524 @ (4.545, -4.545, 13.636) max log p = -3.996524 @ (0.000, 0.000, 0.000) max log p = -3.960246 @ (-1.136, -3.409, -10.227) max log p = -3.956098 @ (0.568, -0.568, -0.568) max log p = -3.950836 @ (-0.852, -0.852, 1.420) Found translation: (-6.0, -0.3, -23.0): log p = -3.951 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.779, old_max_log_p =-3.951 (thresh=-3.9) 1.07500 0.00000 0.00000 -15.91865; 0.00000 0.99317 0.41138 -46.91693; 0.00000 -0.41138 0.99317 35.54391; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.762, old_max_log_p =-3.779 (thresh=-3.8) 0.98587 0.11991 0.04967 -24.15785; -0.15084 1.05852 0.43846 -37.83706; 0.00000 -0.41138 0.99317 35.54391; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-3.762 (thresh=-3.8) 1.07191 -0.02072 -0.00858 -12.03985; -0.01930 0.98524 0.40810 -43.02767; 0.00000 -0.41138 0.99317 35.54391; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-3.745 (thresh=-3.7) 1.07191 -0.02072 -0.00858 -12.03985; -0.01930 0.98524 0.40810 -43.02767; 0.00000 -0.41138 0.99317 35.54391; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.657, old_max_log_p =-3.745 (thresh=-3.7) 1.01207 -0.03003 -0.05049 3.75718; 0.01903 0.95572 0.55463 -61.85587; 0.03217 -0.56915 0.98277 53.05975; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.657 (thresh=-3.7) 1.03104 -0.03059 -0.05143 1.45132; 0.01830 0.99209 0.53197 -63.40742; 0.03216 -0.52749 0.98163 48.25368; 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=-3.623, old_max_log_p =-3.654 (thresh=-3.7) 1.03272 -0.04232 -0.06851 3.69661; 0.03573 0.98399 0.54742 -67.01549; 0.04044 -0.54567 0.97584 49.54727; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.620, old_max_log_p =-3.623 (thresh=-3.6) 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 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 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.620 (old=-4.348) transform before final EM align: 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 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 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000 final transform: 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1066.843815 mri_em_register stimesec 1.396787 mri_em_register ru_maxrss 599000 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158903 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 42 mri_em_register ru_nivcsw 2719 registration took 17 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Wed Jul 6 13:58:25 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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=20.0 skull bounding box = (63, 57, 47) --> (197, 191, 200) using (108, 102, 124) as brain centroid... mean wm in atlas = 107, using box (92,86,105) --> (124, 118,142) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 5.5 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48176; 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 (129, 58, 54) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 204 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 59, 57) --> (134, 168, 196) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 195 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 147, 90) --> (182, 185, 137) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 0 of 36 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 147, 88) --> (133, 185, 138) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 6 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 129, 114) --> (151, 188, 145) Brain_Stem: limiting intensities to 91.0 --> 132.0 0 of 94 (0.0%) samples deleted using 535 total control points for intensity normalization... bias field = 0.900 +- 0.091 0 of 535 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 58, 54) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 370 (0.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 59, 57) --> (134, 168, 196) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 391 (1.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 147, 90) --> (182, 185, 137) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 67 (23.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 147, 88) --> (133, 185, 138) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 54 of 56 (96.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 129, 114) --> (151, 188, 145) Brain_Stem: limiting intensities to 88.0 --> 132.0 33 of 119 (27.7%) samples deleted using 1003 total control points for intensity normalization... bias field = 1.009 +- 0.072 2 of 873 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (129, 58, 54) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 398 (1.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 59, 57) --> (134, 168, 196) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 433 (1.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (133, 147, 90) --> (182, 185, 137) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 90 (35.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (91, 147, 88) --> (133, 185, 138) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 61 of 65 (93.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 129, 114) --> (151, 188, 145) Brain_Stem: limiting intensities to 88.0 --> 132.0 52 of 149 (34.9%) samples deleted using 1135 total control points for intensity normalization... bias field = 1.010 +- 0.066 3 of 971 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Wed Jul 6 14:00:06 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_ca_register -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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) = 1.31 (predicted orig area = 6.1) 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=0.916, neg=0, invalid=4512 0001: dt=297.840745, rms=0.816 (10.962%), neg=0, invalid=4512 0002: dt=187.247525, rms=0.789 (3.277%), neg=0, invalid=4512 0003: dt=268.032902, rms=0.774 (1.954%), neg=0, invalid=4512 0004: dt=160.960000, rms=0.764 (1.255%), neg=0, invalid=4512 0005: dt=369.920000, rms=0.757 (0.948%), neg=0, invalid=4512 0006: dt=137.142857, rms=0.750 (0.841%), neg=0, invalid=4512 0007: dt=517.888000, rms=0.745 (0.709%), neg=0, invalid=4512 0008: dt=136.000000, rms=0.740 (0.637%), neg=0, invalid=4512 0009: dt=443.904000, rms=0.738 (0.335%), neg=0, invalid=4512 0010: dt=142.117647, rms=0.735 (0.428%), neg=0, invalid=4512 0011: dt=369.920000, rms=0.733 (0.204%), neg=0, invalid=4512 0012: dt=369.920000, rms=0.733 (0.077%), neg=0, invalid=4512 0013: dt=369.920000, rms=0.732 (0.043%), neg=0, invalid=4512 0014: dt=369.920000, rms=0.725 (1.036%), neg=0, invalid=4512 0015: dt=369.920000, rms=0.718 (1.001%), neg=0, invalid=4512 0016: dt=369.920000, rms=0.714 (0.508%), neg=0, invalid=4512 0017: dt=369.920000, rms=0.709 (0.652%), neg=0, invalid=4512 0018: dt=369.920000, rms=0.709 (-0.066%), neg=0, invalid=4512 0019: dt=73.984000, rms=0.709 (0.089%), neg=0, invalid=4512 0020: dt=92.480000, rms=0.709 (0.018%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=4512 0021: dt=129.472000, rms=0.707 (0.285%), neg=0, invalid=4512 0022: dt=295.936000, rms=0.706 (0.118%), neg=0, invalid=4512 0023: dt=295.936000, rms=0.705 (0.123%), neg=0, invalid=4512 0024: dt=295.936000, rms=0.704 (0.123%), neg=0, invalid=4512 0025: dt=295.936000, rms=0.703 (0.131%), neg=0, invalid=4512 0026: dt=295.936000, rms=0.702 (0.142%), neg=0, invalid=4512 0027: dt=295.936000, rms=0.701 (0.148%), neg=0, invalid=4512 0028: dt=295.936000, rms=0.700 (0.175%), neg=0, invalid=4512 0029: dt=295.936000, rms=0.699 (0.194%), neg=0, invalid=4512 0030: dt=295.936000, rms=0.698 (0.151%), neg=0, invalid=4512 0031: dt=295.936000, rms=0.696 (0.202%), neg=0, invalid=4512 0032: dt=295.936000, rms=0.695 (0.208%), neg=0, invalid=4512 0033: dt=295.936000, rms=0.694 (0.188%), neg=0, invalid=4512 0034: dt=295.936000, rms=0.692 (0.179%), neg=0, invalid=4512 0035: dt=295.936000, rms=0.691 (0.219%), neg=0, invalid=4512 0036: dt=295.936000, rms=0.690 (0.188%), neg=0, invalid=4512 0037: dt=295.936000, rms=0.689 (0.122%), neg=0, invalid=4512 0038: dt=295.936000, rms=0.688 (0.148%), neg=0, invalid=4512 0039: dt=295.936000, rms=0.686 (0.193%), neg=0, invalid=4512 0040: dt=295.936000, rms=0.686 (0.068%), neg=0, invalid=4512 0041: dt=295.936000, rms=0.685 (0.086%), neg=0, invalid=4512 0042: dt=295.936000, rms=0.684 (0.184%), neg=0, invalid=4512 0043: dt=295.936000, rms=0.683 (0.100%), neg=0, invalid=4512 0044: dt=295.936000, rms=0.683 (0.034%), neg=0, invalid=4512 0045: dt=369.920000, rms=0.682 (0.102%), neg=0, invalid=4512 0046: dt=8.092000, rms=0.682 (-0.004%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.691, neg=0, invalid=4512 0047: dt=60.540541, rms=0.689 (0.335%), neg=0, invalid=4512 0048: dt=331.776000, rms=0.681 (1.072%), neg=0, invalid=4512 0049: dt=123.818512, rms=0.673 (1.200%), neg=0, invalid=4512 0050: dt=75.377778, rms=0.670 (0.436%), neg=0, invalid=4512 0051: dt=90.170040, rms=0.668 (0.342%), neg=0, invalid=4512 0052: dt=92.016064, rms=0.666 (0.320%), neg=0, invalid=4512 0053: dt=71.344262, rms=0.664 (0.215%), neg=0, invalid=4512 0054: dt=71.344262, rms=0.663 (0.243%), neg=0, invalid=4512 0055: dt=71.344262, rms=0.661 (0.313%), neg=0, invalid=4512 0056: dt=71.344262, rms=0.658 (0.451%), neg=0, invalid=4512 0057: dt=71.344262, rms=0.655 (0.467%), neg=0, invalid=4512 0058: dt=71.344262, rms=0.651 (0.603%), neg=0, invalid=4512 0059: dt=71.344262, rms=0.647 (0.514%), neg=0, invalid=4512 0060: dt=71.344262, rms=0.646 (0.188%), neg=0, invalid=4512 0061: dt=71.344262, rms=0.646 (0.057%), neg=0, invalid=4512 0062: dt=71.344262, rms=0.642 (0.618%), neg=0, invalid=4512 0063: dt=71.344262, rms=0.641 (0.088%), neg=0, invalid=4512 0064: dt=71.344262, rms=0.641 (-0.142%), neg=0, invalid=4512 0065: dt=16.164948, rms=0.641 (0.064%), neg=0, invalid=4512 0066: dt=6.480000, rms=0.641 (0.003%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.641, neg=0, invalid=4512 0067: dt=94.100457, rms=0.639 (0.405%), neg=0, invalid=4512 0068: dt=36.288000, rms=0.638 (0.091%), neg=0, invalid=4512 0069: dt=36.288000, rms=0.638 (0.042%), neg=0, invalid=4512 0070: dt=36.288000, rms=0.637 (0.067%), neg=0, invalid=4512 0071: dt=36.288000, rms=0.637 (0.071%), neg=0, invalid=4512 0072: dt=36.288000, rms=0.637 (0.059%), neg=0, invalid=4512 0073: dt=36.288000, rms=0.636 (0.053%), neg=0, invalid=4512 0074: dt=145.152000, rms=0.636 (0.078%), neg=0, invalid=4512 0075: dt=36.288000, rms=0.636 (0.030%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=4512 0076: dt=2.800000, rms=0.662 (0.118%), neg=0, invalid=4512 0077: dt=2.800000, rms=0.662 (0.014%), neg=0, invalid=4512 0078: dt=2.800000, rms=0.662 (0.002%), neg=0, invalid=4512 0079: dt=2.800000, rms=0.662 (-0.033%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=4512 0080: dt=0.175000, rms=0.662 (0.101%), neg=0, invalid=4512 0081: dt=0.100000, rms=0.662 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.736, neg=0, invalid=4512 0082: dt=6.281938, rms=0.718 (2.392%), neg=0, invalid=4512 0083: dt=3.456000, rms=0.717 (0.127%), neg=0, invalid=4512 0084: dt=3.456000, rms=0.717 (-0.019%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.718, neg=0, invalid=4512 0085: dt=0.000000, rms=0.717 (0.075%), neg=0, invalid=4512 0086: dt=0.000000, rms=0.717 (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=0.798, neg=0, invalid=4512 0087: dt=0.448000, rms=0.797 (0.158%), neg=0, invalid=4512 0088: dt=0.768000, rms=0.796 (0.115%), neg=0, invalid=4512 0089: dt=0.768000, rms=0.794 (0.191%), neg=0, invalid=4512 0090: dt=0.768000, rms=0.793 (0.183%), neg=0, invalid=4512 0091: dt=0.768000, rms=0.793 (0.024%), neg=0, invalid=4512 0092: dt=0.768000, rms=0.793 (-0.208%), neg=0, invalid=4512 0093: dt=5.120000, rms=0.787 (0.717%), neg=0, invalid=4512 0094: dt=0.320000, rms=0.787 (0.015%), neg=0, invalid=4512 0095: dt=0.320000, rms=0.787 (-0.012%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.787, neg=0, invalid=4512 0096: dt=0.448000, rms=0.787 (0.106%), neg=0, invalid=4512 0097: dt=0.096000, rms=0.787 (0.001%), neg=0, invalid=4512 0098: dt=0.096000, rms=0.787 (-0.001%), 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=0.724, neg=0, invalid=4512 0099: dt=0.918127, rms=0.704 (2.785%), neg=0, invalid=4512 0100: dt=0.096000, rms=0.703 (0.176%), neg=0, invalid=4512 0101: dt=0.096000, rms=0.703 (-0.088%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=4512 0102: dt=0.028000, rms=0.703 (0.098%), neg=0, invalid=4512 0103: dt=0.016000, rms=0.703 (0.003%), neg=0, invalid=4512 0104: dt=0.016000, rms=0.703 (-0.003%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.08817 (22) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1912 voxels, overlap=0.712) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1912 voxels, peak = 22), gca=22.5 gca peak = 0.15565 (16) mri peak = 0.10874 (21) Right_Lateral_Ventricle (43): linear fit = 1.30 x + 0.0 (1069 voxels, overlap=0.662) Right_Lateral_Ventricle (43): linear fit = 1.30 x + 0.0 (1069 voxels, peak = 21), gca=20.9 gca peak = 0.26829 (96) mri peak = 0.06926 (101) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (706 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (706 voxels, peak = 100), gca=100.3 gca peak = 0.20183 (93) mri peak = 0.08028 (93) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (721 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (721 voxels, peak = 92), gca=91.6 gca peak = 0.21683 (55) mri peak = 0.04948 (73) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (662 voxels, overlap=0.016) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (662 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.08397 (75) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (520 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (520 voxels, peak = 75), gca=74.5 gca peak = 0.11430 (101) mri peak = 0.08998 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (52177 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (52177 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.08468 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (53013 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (53013 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03425 (78) Left_Cerebral_Cortex (3): linear fit = 1.49 x + 0.0 (17657 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.49 x + 0.0 (17657 voxels, peak = 88), gca=87.6 gca peak = 0.15082 (58) mri peak = 0.03769 (84) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (18554 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (18554 voxels, peak = 81), gca=81.5 gca peak = 0.14161 (67) mri peak = 0.09591 (95) Right_Caudate (50): linear fit = 1.40 x + 0.0 (478 voxels, overlap=0.121) Right_Caudate (50): linear fit = 1.40 x + 0.0 (478 voxels, peak = 94), gca=94.1 gca peak = 0.15243 (71) mri peak = 0.09976 (76) Left_Caudate (11): linear fit = 1.05 x + 0.0 (394 voxels, overlap=0.685) Left_Caudate (11): linear fit = 1.05 x + 0.0 (394 voxels, peak = 75), gca=74.9 gca peak = 0.13336 (57) mri peak = 0.05090 (75) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (14950 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (14950 voxels, peak = 77), gca=76.7 gca peak = 0.13252 (56) mri peak = 0.04072 (82) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (20383 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (20383 voxels, peak = 81), gca=81.5 gca peak = 0.18181 (84) mri peak = 0.05249 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7202 voxels, overlap=0.098) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7202 voxels, peak = 91), gca=91.1 gca peak = 0.20573 (83) mri peak = 0.04742 (72) Right_Cerebellum_White_Matter (46): linear fit = 0.93 x + 0.0 (5752 voxels, overlap=0.418) Right_Cerebellum_White_Matter (46): linear fit = 0.93 x + 0.0 (5752 voxels, peak = 77), gca=76.8 gca peak = 0.21969 (57) mri peak = 0.10685 (75) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (367 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (367 voxels, peak = 73), gca=72.7 gca peak = 0.39313 (56) mri peak = 0.10264 (68) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (346 voxels, overlap=0.040) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (346 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.06178 (93) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4669 voxels, overlap=0.763) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4669 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.07302 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3075 voxels, overlap=0.852) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3075 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.08684 (87) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2187 voxels, overlap=0.255) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2187 voxels, peak = 88), gca=88.1 gca peak = 0.14159 (79) mri peak = 0.06961 (86) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2174 voxels, overlap=0.339) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2174 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.08901 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (7531 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.11 x + 0.0 (7531 voxels, peak = 88), gca=88.4 gca peak = 0.13281 (86) mri peak = 0.08791 (93) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (727 voxels, overlap=0.459) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (727 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.07590 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (999 voxels, overlap=0.429) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (999 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.09790 (27) gca peak = 0.15061 (21) mri peak = 0.09742 (27) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (581 voxels, overlap=0.302) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (581 voxels, peak = 35), gca=34.8 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 1.32 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.21 x + 0.0 Right_Pallidum too bright - rescaling by 1.006 (from 1.045) to 100.9 (was 100.3) 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=0.778, neg=0, invalid=4512 0105: dt=101.270588, rms=0.751 (3.397%), neg=0, invalid=4512 0106: dt=181.735849, rms=0.744 (0.997%), neg=0, invalid=4512 0107: dt=517.888000, rms=0.727 (2.261%), neg=0, invalid=4512 0108: dt=27.744000, rms=0.727 (0.009%), neg=0, invalid=4512 0109: dt=27.744000, rms=0.727 (0.008%), neg=0, invalid=4512 0110: dt=27.744000, rms=0.727 (0.010%), neg=0, invalid=4512 0111: dt=27.744000, rms=0.727 (0.013%), neg=0, invalid=4512 0112: dt=27.744000, rms=0.727 (0.026%), neg=0, invalid=4512 0113: dt=27.744000, rms=0.726 (0.062%), neg=0, invalid=4512 0114: dt=27.744000, rms=0.725 (0.121%), neg=0, invalid=4512 0115: dt=27.744000, rms=0.724 (0.184%), neg=0, invalid=4512 0116: dt=27.744000, rms=0.722 (0.236%), neg=0, invalid=4512 0117: dt=27.744000, rms=0.720 (0.263%), neg=0, invalid=4512 0118: dt=27.744000, rms=0.718 (0.262%), neg=0, invalid=4512 0119: dt=27.744000, rms=0.717 (0.239%), neg=0, invalid=4512 0120: dt=27.744000, rms=0.715 (0.205%), neg=0, invalid=4512 0121: dt=27.744000, rms=0.714 (0.168%), neg=0, invalid=4512 0122: dt=27.744000, rms=0.713 (0.128%), neg=0, invalid=4512 0123: dt=27.744000, rms=0.712 (0.094%), neg=0, invalid=4512 0124: dt=27.744000, rms=0.712 (0.068%), neg=0, invalid=4512 0125: dt=27.744000, rms=0.712 (0.057%), neg=0, invalid=4512 0126: dt=27.744000, rms=0.711 (0.062%), neg=0, invalid=4512 0127: dt=27.744000, rms=0.711 (0.081%), neg=0, invalid=4512 0128: dt=27.744000, rms=0.710 (0.108%), neg=0, invalid=4512 0129: dt=27.744000, rms=0.709 (0.133%), neg=0, invalid=4512 0130: dt=27.744000, rms=0.708 (0.152%), neg=0, invalid=4512 0131: dt=27.744000, rms=0.707 (0.160%), neg=0, invalid=4512 0132: dt=27.744000, rms=0.706 (0.160%), neg=0, invalid=4512 0133: dt=27.744000, rms=0.704 (0.150%), neg=0, invalid=4512 0134: dt=27.744000, rms=0.704 (0.135%), neg=0, invalid=4512 0135: dt=27.744000, rms=0.703 (0.120%), neg=0, invalid=4512 0136: dt=27.744000, rms=0.702 (0.107%), neg=0, invalid=4512 0137: dt=27.744000, rms=0.701 (0.094%), neg=0, invalid=4512 0138: dt=27.744000, rms=0.701 (0.086%), neg=0, invalid=4512 0139: dt=27.744000, rms=0.700 (0.084%), neg=0, invalid=4512 0140: dt=27.744000, rms=0.699 (0.086%), neg=0, invalid=4512 0141: dt=27.744000, rms=0.699 (0.092%), neg=0, invalid=4512 0142: dt=27.744000, rms=0.698 (0.100%), neg=0, invalid=4512 0143: dt=27.744000, rms=0.697 (0.107%), neg=0, invalid=4512 0144: dt=27.744000, rms=0.697 (0.111%), neg=0, invalid=4512 0145: dt=27.744000, rms=0.696 (0.110%), neg=0, invalid=4512 0146: dt=27.744000, rms=0.695 (0.107%), neg=0, invalid=4512 0147: dt=27.744000, rms=0.694 (0.100%), neg=0, invalid=4512 0148: dt=27.744000, rms=0.694 (0.091%), neg=0, invalid=4512 0149: dt=27.744000, rms=0.693 (0.083%), neg=0, invalid=4512 0150: dt=27.744000, rms=0.693 (0.074%), neg=0, invalid=4512 0151: dt=27.744000, rms=0.692 (0.069%), neg=0, invalid=4512 0152: dt=27.744000, rms=0.692 (0.065%), neg=0, invalid=4512 0153: dt=27.744000, rms=0.691 (0.065%), neg=0, invalid=4512 0154: dt=27.744000, rms=0.691 (0.066%), neg=0, invalid=4512 0155: dt=27.744000, rms=0.690 (0.067%), neg=0, invalid=4512 0156: dt=27.744000, rms=0.690 (0.070%), neg=0, invalid=4512 0157: dt=27.744000, rms=0.689 (0.071%), neg=0, invalid=4512 0158: dt=27.744000, rms=0.689 (0.071%), neg=0, invalid=4512 0159: dt=27.744000, rms=0.688 (0.069%), neg=0, invalid=4512 0160: dt=27.744000, rms=0.688 (0.065%), neg=0, invalid=4512 0161: dt=27.744000, rms=0.688 (0.061%), neg=0, invalid=4512 0162: dt=27.744000, rms=0.687 (0.058%), neg=0, invalid=4512 0163: dt=27.744000, rms=0.687 (0.054%), neg=0, invalid=4512 0164: dt=27.744000, rms=0.686 (0.051%), neg=0, invalid=4512 0165: dt=27.744000, rms=0.686 (0.048%), neg=0, invalid=4512 0166: dt=27.744000, rms=0.686 (0.047%), neg=0, invalid=4512 0167: dt=27.744000, rms=0.685 (0.047%), neg=0, invalid=4512 0168: dt=27.744000, rms=0.685 (0.047%), neg=0, invalid=4512 0169: dt=27.744000, rms=0.685 (0.047%), neg=0, invalid=4512 0170: dt=27.744000, rms=0.684 (0.048%), neg=0, invalid=4512 0171: dt=27.744000, rms=0.684 (0.047%), neg=0, invalid=4512 0172: dt=27.744000, rms=0.684 (0.047%), neg=0, invalid=4512 0173: dt=27.744000, rms=0.684 (0.046%), neg=0, invalid=4512 0174: dt=27.744000, rms=0.683 (0.046%), neg=0, invalid=4512 0175: dt=27.744000, rms=0.683 (0.044%), neg=0, invalid=4512 0176: dt=27.744000, rms=0.683 (0.042%), neg=0, invalid=4512 0177: dt=27.744000, rms=0.682 (0.041%), neg=0, invalid=4512 0178: dt=27.744000, rms=0.682 (0.039%), neg=0, invalid=4512 0179: dt=27.744000, rms=0.682 (0.038%), neg=0, invalid=4512 0180: dt=27.744000, rms=0.682 (0.037%), neg=0, invalid=4512 0181: dt=27.744000, rms=0.681 (0.037%), neg=0, invalid=4512 0182: dt=27.744000, rms=0.681 (0.038%), neg=0, invalid=4512 0183: dt=27.744000, rms=0.681 (0.037%), neg=0, invalid=4512 0184: dt=27.744000, rms=0.681 (0.037%), neg=0, invalid=4512 0185: dt=27.744000, rms=0.680 (0.037%), neg=0, invalid=4512 0186: dt=27.744000, rms=0.680 (0.037%), neg=0, invalid=4512 0187: dt=27.744000, rms=0.680 (0.036%), neg=0, invalid=4512 0188: dt=27.744000, rms=0.680 (0.034%), neg=0, invalid=4512 0189: dt=27.744000, rms=0.679 (0.033%), neg=0, invalid=4512 0190: dt=27.744000, rms=0.679 (0.032%), neg=0, invalid=4512 0191: dt=27.744000, rms=0.679 (0.031%), neg=0, invalid=4512 0192: dt=27.744000, rms=0.679 (0.031%), neg=0, invalid=4512 0193: dt=27.744000, rms=0.679 (0.031%), neg=0, invalid=4512 0194: dt=27.744000, rms=0.678 (0.030%), neg=0, invalid=4512 0195: dt=27.744000, rms=0.678 (0.029%), neg=0, invalid=4512 0196: dt=27.744000, rms=0.678 (0.029%), neg=0, invalid=4512 0197: dt=27.744000, rms=0.678 (0.030%), neg=0, invalid=4512 0198: dt=27.744000, rms=0.678 (0.029%), neg=0, invalid=4512 0199: dt=27.744000, rms=0.677 (0.030%), neg=0, invalid=4512 0200: dt=27.744000, rms=0.677 (0.028%), neg=0, invalid=4512 0201: dt=27.744000, rms=0.677 (0.028%), neg=0, invalid=4512 0202: dt=27.744000, rms=0.677 (0.028%), neg=0, invalid=4512 0203: dt=27.744000, rms=0.677 (0.028%), neg=0, invalid=4512 0204: dt=27.744000, rms=0.676 (0.028%), neg=0, invalid=4512 0205: dt=27.744000, rms=0.676 (0.026%), neg=0, invalid=4512 0206: dt=27.744000, rms=0.676 (0.026%), neg=0, invalid=4512 0207: dt=27.744000, rms=0.676 (0.027%), neg=0, invalid=4512 0208: dt=27.744000, rms=0.676 (0.026%), neg=0, invalid=4512 0209: dt=27.744000, rms=0.675 (0.026%), neg=0, invalid=4512 0210: dt=27.744000, rms=0.675 (0.025%), neg=0, invalid=4512 0211: dt=27.744000, rms=0.675 (0.025%), neg=0, invalid=4512 0212: dt=27.744000, rms=0.675 (0.025%), neg=0, invalid=4512 0213: dt=27.744000, rms=0.675 (0.025%), neg=0, invalid=4512 0214: dt=18939.904000, rms=0.669 (0.882%), neg=0, invalid=4512 0215: dt=110.976000, rms=0.666 (0.453%), neg=0, invalid=4512 0216: dt=92.480000, rms=0.666 (0.040%), neg=0, invalid=4512 0217: dt=92.480000, rms=0.665 (0.009%), neg=0, invalid=4512 0218: dt=92.480000, rms=0.665 (-0.013%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.666, neg=0, invalid=4512 0219: dt=517.888000, rms=0.663 (0.441%), neg=0, invalid=4512 0220: dt=55.488000, rms=0.663 (0.009%), neg=0, invalid=4512 0221: dt=55.488000, rms=0.663 (0.002%), neg=0, invalid=4512 0222: dt=55.488000, rms=0.663 (-0.007%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.666, neg=0, invalid=4512 0223: dt=145.152000, rms=0.661 (0.747%), neg=0, invalid=4512 0224: dt=231.489362, rms=0.649 (1.737%), neg=0, invalid=4512 0225: dt=73.142857, rms=0.645 (0.648%), neg=0, invalid=4512 0226: dt=36.288000, rms=0.643 (0.218%), neg=0, invalid=4512 0227: dt=36.288000, rms=0.642 (0.177%), neg=0, invalid=4512 0228: dt=7.776000, rms=0.642 (0.038%), neg=0, invalid=4512 0229: dt=0.486000, rms=0.642 (0.002%), neg=0, invalid=4512 0230: dt=0.243000, rms=0.642 (0.001%), neg=0, invalid=4512 0231: dt=0.121500, rms=0.642 (0.001%), neg=0, invalid=4512 0232: dt=0.035437, rms=0.642 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.642, neg=0, invalid=4512 0233: dt=234.170543, rms=0.636 (1.009%), neg=0, invalid=4512 0234: dt=124.416000, rms=0.632 (0.665%), neg=0, invalid=4512 0235: dt=116.760976, rms=0.629 (0.423%), neg=0, invalid=4512 0236: dt=98.461538, rms=0.627 (0.325%), neg=0, invalid=4512 0237: dt=117.760000, rms=0.625 (0.310%), neg=0, invalid=4512 0238: dt=87.355450, rms=0.623 (0.267%), neg=0, invalid=4512 0239: dt=36.288000, rms=0.622 (0.145%), neg=0, invalid=4512 0240: dt=31.104000, rms=0.622 (0.083%), neg=0, invalid=4512 0241: dt=2.268000, rms=0.622 (0.006%), neg=0, invalid=4512 0242: dt=0.141750, rms=0.622 (0.000%), neg=0, invalid=4512 0243: dt=0.070875, rms=0.622 (0.000%), neg=0, invalid=4512 0244: dt=0.035437, rms=0.622 (0.000%), neg=0, invalid=4512 0245: dt=0.030375, rms=0.622 (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=0.631, neg=0, invalid=4512 0246: dt=0.002344, rms=0.631 (0.054%), neg=0, invalid=4512 0247: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=4512 0248: dt=0.000244, rms=0.631 (0.000%), neg=0, invalid=4512 0249: dt=0.000008, rms=0.631 (0.000%), neg=0, invalid=4512 0250: dt=0.000004, rms=0.631 (0.000%), neg=0, invalid=4512 0251: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=4512 0252: dt=44.800000, rms=0.613 (2.954%), neg=0, invalid=4512 0253: dt=44.800000, rms=0.600 (2.063%), neg=0, invalid=4512 0254: dt=11.200000, rms=0.598 (0.375%), neg=0, invalid=4512 0255: dt=8.000000, rms=0.596 (0.262%), neg=0, invalid=4512 0256: dt=0.175000, rms=0.596 (0.005%), neg=0, invalid=4512 0257: dt=0.175000, rms=0.596 (0.005%), neg=0, invalid=4512 0258: dt=0.087500, rms=0.596 (0.003%), neg=0, invalid=4512 0259: dt=0.010937, rms=0.596 (0.000%), neg=0, invalid=4512 0260: dt=0.002734, rms=0.596 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=4512 0261: dt=11.520000, rms=0.605 (2.997%), neg=0, invalid=4512 0262: dt=3.456000, rms=0.602 (0.481%), neg=0, invalid=4512 0263: dt=0.063000, rms=0.602 (0.007%), neg=0, invalid=4512 0264: dt=0.063000, rms=0.602 (0.008%), neg=0, invalid=4512 0265: dt=0.031500, rms=0.602 (0.004%), neg=0, invalid=4512 0266: dt=0.015750, rms=0.602 (0.002%), neg=0, invalid=4512 0267: dt=0.003938, rms=0.602 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=4512 0268: dt=0.000984, rms=0.602 (0.041%), neg=0, invalid=4512 0269: dt=0.000630, rms=0.602 (0.000%), neg=0, invalid=4512 0270: dt=0.000020, rms=0.602 (0.000%), neg=0, invalid=4512 0271: dt=0.000005, rms=0.602 (0.000%), neg=0, invalid=4512 0272: dt=0.000002, rms=0.602 (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=0.655, neg=0, invalid=4512 0273: dt=1.976744, rms=0.653 (0.359%), neg=0, invalid=4512 0274: dt=3.072000, rms=0.652 (0.175%), neg=0, invalid=4512 0275: dt=1.792000, rms=0.651 (0.087%), neg=0, invalid=4512 0276: dt=1.792000, rms=0.651 (0.085%), neg=0, invalid=4512 0277: dt=1.792000, rms=0.650 (0.079%), neg=0, invalid=4512 0278: dt=1.792000, rms=0.650 (0.076%), neg=0, invalid=4512 0279: dt=5.120000, rms=0.648 (0.189%), neg=0, invalid=4512 0280: dt=1.792000, rms=0.648 (0.070%), neg=0, invalid=4512 0281: dt=7.168000, rms=0.646 (0.234%), neg=0, invalid=4512 0282: dt=5.120000, rms=0.646 (0.136%), neg=0, invalid=4512 0283: dt=5.120000, rms=0.645 (0.157%), neg=0, invalid=4512 0284: dt=1.792000, rms=0.644 (0.052%), neg=0, invalid=4512 0285: dt=5.120000, rms=0.643 (0.129%), neg=0, invalid=4512 0286: dt=5.120000, rms=0.643 (0.127%), neg=0, invalid=4512 0287: dt=1.792000, rms=0.642 (0.041%), neg=0, invalid=4512 0288: dt=1.792000, rms=0.642 (0.041%), neg=0, invalid=4512 0289: dt=1.792000, rms=0.642 (0.072%), neg=0, invalid=4512 0290: dt=1.792000, rms=0.641 (0.102%), neg=0, invalid=4512 0291: dt=1.792000, rms=0.640 (0.112%), neg=0, invalid=4512 0292: dt=1.792000, rms=0.639 (0.120%), neg=0, invalid=4512 0293: dt=1.792000, rms=0.639 (0.107%), neg=0, invalid=4512 0294: dt=1.792000, rms=0.638 (0.096%), neg=0, invalid=4512 0295: dt=1.792000, rms=0.638 (0.077%), neg=0, invalid=4512 0296: dt=1.792000, rms=0.637 (0.067%), neg=0, invalid=4512 0297: dt=1.792000, rms=0.637 (0.066%), neg=0, invalid=4512 0298: dt=1.792000, rms=0.636 (0.067%), neg=0, invalid=4512 0299: dt=1.792000, rms=0.636 (0.071%), neg=0, invalid=4512 0300: dt=1.792000, rms=0.635 (0.072%), neg=0, invalid=4512 0301: dt=1.792000, rms=0.635 (0.074%), neg=0, invalid=4512 0302: dt=1.792000, rms=0.635 (0.072%), neg=0, invalid=4512 0303: dt=1.792000, rms=0.634 (0.072%), neg=0, invalid=4512 0304: dt=1.792000, rms=0.634 (0.079%), neg=0, invalid=4512 0305: dt=1.792000, rms=0.633 (0.081%), neg=0, invalid=4512 0306: dt=1.792000, rms=0.633 (0.079%), neg=0, invalid=4512 0307: dt=1.792000, rms=0.632 (0.078%), neg=0, invalid=4512 0308: dt=1.792000, rms=0.632 (0.077%), neg=0, invalid=4512 0309: dt=1.792000, rms=0.631 (0.072%), neg=0, invalid=4512 0310: dt=1.792000, rms=0.631 (0.068%), neg=0, invalid=4512 0311: dt=1.792000, rms=0.630 (0.064%), neg=0, invalid=4512 0312: dt=1.792000, rms=0.630 (0.060%), neg=0, invalid=4512 0313: dt=1.792000, rms=0.630 (0.055%), neg=0, invalid=4512 0314: dt=1.792000, rms=0.629 (0.051%), neg=0, invalid=4512 0315: dt=1.792000, rms=0.629 (0.043%), neg=0, invalid=4512 0316: dt=1.792000, rms=0.629 (0.036%), neg=0, invalid=4512 0317: dt=1.792000, rms=0.629 (0.031%), neg=0, invalid=4512 0318: dt=1.792000, rms=0.628 (0.027%), neg=0, invalid=4512 0319: dt=1.792000, rms=0.628 (0.026%), neg=0, invalid=4512 0320: dt=1.792000, rms=0.628 (0.020%), neg=0, invalid=4512 0321: dt=1.792000, rms=0.628 (0.019%), neg=0, invalid=4512 0322: dt=1.792000, rms=0.628 (0.004%), neg=0, invalid=4512 0323: dt=1.792000, rms=0.628 (0.002%), neg=0, invalid=4512 0324: dt=1.792000, rms=0.628 (0.001%), neg=0, invalid=4512 0325: dt=1.792000, rms=0.628 (0.004%), neg=0, invalid=4512 0326: dt=1.792000, rms=0.628 (0.004%), neg=0, invalid=4512 0327: dt=1.792000, rms=0.628 (0.006%), neg=0, invalid=4512 0328: dt=1.792000, rms=0.628 (0.004%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.628, neg=0, invalid=4512 0329: dt=7.168000, rms=0.622 (0.950%), neg=0, invalid=4512 0330: dt=0.000000, rms=0.622 (-0.002%), neg=0, invalid=4512 0331: dt=0.100000, rms=0.622 (-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=0.607, neg=0, invalid=4512 0332: dt=0.448000, rms=0.588 (3.165%), neg=0, invalid=4512 0333: dt=0.448000, rms=0.581 (1.192%), neg=0, invalid=4512 0334: dt=0.448000, rms=0.576 (0.696%), neg=0, invalid=4512 0335: dt=0.448000, rms=0.574 (0.463%), neg=0, invalid=4512 0336: dt=0.448000, rms=0.572 (0.349%), neg=0, invalid=4512 0337: dt=0.448000, rms=0.570 (0.264%), neg=0, invalid=4512 0338: dt=0.448000, rms=0.569 (0.220%), neg=0, invalid=4512 0339: dt=0.562500, rms=0.568 (0.214%), neg=0, invalid=4512 0340: dt=0.500000, rms=0.567 (0.167%), neg=0, invalid=4512 0341: dt=0.448000, rms=0.566 (0.114%), neg=0, invalid=4512 0342: dt=0.448000, rms=0.566 (0.108%), neg=0, invalid=4512 0343: dt=0.448000, rms=0.565 (0.086%), neg=0, invalid=4512 0344: dt=0.448000, rms=0.565 (0.085%), neg=0, invalid=4512 0345: dt=0.448000, rms=0.564 (0.065%), neg=0, invalid=4512 0346: dt=0.448000, rms=0.564 (0.071%), neg=0, invalid=4512 0347: dt=0.448000, rms=0.564 (0.050%), neg=0, invalid=4512 0348: dt=0.448000, rms=0.563 (0.058%), neg=0, invalid=4512 0349: dt=0.448000, rms=0.563 (0.040%), neg=0, invalid=4512 0350: dt=0.448000, rms=0.563 (0.050%), neg=0, invalid=4512 0351: dt=0.448000, rms=0.562 (0.078%), neg=0, invalid=4512 0352: dt=0.448000, rms=0.562 (0.094%), neg=0, invalid=4512 0353: dt=0.448000, rms=0.561 (0.113%), neg=0, invalid=4512 0354: dt=0.448000, rms=0.561 (0.118%), neg=0, invalid=4512 0355: dt=0.448000, rms=0.560 (0.099%), neg=0, invalid=4512 0356: dt=0.448000, rms=0.559 (0.084%), neg=0, invalid=4512 0357: dt=0.448000, rms=0.559 (0.073%), neg=0, invalid=4512 0358: dt=0.448000, rms=0.559 (0.055%), neg=0, invalid=4512 0359: dt=0.448000, rms=0.559 (0.034%), neg=0, invalid=4512 0360: dt=0.448000, rms=0.558 (0.014%), neg=0, invalid=4512 0361: dt=0.448000, rms=0.558 (0.012%), neg=0, invalid=4512 0362: dt=0.192000, rms=0.558 (0.001%), neg=0, invalid=4512 0363: dt=0.192000, rms=0.558 (0.003%), neg=0, invalid=4512 0364: dt=0.192000, rms=0.558 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=4512 0365: dt=0.448000, rms=0.553 (1.007%), neg=0, invalid=4512 0366: dt=0.448000, rms=0.553 (0.100%), neg=0, invalid=4512 0367: dt=0.448000, rms=0.552 (0.008%), neg=0, invalid=4512 0368: dt=0.448000, rms=0.552 (-0.027%), 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=0.548, neg=0, invalid=4512 0369: dt=0.000000, rms=0.548 (0.056%), neg=0, invalid=4512 0370: dt=0.000000, rms=0.548 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=4512 0371: dt=129.472000, rms=0.547 (0.202%), neg=0, invalid=4512 0372: dt=129.472000, rms=0.547 (0.035%), neg=0, invalid=4512 0373: dt=129.472000, rms=0.547 (0.044%), neg=0, invalid=4512 0374: dt=129.472000, rms=0.546 (0.062%), neg=0, invalid=4512 0375: dt=129.472000, rms=0.546 (0.041%), neg=0, invalid=4512 0376: dt=129.472000, rms=0.546 (0.037%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=4512 0377: dt=25.920000, rms=0.546 (0.144%), neg=0, invalid=4512 0378: dt=25.920000, rms=0.545 (0.043%), neg=0, invalid=4512 0379: dt=25.920000, rms=0.545 (0.041%), neg=0, invalid=4512 0380: dt=25.920000, rms=0.545 (0.022%), neg=0, invalid=4512 0381: dt=25.920000, rms=0.545 (-0.031%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=4512 0382: dt=103.680000, rms=0.540 (0.992%), neg=0, invalid=4512 0383: dt=36.288000, rms=0.539 (0.163%), neg=0, invalid=4512 0384: dt=36.288000, rms=0.539 (0.079%), neg=0, invalid=4512 0385: dt=36.288000, rms=0.538 (0.129%), neg=0, invalid=4512 0386: dt=36.288000, rms=0.537 (0.179%), neg=0, invalid=4512 0387: dt=36.288000, rms=0.536 (0.224%), neg=0, invalid=4512 0388: dt=36.288000, rms=0.534 (0.234%), neg=0, invalid=4512 0389: dt=36.288000, rms=0.533 (0.209%), neg=0, invalid=4512 0390: dt=36.288000, rms=0.532 (0.182%), neg=0, invalid=4512 0391: dt=36.288000, rms=0.531 (0.159%), neg=0, invalid=4512 0392: dt=36.288000, rms=0.531 (0.140%), neg=0, invalid=4512 0393: dt=36.288000, rms=0.530 (0.130%), neg=0, invalid=4512 0394: dt=36.288000, rms=0.529 (0.134%), neg=0, invalid=4512 0395: dt=36.288000, rms=0.529 (0.131%), neg=0, invalid=4512 0396: dt=36.288000, rms=0.528 (0.122%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0397: dt=36.288000, rms=0.527 (0.102%), neg=0, invalid=4512 0398: dt=124.416000, rms=0.527 (0.026%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=124.416000, rms=0.527 (0.013%), neg=0, invalid=4512 0400: dt=124.416000, rms=0.527 (0.016%), neg=0, invalid=4512 0401: dt=124.416000, rms=0.527 (-0.023%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.529, neg=0, invalid=4512 iter 0, gcam->neg = 6 after 0 iterations, nbhd size=0, neg = 0 0402: dt=28.972043, rms=0.526 (0.604%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0403: dt=64.231884, rms=0.522 (0.732%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0404: dt=30.735967, rms=0.519 (0.531%), neg=0, invalid=4512 iter 0, gcam->neg = 19 after 9 iterations, nbhd size=1, neg = 0 0405: dt=91.836431, rms=0.515 (0.693%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0406: dt=24.131148, rms=0.514 (0.323%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0407: dt=44.800000, rms=0.512 (0.252%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0408: dt=25.600000, rms=0.512 (0.126%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0409: dt=25.600000, rms=0.511 (0.138%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0410: dt=25.600000, rms=0.510 (0.188%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 0411: dt=25.600000, rms=0.509 (0.239%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0412: dt=25.600000, rms=0.508 (0.273%), neg=0, invalid=4512 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 0413: dt=25.600000, rms=0.506 (0.321%), neg=0, invalid=4512 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0414: dt=25.600000, rms=0.505 (0.254%), neg=0, invalid=4512 iter 0, gcam->neg = 20 after 10 iterations, nbhd size=1, neg = 0 0415: dt=25.600000, rms=0.503 (0.254%), neg=0, invalid=4512 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=1, neg = 0 0416: dt=25.600000, rms=0.502 (0.243%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0417: dt=25.600000, rms=0.501 (0.220%), neg=0, invalid=4512 iter 0, gcam->neg = 27 after 8 iterations, nbhd size=1, neg = 0 0418: dt=25.600000, rms=0.500 (0.142%), neg=0, invalid=4512 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0419: dt=25.600000, rms=0.500 (0.137%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0420: dt=25.600000, rms=0.499 (0.125%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0421: dt=25.600000, rms=0.499 (0.104%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 13 iterations, nbhd size=1, neg = 0 0422: dt=25.600000, rms=0.498 (0.043%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0423: dt=44.800000, rms=0.498 (0.053%), neg=0, invalid=4512 0424: dt=11.200000, rms=0.498 (0.012%), neg=0, invalid=4512 0425: dt=11.200000, rms=0.498 (0.012%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=11.200000, rms=0.498 (0.018%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0427: dt=11.200000, rms=0.498 (0.018%), neg=0, invalid=4512 0428: dt=11.200000, rms=0.498 (0.023%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=0, neg = 0 0429: dt=11.200000, rms=0.498 (0.018%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=4512 0430: dt=60.717949, rms=0.494 (0.816%), neg=0, invalid=4512 0431: dt=25.600000, rms=0.493 (0.185%), neg=0, invalid=4512 0432: dt=25.600000, rms=0.492 (0.074%), neg=0, invalid=4512 0433: dt=25.600000, rms=0.492 (0.119%), neg=0, invalid=4512 0434: dt=25.600000, rms=0.491 (0.112%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0435: dt=25.600000, rms=0.491 (0.065%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0436: dt=32.000000, rms=0.491 (0.035%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.505, neg=0, invalid=4512 0437: dt=0.000135, rms=0.504 (0.058%), neg=0, invalid=4512 0438: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=4512 0439: dt=2.304000, rms=0.504 (0.096%), neg=0, invalid=4512 0440: dt=1.008000, rms=0.504 (0.008%), neg=0, invalid=4512 0441: dt=1.008000, rms=0.504 (0.003%), neg=0, invalid=4512 0442: dt=1.008000, rms=0.504 (-0.013%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=4512 0443: dt=1.536000, rms=0.525 (0.448%), neg=0, invalid=4512 0444: dt=0.384000, rms=0.525 (0.018%), neg=0, invalid=4512 0445: dt=0.384000, rms=0.525 (-0.002%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=4512 0446: dt=1.536000, rms=0.524 (0.302%), neg=0, invalid=4512 0447: dt=1.024000, rms=0.524 (0.043%), neg=0, invalid=4512 0448: dt=1.024000, rms=0.524 (-0.002%), 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=0.505, neg=0, invalid=4512 iter 0, gcam->neg = 1224 after 14 iterations, nbhd size=1, neg = 0 0449: dt=2.435570, rms=0.471 (6.818%), neg=0, invalid=4512 0450: dt=0.112000, rms=0.470 (0.196%), neg=0, invalid=4512 0451: dt=0.112000, rms=0.470 (0.021%), neg=0, invalid=4512 0452: dt=0.112000, rms=0.470 (-0.329%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=4512 0453: dt=0.080000, rms=0.469 (0.111%), neg=0, invalid=4512 0454: dt=0.007000, rms=0.469 (0.000%), neg=0, invalid=4512 0455: dt=0.007000, rms=0.469 (0.000%), neg=0, invalid=4512 0456: dt=0.007000, rms=0.469 (-0.001%), neg=0, invalid=4512 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=4512 0457: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=4512 0458: dt=73.984000, rms=0.454 (0.013%), neg=0, invalid=4512 0459: dt=92.480000, rms=0.454 (0.003%), neg=0, invalid=4512 0460: dt=92.480000, rms=0.454 (0.001%), neg=0, invalid=4512 0461: dt=92.480000, rms=0.454 (-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=0.454, neg=0, invalid=4512 0462: dt=2.268000, rms=0.454 (0.001%), neg=0, invalid=4512 0463: dt=0.567000, rms=0.454 (0.000%), neg=0, invalid=4512 0464: dt=0.567000, rms=0.454 (0.000%), neg=0, invalid=4512 0465: dt=0.567000, rms=0.454 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=4512 0466: dt=145.152000, rms=0.454 (0.138%), neg=0, invalid=4512 0467: dt=145.152000, rms=0.453 (0.161%), neg=0, invalid=4512 0468: dt=36.288000, rms=0.453 (0.049%), neg=0, invalid=4512 0469: dt=36.288000, rms=0.453 (0.020%), neg=0, invalid=4512 0470: dt=36.288000, rms=0.453 (0.032%), neg=0, invalid=4512 0471: dt=36.288000, rms=0.452 (0.044%), neg=0, invalid=4512 0472: dt=36.288000, rms=0.452 (0.059%), neg=0, invalid=4512 0473: dt=36.288000, rms=0.452 (0.065%), neg=0, invalid=4512 0474: dt=36.288000, rms=0.452 (0.063%), neg=0, invalid=4512 0475: dt=36.288000, rms=0.451 (0.058%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=4512 0476: dt=11.200000, rms=0.451 (0.134%), neg=0, invalid=4512 0477: dt=11.200000, rms=0.451 (0.071%), neg=0, invalid=4512 0478: dt=11.200000, rms=0.451 (0.053%), neg=0, invalid=4512 0479: dt=11.200000, rms=0.451 (0.033%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0480: dt=11.200000, rms=0.451 (-0.031%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=4512 0481: dt=52.253165, rms=0.446 (0.991%), neg=0, invalid=4512 0482: dt=32.000000, rms=0.445 (0.330%), neg=0, invalid=4512 0483: dt=44.800000, rms=0.444 (0.260%), neg=0, invalid=4512 0484: dt=32.000000, rms=0.443 (0.159%), neg=0, invalid=4512 0485: dt=32.000000, rms=0.442 (0.141%), neg=0, invalid=4512 0486: dt=32.000000, rms=0.441 (0.215%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0487: dt=32.000000, rms=0.440 (0.277%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0488: dt=32.000000, rms=0.439 (0.260%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0489: dt=32.000000, rms=0.438 (0.270%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0490: dt=32.000000, rms=0.437 (0.230%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0491: dt=32.000000, rms=0.436 (0.222%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0492: dt=32.000000, rms=0.435 (0.168%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0493: dt=32.000000, rms=0.434 (0.154%), neg=0, invalid=4512 0494: dt=32.000000, rms=0.434 (0.120%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 4 iterations, nbhd size=0, neg = 0 0495: dt=32.000000, rms=0.433 (0.112%), neg=0, invalid=4512 0496: dt=11.200000, rms=0.433 (0.003%), neg=0, invalid=4512 0497: dt=11.200000, rms=0.433 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=4512 0498: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=4512 0499: dt=0.000000, rms=0.440 (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=0.452, neg=0, invalid=4512 0500: dt=0.000000, rms=0.452 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=4512 0501: dt=0.448000, rms=0.452 (0.067%), neg=0, invalid=4512 0502: dt=0.320000, rms=0.452 (0.014%), neg=0, invalid=4512 0503: dt=0.320000, rms=0.452 (-0.009%), 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=0.434, neg=0, invalid=4512 iter 0, gcam->neg = 852 after 13 iterations, nbhd size=1, neg = 0 0504: dt=1.625813, rms=0.422 (2.813%), neg=0, invalid=4512 0505: dt=0.007000, rms=0.422 (0.001%), neg=0, invalid=4512 0506: dt=0.007000, rms=0.422 (0.000%), neg=0, invalid=4512 0507: dt=0.007000, rms=0.422 (-0.002%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=4512 0508: dt=0.112000, rms=0.421 (0.074%), neg=0, invalid=4512 0509: dt=0.028000, rms=0.421 (0.003%), neg=0, invalid=4512 0510: dt=0.028000, rms=0.421 (-0.001%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 4 hours, 48 minutes and 23 seconds. mri_ca_register utimesec 17288.217791 mri_ca_register stimesec 11.042321 mri_ca_register ru_maxrss 1342252 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4867090 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 138 mri_ca_register ru_nivcsw 25329 FSRUNTIME@ mri_ca_register 4.8064 hours 1 threads #-------------------------------------- #@# SubCort Seg Wed Jul 6 18:48:29 EDT 2016 mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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-0-92 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/AD01/mri mri_ca_label -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca... reading input volume from norm.mgz... average std[0] = 7.3 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 6.12 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 = 0.08372 (22) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (5677 voxels, overlap=0.944) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (5677 voxels, peak = 22), gca=22.5 gca peak = 0.17677 (13) mri peak = 0.08427 (21) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (4653 voxels, overlap=0.408) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (4653 voxels, peak = 19), gca=19.4 gca peak = 0.28129 (95) mri peak = 0.08421 (94) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (616 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (616 voxels, peak = 93), gca=92.6 gca peak = 0.16930 (96) mri peak = 0.09503 (104) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (659 voxels, overlap=0.875) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (659 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.09329 (71) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (857 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (857 voxels, peak = 70), gca=69.6 gca peak = 0.30264 (59) mri peak = 0.09032 (74) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (773 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (773 voxels, peak = 75), gca=75.2 gca peak = 0.07580 (103) mri peak = 0.09535 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26633 voxels, overlap=0.781) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26633 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.09636 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (23492 voxels, overlap=0.659) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (23492 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04063 (82) Left_Cerebral_Cortex (3): linear fit = 1.40 x + 0.0 (22955 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.40 x + 0.0 (22955 voxels, peak = 81), gca=81.5 gca peak = 0.11620 (58) mri peak = 0.04223 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (21881 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (21881 voxels, peak = 78), gca=78.0 gca peak = 0.30970 (66) mri peak = 0.09498 (82) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1114 voxels, overlap=0.023) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1114 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.09538 (80) Left_Caudate (11): linear fit = 1.09 x + 0.0 (655 voxels, overlap=0.573) Left_Caudate (11): linear fit = 1.09 x + 0.0 (655 voxels, peak = 75), gca=74.9 gca peak = 0.13902 (56) mri peak = 0.07257 (75) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (23773 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (23773 voxels, peak = 74), gca=74.2 gca peak = 0.14777 (55) mri peak = 0.06364 (77) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (21118 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (21118 voxels, peak = 77), gca=77.3 gca peak = 0.16765 (84) mri peak = 0.11063 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4247 voxels, overlap=0.637) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4247 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.06919 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (6758 voxels, overlap=0.557) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (6758 voxels, peak = 94), gca=94.5 gca peak = 0.29869 (57) mri peak = 0.11950 (71) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (408 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (408 voxels, peak = 72), gca=71.5 gca peak = 0.33601 (57) mri peak = 0.10298 (70) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (366 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (366 voxels, peak = 70), gca=70.4 gca peak = 0.11131 (90) mri peak = 0.07435 (90) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3415 voxels, overlap=0.911) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3415 voxels, peak = 93), gca=93.1 gca peak = 0.11793 (83) mri peak = 0.08018 (84) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3356 voxels, overlap=0.863) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3356 voxels, peak = 86), gca=85.9 gca peak = 0.08324 (81) mri peak = 0.10278 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1186 voxels, overlap=0.293) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1186 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.09310 (85) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1465 voxels, overlap=0.445) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1465 voxels, peak = 85), gca=85.1 gca peak = 0.08424 (78) mri peak = 0.08302 (86) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11147 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11147 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.07289 (92) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1063 voxels, overlap=0.785) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1063 voxels, peak = 97), gca=96.6 gca peak = 0.14500 (87) mri peak = 0.06777 (97) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1246 voxels, overlap=0.526) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1246 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.13913 (25) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (230 voxels, overlap=0.968) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (230 voxels, peak = 22), gca=22.4 gca peak = 0.19357 (14) mri peak = 0.13102 (21) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (143 voxels, overlap=0.632) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (143 voxels, peak = 20), gca=19.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.30 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.24 x + 0.0 Left_Pallidum too bright - rescaling by 0.978 (from 1.075) to 100.9 (was 103.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13947 (23) mri peak = 0.08372 (22) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (5677 voxels, overlap=0.921) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (5677 voxels, peak = 24), gca=24.5 gca peak = 0.14738 (19) mri peak = 0.08427 (21) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (4653 voxels, overlap=0.728) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (4653 voxels, peak = 19), gca=19.5 gca peak = 0.25109 (91) mri peak = 0.08421 (94) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (616 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (616 voxels, peak = 92), gca=92.4 gca peak = 0.14807 (100) mri peak = 0.09503 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (659 voxels, peak = 100), gca=100.5 gca peak = 0.20071 (70) mri peak = 0.09329 (71) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (857 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (857 voxels, peak = 69), gca=69.0 gca peak = 0.22957 (72) mri peak = 0.09032 (74) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (773 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (773 voxels, peak = 72), gca=72.0 gca peak = 0.07830 (102) mri peak = 0.09535 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26633 voxels, overlap=0.763) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26633 voxels, peak = 102), gca=102.0 gca peak = 0.07854 (106) mri peak = 0.09636 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23492 voxels, overlap=0.724) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (23492 voxels, peak = 106), gca=106.0 gca peak = 0.06965 (81) mri peak = 0.04063 (82) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (22955 voxels, overlap=0.958) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (22955 voxels, peak = 80), gca=79.8 gca peak = 0.08769 (78) mri peak = 0.04223 (79) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (21881 voxels, overlap=0.950) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (21881 voxels, peak = 79), gca=79.2 gca peak = 0.21544 (80) mri peak = 0.09498 (82) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1114 voxels, overlap=1.006) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1114 voxels, peak = 81), gca=81.2 gca peak = 0.16156 (84) mri peak = 0.09538 (80) Left_Caudate (11): linear fit = 0.99 x + 0.0 (655 voxels, overlap=1.002) Left_Caudate (11): linear fit = 0.99 x + 0.0 (655 voxels, peak = 83), gca=82.7 gca peak = 0.10862 (74) mri peak = 0.07257 (75) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23773 voxels, overlap=0.946) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23773 voxels, peak = 74), gca=74.0 gca peak = 0.10566 (77) mri peak = 0.06364 (77) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (21118 voxels, overlap=0.927) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (21118 voxels, peak = 76), gca=75.8 gca peak = 0.15888 (90) mri peak = 0.11063 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4247 voxels, overlap=0.939) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4247 voxels, peak = 91), gca=91.3 gca peak = 0.14907 (95) mri peak = 0.06919 (91) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6758 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6758 voxels, peak = 94), gca=93.6 gca peak = 0.29345 (73) mri peak = 0.11950 (71) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (408 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (408 voxels, peak = 72), gca=71.9 gca peak = 0.34032 (70) mri peak = 0.10298 (70) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (366 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (366 voxels, peak = 72), gca=72.4 gca peak = 0.11173 (93) mri peak = 0.07435 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3415 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3415 voxels, peak = 93), gca=92.5 gca peak = 0.09898 (86) mri peak = 0.08018 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3356 voxels, overlap=0.964) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3356 voxels, peak = 86), gca=85.6 gca peak = 0.08254 (92) mri peak = 0.10278 (89) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1186 voxels, overlap=0.801) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1186 voxels, peak = 92), gca=91.5 gca peak = 0.08077 (85) mri peak = 0.09310 (85) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1465 voxels, overlap=0.891) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1465 voxels, peak = 85), gca=84.6 gca peak = 0.07886 (86) mri peak = 0.08302 (86) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11147 voxels, overlap=0.728) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11147 voxels, peak = 85), gca=84.7 gca peak = 0.10980 (96) mri peak = 0.07289 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=0.879) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 96), gca=95.5 gca peak = 0.16838 (92) mri peak = 0.06777 (97) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1246 voxels, overlap=0.887) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1246 voxels, peak = 94), gca=94.3 gca peak = 0.21376 (24) mri peak = 0.13913 (25) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (230 voxels, overlap=1.009) Third_Ventricle (14): linear fit = 0.95 x + 0.0 (230 voxels, peak = 23), gca=22.9 gca peak = 0.14887 (21) mri peak = 0.13102 (21) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (143 voxels, overlap=0.783) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (143 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16097 (41) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.17176 (45) gca peak Left_Accumbens_area = 0.60769 (68) gca peak Left_undetermined = 0.96707 (27) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11916 (35) gca peak Right_Inf_Lat_Vent = 0.19572 (29) gca peak Right_Accumbens_area = 0.35854 (79) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.87083 (39) gca peak WM_hypointensities = 0.07714 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.68898 (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 1.00 x + 0.0 Left_Pallidum too bright - rescaling by 1.004 (from 1.005) to 100.9 (was 100.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 59816 voxels changed in iteration 0 of unlikely voxel relabeling 182 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 71758 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels) 450 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 74928 changed. image ll: -2.112, PF=0.500 pass 2: 18965 changed. image ll: -2.111, PF=0.500 pass 3: 5131 changed. pass 4: 1731 changed. 54337 voxels changed in iteration 0 of unlikely voxel relabeling 263 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 7177 voxels changed in iteration 0 of unlikely voxel relabeling 107 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5704 voxels changed in iteration 0 of unlikely voxel relabeling 130 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 10 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5416 voxels changed in iteration 0 of unlikely voxel relabeling 43 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 MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... mri_ca_label utimesec 4811.799495 mri_ca_label stimesec 1.950703 mri_ca_label ru_maxrss 2114008 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 644437 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 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 204 mri_ca_label ru_nivcsw 7080 auto-labeling took 80 minutes and 15 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/cc_up.lta AD01 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/AD01/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/norm.mgz 19745 voxels in left wm, 34163 in right wm, xrange [126, 135] searching rotation angles z=[-8 6], y=[-10 4] searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 global minimum found at slice 130.6, rotations (-3.06, -1.25) final transformation (x=130.6, yr=-3.064, zr=-1.251): 0.99833 0.02183 -0.05344 1.20926; -0.02180 0.99976 0.00117 32.74471; 0.05346 -0.00000 0.99857 14.17213; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 127 cc center is found at 127 98 107 eigenvectors: 0.00103 -0.00143 1.00000; -0.31034 -0.95062 -0.00104; 0.95062 -0.31034 -0.00142; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Wed Jul 6 20:09:30 EDT 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jul 6 20:09:30 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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... 396 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 87 (87), valley at 51 (51) csf peak at 39, setting threshold to 71 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 87 (87), valley at 49 (49) csf peak at 44, setting threshold to 72 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 55 seconds. #-------------------------------------------- #@# Mask BFS Wed Jul 6 20:13:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1386248 voxels in mask (pct= 8.26) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jul 6 20:13:30 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 (103.0): 103.9 +- 6.0 [79.0 --> 125.0] GM (71.0) : 67.8 +- 12.6 [30.0 --> 95.0] setting bottom of white matter range to 80.4 setting top of gray matter range to 93.0 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... 5843 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2584 filled 1127 bright non-wm voxels segmented. 5090 diagonally connected voxels added... white matter segmentation took 2.1 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 0.62 minutes reading wm segmentation from wm.seg.mgz... 75 voxels added to wm to prevent paths from MTL structures to cortex 3177 additional wm voxels added 0 additional wm voxels added SEG EDIT: 65875 voxels turned on, 60488 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 113 new 113 115,126,128 old 113 new 113 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 21 found - 21 modified | TOTAL: 38 pass 2 (xy-): 0 found - 21 modified | TOTAL: 38 pass 1 (yz+): 23 found - 23 modified | TOTAL: 61 pass 2 (yz+): 0 found - 23 modified | TOTAL: 61 pass 1 (yz-): 14 found - 14 modified | TOTAL: 75 pass 2 (yz-): 0 found - 14 modified | TOTAL: 75 pass 1 (xz+): 18 found - 18 modified | TOTAL: 93 pass 2 (xz+): 0 found - 18 modified | TOTAL: 93 pass 1 (xz-): 26 found - 26 modified | TOTAL: 119 pass 2 (xz-): 0 found - 26 modified | TOTAL: 119 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 35 found - 35 modified | TOTAL: 55 pass 2 (+++): 0 found - 35 modified | TOTAL: 55 pass 1 (+++): 32 found - 32 modified | TOTAL: 87 pass 2 (+++): 0 found - 32 modified | TOTAL: 87 pass 1 (+++): 26 found - 26 modified | TOTAL: 113 pass 2 (+++): 0 found - 26 modified | TOTAL: 113 Iteration Number : 1 pass 1 (++): 74 found - 74 modified | TOTAL: 74 pass 2 (++): 0 found - 74 modified | TOTAL: 74 pass 1 (+-): 76 found - 76 modified | TOTAL: 150 pass 2 (+-): 0 found - 76 modified | TOTAL: 150 pass 1 (--): 75 found - 75 modified | TOTAL: 225 pass 2 (--): 0 found - 75 modified | TOTAL: 225 pass 1 (-+): 71 found - 71 modified | TOTAL: 296 pass 2 (-+): 0 found - 71 modified | TOTAL: 296 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 8 found - 8 modified | TOTAL: 17 pass 2 (xy-): 0 found - 8 modified | TOTAL: 17 pass 1 (yz+): 9 found - 9 modified | TOTAL: 26 pass 2 (yz+): 0 found - 9 modified | TOTAL: 26 pass 1 (yz-): 10 found - 10 modified | TOTAL: 36 pass 2 (yz-): 0 found - 10 modified | TOTAL: 36 pass 1 (xz+): 7 found - 7 modified | TOTAL: 43 pass 2 (xz+): 0 found - 7 modified | TOTAL: 43 pass 1 (xz-): 3 found - 3 modified | TOTAL: 46 pass 2 (xz-): 0 found - 3 modified | TOTAL: 46 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 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 3 found - 3 modified | TOTAL: 9 pass 2 (+-): 0 found - 3 modified | TOTAL: 9 pass 1 (--): 3 found - 3 modified | TOTAL: 12 pass 2 (--): 0 found - 3 modified | TOTAL: 12 pass 1 (-+): 2 found - 2 modified | TOTAL: 14 pass 2 (-+): 0 found - 2 modified | TOTAL: 14 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 591 (out of 534056: 0.110663) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jul 6 20:16:18 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48177; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03151 -0.04227 -0.06843 3.84080; 0.03577 0.98514 0.54806 -67.23380; 0.04049 -0.54631 0.97698 49.48177; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1091 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (125, 122, 151), TAL = (3.0, 23.0, 6.0) talairach voxel to voxel transform 0.96604 0.06024 0.03387 -1.33629; -0.00977 0.77362 -0.43467 73.55894; -0.04549 0.43010 0.77910 -9.45949; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 122, 151) --> (3.0, 23.0, 6.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (3.00, 23.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 23.00, 6.00) SRC: (114.49, 101.26, 155.79) search lh wm seed point around talairach space (-15.00, 23.00, 6.00), SRC: (149.27, 100.91, 154.15) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Jul 6 20:17:11 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 15 (out of 264065: 0.005680) 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 1.781 2016/06/13 21:20:50 fischl Exp $ slice 60: 3477 vertices, 3736 faces slice 70: 12822 vertices, 13244 faces slice 80: 24579 vertices, 25068 faces slice 90: 36819 vertices, 37294 faces slice 100: 48415 vertices, 48855 faces slice 110: 60104 vertices, 60556 faces slice 120: 70710 vertices, 71173 faces slice 130: 81562 vertices, 82033 faces slice 140: 91796 vertices, 92244 faces slice 150: 101928 vertices, 102450 faces slice 160: 111928 vertices, 112463 faces slice 170: 120057 vertices, 120469 faces slice 180: 125129 vertices, 125478 faces slice 190: 128356 vertices, 128617 faces slice 200: 128790 vertices, 128994 faces slice 210: 128790 vertices, 128994 faces slice 220: 128790 vertices, 128994 faces slice 230: 128790 vertices, 128994 faces slice 240: 128790 vertices, 128994 faces slice 250: 128790 vertices, 128994 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... 128790 voxel in cpt #1: X=-204 [v=128790,e=386982,f=257988] located at (-30.671978, -13.010459, 14.279253) For the whole surface: X=-204 [v=128790,e=386982,f=257988] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Jul 6 20:17:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 3 found - 3 modified | TOTAL: 6 pass 2 (yz-): 0 found - 3 modified | TOTAL: 6 pass 1 (xz+): 3 found - 3 modified | TOTAL: 9 pass 2 (xz+): 0 found - 3 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 250641: 0.005187) 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 1.781 2016/06/13 21:20:50 fischl Exp $ slice 60: 1731 vertices, 1955 faces slice 70: 9836 vertices, 10176 faces slice 80: 20896 vertices, 21305 faces slice 90: 32333 vertices, 32733 faces slice 100: 43028 vertices, 43421 faces slice 110: 53294 vertices, 53699 faces slice 120: 64103 vertices, 64562 faces slice 130: 75166 vertices, 75616 faces slice 140: 85643 vertices, 86100 faces slice 150: 96183 vertices, 96645 faces slice 160: 105955 vertices, 106368 faces slice 170: 114457 vertices, 114841 faces slice 180: 121072 vertices, 121382 faces slice 190: 125627 vertices, 125869 faces slice 200: 126436 vertices, 126574 faces slice 210: 126436 vertices, 126574 faces slice 220: 126436 vertices, 126574 faces slice 230: 126436 vertices, 126574 faces slice 240: 126436 vertices, 126574 faces slice 250: 126436 vertices, 126574 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... 126436 voxel in cpt #1: X=-138 [v=126436,e=379722,f=253148] located at (24.792654, -9.078277, 18.487473) For the whole surface: X=-138 [v=126436,e=379722,f=253148] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jul 6 20:17:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Jul 6 20:17:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Jul 6 20:17:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.9 mm, total surface area = 65396 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes step 000: RMS=0.173 (target=0.015) step 005: RMS=0.132 (target=0.015) step 010: RMS=0.102 (target=0.015) step 015: RMS=0.089 (target=0.015) step 020: RMS=0.078 (target=0.015) step 025: RMS=0.072 (target=0.015) step 030: RMS=0.067 (target=0.015) step 035: RMS=0.062 (target=0.015) step 040: RMS=0.060 (target=0.015) step 045: RMS=0.057 (target=0.015) step 050: RMS=0.057 (target=0.015) step 055: RMS=0.056 (target=0.015) step 060: RMS=0.055 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 61.739614 mris_inflate stimesec 0.091986 mris_inflate ru_maxrss 166588 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22131 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 93 mris_inflate ru_nivcsw 160 #-------------------------------------------- #@# Inflation1 rh Wed Jul 6 20:18:45 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.7 mm, total surface area = 64079 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.0 minutes step 000: RMS=0.173 (target=0.015) step 005: RMS=0.132 (target=0.015) step 010: RMS=0.104 (target=0.015) step 015: RMS=0.088 (target=0.015) step 020: RMS=0.078 (target=0.015) step 025: RMS=0.071 (target=0.015) step 030: RMS=0.066 (target=0.015) step 035: RMS=0.061 (target=0.015) step 040: RMS=0.059 (target=0.015) step 045: RMS=0.057 (target=0.015) step 050: RMS=0.055 (target=0.015) step 055: RMS=0.055 (target=0.015) step 060: RMS=0.054 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 59.751916 mris_inflate stimesec 0.096985 mris_inflate ru_maxrss 163672 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 21408 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 31 mris_inflate ru_nivcsw 70 #-------------------------------------------- #@# QSphere lh Wed Jul 6 20:19:45 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.59 (0.00-->7.29) (max @ vno 98630 --> 98645) face area 0.03 +- 0.04 (-0.24-->0.74) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.366... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.201, avgs=0 005/300: dt: 0.9000, rms radial error=173.944, avgs=0 010/300: dt: 0.9000, rms radial error=173.394, avgs=0 015/300: dt: 0.9000, rms radial error=172.671, avgs=0 020/300: dt: 0.9000, rms radial error=171.848, avgs=0 025/300: dt: 0.9000, rms radial error=170.967, avgs=0 030/300: dt: 0.9000, rms radial error=170.054, avgs=0 035/300: dt: 0.9000, rms radial error=169.129, avgs=0 040/300: dt: 0.9000, rms radial error=168.197, avgs=0 045/300: dt: 0.9000, rms radial error=167.263, avgs=0 050/300: dt: 0.9000, rms radial error=166.331, avgs=0 055/300: dt: 0.9000, rms radial error=165.405, avgs=0 060/300: dt: 0.9000, rms radial error=164.482, avgs=0 065/300: dt: 0.9000, rms radial error=163.561, avgs=0 070/300: dt: 0.9000, rms radial error=162.645, avgs=0 075/300: dt: 0.9000, rms radial error=161.734, avgs=0 080/300: dt: 0.9000, rms radial error=160.827, avgs=0 085/300: dt: 0.9000, rms radial error=159.925, avgs=0 090/300: dt: 0.9000, rms radial error=159.028, avgs=0 095/300: dt: 0.9000, rms radial error=158.136, avgs=0 100/300: dt: 0.9000, rms radial error=157.248, avgs=0 105/300: dt: 0.9000, rms radial error=156.365, avgs=0 110/300: dt: 0.9000, rms radial error=155.487, avgs=0 115/300: dt: 0.9000, rms radial error=154.614, avgs=0 120/300: dt: 0.9000, rms radial error=153.745, avgs=0 125/300: dt: 0.9000, rms radial error=152.880, avgs=0 130/300: dt: 0.9000, rms radial error=152.021, avgs=0 135/300: dt: 0.9000, rms radial error=151.166, avgs=0 140/300: dt: 0.9000, rms radial error=150.315, avgs=0 145/300: dt: 0.9000, rms radial error=149.470, avgs=0 150/300: dt: 0.9000, rms radial error=148.629, avgs=0 155/300: dt: 0.9000, rms radial error=147.792, avgs=0 160/300: dt: 0.9000, rms radial error=146.960, avgs=0 165/300: dt: 0.9000, rms radial error=146.132, avgs=0 170/300: dt: 0.9000, rms radial error=145.309, avgs=0 175/300: dt: 0.9000, rms radial error=144.491, avgs=0 180/300: dt: 0.9000, rms radial error=143.677, avgs=0 185/300: dt: 0.9000, rms radial error=142.867, avgs=0 190/300: dt: 0.9000, rms radial error=142.062, avgs=0 195/300: dt: 0.9000, rms radial error=141.262, avgs=0 200/300: dt: 0.9000, rms radial error=140.465, avgs=0 205/300: dt: 0.9000, rms radial error=139.673, avgs=0 210/300: dt: 0.9000, rms radial error=138.886, avgs=0 215/300: dt: 0.9000, rms radial error=138.102, avgs=0 220/300: dt: 0.9000, rms radial error=137.323, avgs=0 225/300: dt: 0.9000, rms radial error=136.548, avgs=0 230/300: dt: 0.9000, rms radial error=135.777, avgs=0 235/300: dt: 0.9000, rms radial error=135.011, avgs=0 240/300: dt: 0.9000, rms radial error=134.249, avgs=0 245/300: dt: 0.9000, rms radial error=133.491, avgs=0 250/300: dt: 0.9000, rms radial error=132.737, avgs=0 255/300: dt: 0.9000, rms radial error=131.988, avgs=0 260/300: dt: 0.9000, rms radial error=131.244, avgs=0 265/300: dt: 0.9000, rms radial error=130.503, avgs=0 270/300: dt: 0.9000, rms radial error=129.767, avgs=0 275/300: dt: 0.9000, rms radial error=129.035, avgs=0 280/300: dt: 0.9000, rms radial error=128.306, avgs=0 285/300: dt: 0.9000, rms radial error=127.582, avgs=0 290/300: dt: 0.9000, rms radial error=126.862, avgs=0 295/300: dt: 0.9000, rms radial error=126.146, avgs=0 300/300: dt: 0.9000, rms radial error=125.434, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14317.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 2210.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 3 (K=160.0), pass 1, starting sse = 218.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00651 epoch 4 (K=640.0), pass 1, starting sse = 20.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00563 final distance error %24.97 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours mris_sphere utimesec 350.244754 mris_sphere stimesec 0.136979 mris_sphere ru_maxrss 166800 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 21671 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 99 mris_sphere ru_nivcsw 422 FSRUNTIME@ mris_sphere 0.0973 hours 1 threads #-------------------------------------------- #@# QSphere rh Wed Jul 6 20:25:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.61 (0.00-->7.34) (max @ vno 98923 --> 98924) face area 0.03 +- 0.04 (-0.43-->0.97) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.369... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=173.927, avgs=0 005/300: dt: 0.9000, rms radial error=173.674, avgs=0 010/300: dt: 0.9000, rms radial error=173.132, avgs=0 015/300: dt: 0.9000, rms radial error=172.419, avgs=0 020/300: dt: 0.9000, rms radial error=171.605, avgs=0 025/300: dt: 0.9000, rms radial error=170.734, avgs=0 030/300: dt: 0.9000, rms radial error=169.825, avgs=0 035/300: dt: 0.9000, rms radial error=168.899, avgs=0 040/300: dt: 0.9000, rms radial error=167.966, avgs=0 045/300: dt: 0.9000, rms radial error=167.030, avgs=0 050/300: dt: 0.9000, rms radial error=166.094, avgs=0 055/300: dt: 0.9000, rms radial error=165.161, avgs=0 060/300: dt: 0.9000, rms radial error=164.231, avgs=0 065/300: dt: 0.9000, rms radial error=163.305, avgs=0 070/300: dt: 0.9000, rms radial error=162.385, avgs=0 075/300: dt: 0.9000, rms radial error=161.469, avgs=0 080/300: dt: 0.9000, rms radial error=160.558, avgs=0 085/300: dt: 0.9000, rms radial error=159.652, avgs=0 090/300: dt: 0.9000, rms radial error=158.752, avgs=0 095/300: dt: 0.9000, rms radial error=157.863, avgs=0 100/300: dt: 0.9000, rms radial error=156.980, avgs=0 105/300: dt: 0.9000, rms radial error=156.101, avgs=0 110/300: dt: 0.9000, rms radial error=155.227, avgs=0 115/300: dt: 0.9000, rms radial error=154.357, avgs=0 120/300: dt: 0.9000, rms radial error=153.492, avgs=0 125/300: dt: 0.9000, rms radial error=152.628, avgs=0 130/300: dt: 0.9000, rms radial error=151.769, avgs=0 135/300: dt: 0.9000, rms radial error=150.914, avgs=0 140/300: dt: 0.9000, rms radial error=150.063, avgs=0 145/300: dt: 0.9000, rms radial error=149.217, avgs=0 150/300: dt: 0.9000, rms radial error=148.376, avgs=0 155/300: dt: 0.9000, rms radial error=147.541, avgs=0 160/300: dt: 0.9000, rms radial error=146.709, avgs=0 165/300: dt: 0.9000, rms radial error=145.882, avgs=0 170/300: dt: 0.9000, rms radial error=145.060, avgs=0 175/300: dt: 0.9000, rms radial error=144.243, avgs=0 180/300: dt: 0.9000, rms radial error=143.430, avgs=0 185/300: dt: 0.9000, rms radial error=142.621, avgs=0 190/300: dt: 0.9000, rms radial error=141.817, avgs=0 195/300: dt: 0.9000, rms radial error=141.017, avgs=0 200/300: dt: 0.9000, rms radial error=140.222, avgs=0 205/300: dt: 0.9000, rms radial error=139.431, avgs=0 210/300: dt: 0.9000, rms radial error=138.644, avgs=0 215/300: dt: 0.9000, rms radial error=137.862, avgs=0 220/300: dt: 0.9000, rms radial error=137.084, avgs=0 225/300: dt: 0.9000, rms radial error=136.311, avgs=0 230/300: dt: 0.9000, rms radial error=135.541, avgs=0 235/300: dt: 0.9000, rms radial error=134.776, avgs=0 240/300: dt: 0.9000, rms radial error=134.016, avgs=0 245/300: dt: 0.9000, rms radial error=133.259, avgs=0 250/300: dt: 0.9000, rms radial error=132.507, avgs=0 255/300: dt: 0.9000, rms radial error=131.759, avgs=0 260/300: dt: 0.9000, rms radial error=131.015, avgs=0 265/300: dt: 0.9000, rms radial error=130.275, avgs=0 270/300: dt: 0.9000, rms radial error=129.539, avgs=0 275/300: dt: 0.9000, rms radial error=128.808, avgs=0 280/300: dt: 0.9000, rms radial error=128.081, avgs=0 285/300: dt: 0.9000, rms radial error=127.358, avgs=0 290/300: dt: 0.9000, rms radial error=126.639, avgs=0 295/300: dt: 0.9000, rms radial error=125.924, avgs=0 300/300: dt: 0.9000, rms radial error=125.213, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14017.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 2 (K=40.0), pass 1, starting sse = 2165.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 215.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00402 epoch 4 (K=640.0), pass 1, starting sse = 19.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/13 = 0.00639 final distance error %25.59 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 326.005439 mris_sphere stimesec 0.110983 mris_sphere ru_maxrss 163892 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 21458 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 379 FSRUNTIME@ mris_sphere 0.0906 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Wed Jul 6 20:31:02 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Jul 6 20:31:02 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Jul 6 20:31:02 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-204 (nv=128790, nf=257988, ne=386982, g=103) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 12209 ambiguous faces found in tessellation segmenting defects... 94 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 23 into 21 -merging segment 72 into 69 92 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0741 (-4.5371) -vertex loglikelihood: -6.2282 (-3.1141) -normal dot loglikelihood: -3.6619 (-3.6619) -quad curv loglikelihood: -6.1922 (-3.0961) Total Loglikelihood : -25.1565 CORRECTING DEFECT 0 (vertices=17, convex hull=45, v0=1547) After retessellation of defect 0 (v0=1547), euler #=-89 (121459,361503,239955) : difference with theory (-89) = 0 CORRECTING DEFECT 1 (vertices=22, convex hull=44, v0=2227) After retessellation of defect 1 (v0=2227), euler #=-88 (121472,361557,239997) : difference with theory (-88) = 0 CORRECTING DEFECT 2 (vertices=23, convex hull=55, v0=2598) After retessellation of defect 2 (v0=2598), euler #=-87 (121483,361612,240042) : difference with theory (-87) = 0 CORRECTING DEFECT 3 (vertices=21, convex hull=69, v0=2967) After retessellation of defect 3 (v0=2967), euler #=-86 (121495,361676,240095) : difference with theory (-86) = 0 CORRECTING DEFECT 4 (vertices=84, convex hull=107, v0=6318) After retessellation of defect 4 (v0=6318), euler #=-85 (121527,361814,240202) : difference with theory (-85) = 0 CORRECTING DEFECT 5 (vertices=54, convex hull=85, v0=9125) After retessellation of defect 5 (v0=9125), euler #=-84 (121536,361881,240261) : difference with theory (-84) = 0 CORRECTING DEFECT 6 (vertices=31, convex hull=63, v0=10127) After retessellation of defect 6 (v0=10127), euler #=-83 (121549,361944,240312) : difference with theory (-83) = 0 CORRECTING DEFECT 7 (vertices=24, convex hull=42, v0=11054) After retessellation of defect 7 (v0=11054), euler #=-82 (121559,361989,240348) : difference with theory (-82) = 0 CORRECTING DEFECT 8 (vertices=23, convex hull=62, v0=12619) After retessellation of defect 8 (v0=12619), euler #=-81 (121570,362049,240398) : difference with theory (-81) = 0 CORRECTING DEFECT 9 (vertices=37, convex hull=58, v0=16612) After retessellation of defect 9 (v0=16612), euler #=-80 (121592,362138,240466) : difference with theory (-80) = 0 CORRECTING DEFECT 10 (vertices=62, convex hull=98, v0=17111) After retessellation of defect 10 (v0=17111), euler #=-79 (121618,362258,240561) : difference with theory (-79) = 0 CORRECTING DEFECT 11 (vertices=66, convex hull=66, v0=19293) After retessellation of defect 11 (v0=19293), euler #=-78 (121638,362345,240629) : difference with theory (-78) = 0 CORRECTING DEFECT 12 (vertices=1011, convex hull=130, v0=25938) After retessellation of defect 12 (v0=25938), euler #=-77 (121671,362503,240755) : difference with theory (-77) = 0 CORRECTING DEFECT 13 (vertices=21, convex hull=38, v0=29044) After retessellation of defect 13 (v0=29044), euler #=-76 (121682,362548,240790) : difference with theory (-76) = 0 CORRECTING DEFECT 14 (vertices=51, convex hull=70, v0=29414) After retessellation of defect 14 (v0=29414), euler #=-75 (121697,362621,240849) : difference with theory (-75) = 0 CORRECTING DEFECT 15 (vertices=451, convex hull=339, v0=29651) After retessellation of defect 15 (v0=29651), euler #=-74 (121833,363200,241293) : difference with theory (-74) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=22, v0=37536) After retessellation of defect 16 (v0=37536), euler #=-73 (121834,363210,241303) : difference with theory (-73) = 0 CORRECTING DEFECT 17 (vertices=21, convex hull=45, v0=38394) After retessellation of defect 17 (v0=38394), euler #=-72 (121842,363249,241335) : difference with theory (-72) = 0 CORRECTING DEFECT 18 (vertices=11, convex hull=20, v0=39964) After retessellation of defect 18 (v0=39964), euler #=-71 (121842,363255,241342) : difference with theory (-71) = 0 CORRECTING DEFECT 19 (vertices=28, convex hull=55, v0=42251) After retessellation of defect 19 (v0=42251), euler #=-70 (121854,363311,241387) : difference with theory (-70) = 0 CORRECTING DEFECT 20 (vertices=36, convex hull=67, v0=42626) After retessellation of defect 20 (v0=42626), euler #=-69 (121869,363383,241445) : difference with theory (-69) = 0 CORRECTING DEFECT 21 (vertices=80, convex hull=147, v0=42746) After retessellation of defect 21 (v0=42746), euler #=-67 (121899,363539,241573) : difference with theory (-68) = -1 CORRECTING DEFECT 22 (vertices=46, convex hull=54, v0=46369) After retessellation of defect 22 (v0=46369), euler #=-66 (121908,363583,241609) : difference with theory (-67) = -1 CORRECTING DEFECT 23 (vertices=63, convex hull=78, v0=47240) After retessellation of defect 23 (v0=47240), euler #=-65 (121925,363665,241675) : difference with theory (-66) = -1 CORRECTING DEFECT 24 (vertices=25, convex hull=57, v0=48025) After retessellation of defect 24 (v0=48025), euler #=-64 (121940,363730,241726) : difference with theory (-65) = -1 CORRECTING DEFECT 25 (vertices=25, convex hull=57, v0=54723) After retessellation of defect 25 (v0=54723), euler #=-63 (121953,363796,241780) : difference with theory (-64) = -1 CORRECTING DEFECT 26 (vertices=51, convex hull=52, v0=55170) After retessellation of defect 26 (v0=55170), euler #=-62 (121970,363870,241838) : difference with theory (-63) = -1 CORRECTING DEFECT 27 (vertices=38, convex hull=62, v0=56362) After retessellation of defect 27 (v0=56362), euler #=-61 (121991,363956,241904) : difference with theory (-62) = -1 CORRECTING DEFECT 28 (vertices=284, convex hull=71, v0=58972) After retessellation of defect 28 (v0=58972), euler #=-60 (122007,364034,241967) : difference with theory (-61) = -1 CORRECTING DEFECT 29 (vertices=31, convex hull=51, v0=59405) After retessellation of defect 29 (v0=59405), euler #=-59 (122028,364115,242028) : difference with theory (-60) = -1 CORRECTING DEFECT 30 (vertices=47, convex hull=42, v0=59407) After retessellation of defect 30 (v0=59407), euler #=-58 (122039,364169,242072) : difference with theory (-59) = -1 CORRECTING DEFECT 31 (vertices=72, convex hull=82, v0=69337) After retessellation of defect 31 (v0=69337), euler #=-57 (122072,364308,242179) : difference with theory (-58) = -1 CORRECTING DEFECT 32 (vertices=20, convex hull=51, v0=72879) After retessellation of defect 32 (v0=72879), euler #=-56 (122086,364367,242225) : difference with theory (-57) = -1 CORRECTING DEFECT 33 (vertices=99, convex hull=55, v0=73800) After retessellation of defect 33 (v0=73800), euler #=-55 (122109,364457,242293) : difference with theory (-56) = -1 CORRECTING DEFECT 34 (vertices=24, convex hull=43, v0=74613) After retessellation of defect 34 (v0=74613), euler #=-54 (122121,364505,242330) : difference with theory (-55) = -1 CORRECTING DEFECT 35 (vertices=52, convex hull=105, v0=74729) After retessellation of defect 35 (v0=74729), euler #=-53 (122151,364642,242438) : difference with theory (-54) = -1 CORRECTING DEFECT 36 (vertices=5, convex hull=18, v0=75713) After retessellation of defect 36 (v0=75713), euler #=-52 (122151,364646,242443) : difference with theory (-53) = -1 CORRECTING DEFECT 37 (vertices=117, convex hull=105, v0=76170) After retessellation of defect 37 (v0=76170), euler #=-51 (122181,364784,242552) : difference with theory (-52) = -1 CORRECTING DEFECT 38 (vertices=6, convex hull=13, v0=76666) After retessellation of defect 38 (v0=76666), euler #=-50 (122181,364788,242557) : difference with theory (-51) = -1 CORRECTING DEFECT 39 (vertices=20, convex hull=62, v0=76751) After retessellation of defect 39 (v0=76751), euler #=-49 (122192,364846,242605) : difference with theory (-50) = -1 CORRECTING DEFECT 40 (vertices=154, convex hull=136, v0=79276) After retessellation of defect 40 (v0=79276), euler #=-48 (122204,364951,242699) : difference with theory (-49) = -1 CORRECTING DEFECT 41 (vertices=48, convex hull=59, v0=79431) After retessellation of defect 41 (v0=79431), euler #=-47 (122221,365026,242758) : difference with theory (-48) = -1 CORRECTING DEFECT 42 (vertices=27, convex hull=52, v0=79895) After retessellation of defect 42 (v0=79895), euler #=-46 (122230,365075,242799) : difference with theory (-47) = -1 CORRECTING DEFECT 43 (vertices=79, convex hull=65, v0=82199) After retessellation of defect 43 (v0=82199), euler #=-45 (122257,365183,242881) : difference with theory (-46) = -1 CORRECTING DEFECT 44 (vertices=58, convex hull=72, v0=83005) After retessellation of defect 44 (v0=83005), euler #=-44 (122278,365276,242954) : difference with theory (-45) = -1 CORRECTING DEFECT 45 (vertices=410, convex hull=286, v0=84252) After retessellation of defect 45 (v0=84252), euler #=-43 (122294,365459,243122) : difference with theory (-44) = -1 CORRECTING DEFECT 46 (vertices=31, convex hull=49, v0=85896) After retessellation of defect 46 (v0=85896), euler #=-42 (122303,365507,243162) : difference with theory (-43) = -1 CORRECTING DEFECT 47 (vertices=24, convex hull=36, v0=88752) After retessellation of defect 47 (v0=88752), euler #=-41 (122310,365539,243188) : difference with theory (-42) = -1 CORRECTING DEFECT 48 (vertices=19, convex hull=39, v0=92295) After retessellation of defect 48 (v0=92295), euler #=-40 (122321,365585,243224) : difference with theory (-41) = -1 CORRECTING DEFECT 49 (vertices=63, convex hull=86, v0=92428) After retessellation of defect 49 (v0=92428), euler #=-39 (122357,365727,243331) : difference with theory (-40) = -1 CORRECTING DEFECT 50 (vertices=44, convex hull=77, v0=92836) After retessellation of defect 50 (v0=92836), euler #=-38 (122378,365817,243401) : difference with theory (-39) = -1 CORRECTING DEFECT 51 (vertices=6, convex hull=18, v0=93372) After retessellation of defect 51 (v0=93372), euler #=-37 (122379,365825,243409) : difference with theory (-38) = -1 CORRECTING DEFECT 52 (vertices=15, convex hull=35, v0=93646) After retessellation of defect 52 (v0=93646), euler #=-36 (122384,365850,243430) : difference with theory (-37) = -1 CORRECTING DEFECT 53 (vertices=45, convex hull=59, v0=94218) After retessellation of defect 53 (v0=94218), euler #=-35 (122402,365927,243490) : difference with theory (-36) = -1 CORRECTING DEFECT 54 (vertices=29, convex hull=64, v0=94345) After retessellation of defect 54 (v0=94345), euler #=-34 (122420,366004,243550) : difference with theory (-35) = -1 CORRECTING DEFECT 55 (vertices=120, convex hull=112, v0=94534) After retessellation of defect 55 (v0=94534), euler #=-33 (122483,366242,243726) : difference with theory (-34) = -1 CORRECTING DEFECT 56 (vertices=22, convex hull=33, v0=94648) After retessellation of defect 56 (v0=94648), euler #=-32 (122486,366263,243745) : difference with theory (-33) = -1 CORRECTING DEFECT 57 (vertices=66, convex hull=84, v0=94814) After retessellation of defect 57 (v0=94814), euler #=-31 (122504,366355,243820) : difference with theory (-32) = -1 CORRECTING DEFECT 58 (vertices=28, convex hull=51, v0=95411) After retessellation of defect 58 (v0=95411), euler #=-30 (122513,366403,243860) : difference with theory (-31) = -1 CORRECTING DEFECT 59 (vertices=51, convex hull=77, v0=96689) After retessellation of defect 59 (v0=96689), euler #=-29 (122539,366510,243942) : difference with theory (-30) = -1 CORRECTING DEFECT 60 (vertices=8, convex hull=32, v0=96717) After retessellation of defect 60 (v0=96717), euler #=-28 (122541,366527,243958) : difference with theory (-29) = -1 CORRECTING DEFECT 61 (vertices=51, convex hull=72, v0=96937) After retessellation of defect 61 (v0=96937), euler #=-27 (122566,366635,244042) : difference with theory (-28) = -1 CORRECTING DEFECT 62 (vertices=33, convex hull=76, v0=98381) After retessellation of defect 62 (v0=98381), euler #=-26 (122583,366713,244104) : difference with theory (-27) = -1 CORRECTING DEFECT 63 (vertices=249, convex hull=193, v0=98562) After retessellation of defect 63 (v0=98562), euler #=-25 (122694,367152,244433) : difference with theory (-26) = -1 CORRECTING DEFECT 64 (vertices=25, convex hull=52, v0=98977) After retessellation of defect 64 (v0=98977), euler #=-24 (122703,367200,244473) : difference with theory (-25) = -1 CORRECTING DEFECT 65 (vertices=60, convex hull=50, v0=99593) After retessellation of defect 65 (v0=99593), euler #=-23 (122705,367230,244502) : difference with theory (-24) = -1 CORRECTING DEFECT 66 (vertices=38, convex hull=82, v0=100142) After retessellation of defect 66 (v0=100142), euler #=-22 (122724,367321,244575) : difference with theory (-23) = -1 CORRECTING DEFECT 67 (vertices=30, convex hull=36, v0=100731) After retessellation of defect 67 (v0=100731), euler #=-21 (122735,367370,244614) : difference with theory (-22) = -1 CORRECTING DEFECT 68 (vertices=818, convex hull=206, v0=100860) After retessellation of defect 68 (v0=100860), euler #=-19 (122789,367635,244827) : difference with theory (-21) = -2 CORRECTING DEFECT 69 (vertices=30, convex hull=49, v0=101752) After retessellation of defect 69 (v0=101752), euler #=-18 (122803,367694,244873) : difference with theory (-20) = -2 CORRECTING DEFECT 70 (vertices=6, convex hull=23, v0=104490) After retessellation of defect 70 (v0=104490), euler #=-17 (122804,367705,244884) : difference with theory (-19) = -2 CORRECTING DEFECT 71 (vertices=38, convex hull=84, v0=106857) After retessellation of defect 71 (v0=106857), euler #=-16 (122822,367790,244952) : difference with theory (-18) = -2 CORRECTING DEFECT 72 (vertices=22, convex hull=66, v0=108021) After retessellation of defect 72 (v0=108021), euler #=-15 (122834,367850,245001) : difference with theory (-17) = -2 CORRECTING DEFECT 73 (vertices=355, convex hull=115, v0=108606) After retessellation of defect 73 (v0=108606), euler #=-14 (122861,367996,245121) : difference with theory (-16) = -2 CORRECTING DEFECT 74 (vertices=52, convex hull=90, v0=109419) After retessellation of defect 74 (v0=109419), euler #=-13 (122895,368135,245227) : difference with theory (-15) = -2 CORRECTING DEFECT 75 (vertices=24, convex hull=48, v0=111127) After retessellation of defect 75 (v0=111127), euler #=-12 (122903,368177,245262) : difference with theory (-14) = -2 CORRECTING DEFECT 76 (vertices=41, convex hull=25, v0=112573) After retessellation of defect 76 (v0=112573), euler #=-11 (122907,368198,245280) : difference with theory (-13) = -2 CORRECTING DEFECT 77 (vertices=18, convex hull=40, v0=113094) After retessellation of defect 77 (v0=113094), euler #=-10 (122917,368241,245314) : difference with theory (-12) = -2 CORRECTING DEFECT 78 (vertices=91, convex hull=52, v0=113364) After retessellation of defect 78 (v0=113364), euler #=-9 (122925,368283,245349) : difference with theory (-11) = -2 CORRECTING DEFECT 79 (vertices=31, convex hull=49, v0=113517) After retessellation of defect 79 (v0=113517), euler #=-8 (122936,368334,245390) : difference with theory (-10) = -2 CORRECTING DEFECT 80 (vertices=40, convex hull=40, v0=113578) After retessellation of defect 80 (v0=113578), euler #=-7 (122949,368384,245428) : difference with theory (-9) = -2 CORRECTING DEFECT 81 (vertices=38, convex hull=61, v0=116271) After retessellation of defect 81 (v0=116271), euler #=-6 (122964,368450,245480) : difference with theory (-8) = -2 CORRECTING DEFECT 82 (vertices=265, convex hull=269, v0=117794) After retessellation of defect 82 (v0=117794), euler #=-7 (123084,368968,245877) : difference with theory (-7) = 0 CORRECTING DEFECT 83 (vertices=31, convex hull=65, v0=118232) After retessellation of defect 83 (v0=118232), euler #=-6 (123104,369051,245941) : difference with theory (-6) = 0 CORRECTING DEFECT 84 (vertices=76, convex hull=73, v0=119079) After retessellation of defect 84 (v0=119079), euler #=-5 (123115,369115,245995) : difference with theory (-5) = 0 CORRECTING DEFECT 85 (vertices=28, convex hull=67, v0=119667) After retessellation of defect 85 (v0=119667), euler #=-4 (123124,369168,246040) : difference with theory (-4) = 0 CORRECTING DEFECT 86 (vertices=56, convex hull=108, v0=119933) After retessellation of defect 86 (v0=119933), euler #=-3 (123147,369282,246132) : difference with theory (-3) = 0 CORRECTING DEFECT 87 (vertices=70, convex hull=85, v0=122515) After retessellation of defect 87 (v0=122515), euler #=-2 (123180,369419,246237) : difference with theory (-2) = 0 CORRECTING DEFECT 88 (vertices=47, convex hull=66, v0=124969) After retessellation of defect 88 (v0=124969), euler #=-1 (123192,369480,246287) : difference with theory (-1) = 0 CORRECTING DEFECT 89 (vertices=30, convex hull=67, v0=126283) After retessellation of defect 89 (v0=126283), euler #=0 (123209,369560,246351) : difference with theory (0) = 0 CORRECTING DEFECT 90 (vertices=47, convex hull=90, v0=128287) After retessellation of defect 90 (v0=128287), euler #=1 (123231,369664,246434) : difference with theory (1) = 0 CORRECTING DEFECT 91 (vertices=40, convex hull=56, v0=128550) After retessellation of defect 91 (v0=128550), euler #=2 (123245,369729,246486) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.07-->13.28) (max @ vno 75226 --> 87030) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.07-->13.28) (max @ vno 75226 --> 87030) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 267 mutations (30.7%), 604 crossovers (69.3%), 577 vertices were eliminated building final representation... 5545 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123245, nf=246486, ne=369729, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 72.1 minutes 0 defective edges removing intersecting faces 000: 594 intersecting 001: 21 intersecting mris_fix_topology utimesec 4323.256765 mris_fix_topology stimesec 0.618905 mris_fix_topology ru_maxrss 404884 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 53177 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 145 mris_fix_topology ru_nivcsw 7665 FSRUNTIME@ mris_fix_topology lh 1.2014 hours 1 threads #@# Fix Topology rh Wed Jul 6 21:43:07 EDT 2016 mris_fix_topology -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-138 (nv=126436, nf=253148, ne=379722, g=70) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 8777 ambiguous faces found in tessellation segmenting defects... 79 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 39 into 46 -merging segment 52 into 51 77 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9785 (-4.4893) -vertex loglikelihood: -6.1058 (-3.0529) -normal dot loglikelihood: -3.6292 (-3.6292) -quad curv loglikelihood: -6.2908 (-3.1454) Total Loglikelihood : -25.0043 CORRECTING DEFECT 0 (vertices=37, convex hull=48, v0=1416) After retessellation of defect 0 (v0=1416), euler #=-75 (121054,360879,239750) : difference with theory (-74) = 1 CORRECTING DEFECT 1 (vertices=68, convex hull=89, v0=2990) After retessellation of defect 1 (v0=2990), euler #=-74 (121074,360976,239828) : difference with theory (-73) = 1 CORRECTING DEFECT 2 (vertices=160, convex hull=128, v0=3615) After retessellation of defect 2 (v0=3615), euler #=-73 (121110,361137,239954) : difference with theory (-72) = 1 CORRECTING DEFECT 3 (vertices=28, convex hull=67, v0=6649) After retessellation of defect 3 (v0=6649), euler #=-72 (121124,361205,240009) : difference with theory (-71) = 1 CORRECTING DEFECT 4 (vertices=27, convex hull=15, v0=7739) After retessellation of defect 4 (v0=7739), euler #=-71 (121124,361207,240012) : difference with theory (-70) = 1 CORRECTING DEFECT 5 (vertices=44, convex hull=83, v0=13591) After retessellation of defect 5 (v0=13591), euler #=-70 (121155,361334,240109) : difference with theory (-69) = 1 CORRECTING DEFECT 6 (vertices=35, convex hull=76, v0=14258) After retessellation of defect 6 (v0=14258), euler #=-69 (121168,361406,240169) : difference with theory (-68) = 1 CORRECTING DEFECT 7 (vertices=23, convex hull=65, v0=16499) After retessellation of defect 7 (v0=16499), euler #=-68 (121178,361462,240216) : difference with theory (-67) = 1 CORRECTING DEFECT 8 (vertices=33, convex hull=60, v0=25093) After retessellation of defect 8 (v0=25093), euler #=-67 (121189,361518,240262) : difference with theory (-66) = 1 CORRECTING DEFECT 9 (vertices=37, convex hull=64, v0=27077) After retessellation of defect 9 (v0=27077), euler #=-66 (121207,361596,240323) : difference with theory (-65) = 1 CORRECTING DEFECT 10 (vertices=843, convex hull=160, v0=27716) After retessellation of defect 10 (v0=27716), euler #=-65 (121279,361879,240535) : difference with theory (-64) = 1 CORRECTING DEFECT 11 (vertices=22, convex hull=25, v0=28516) After retessellation of defect 11 (v0=28516), euler #=-64 (121283,361898,240551) : difference with theory (-63) = 1 CORRECTING DEFECT 12 (vertices=61, convex hull=38, v0=29828) After retessellation of defect 12 (v0=29828), euler #=-63 (121292,361937,240582) : difference with theory (-62) = 1 CORRECTING DEFECT 13 (vertices=39, convex hull=27, v0=31191) After retessellation of defect 13 (v0=31191), euler #=-62 (121297,361963,240604) : difference with theory (-61) = 1 CORRECTING DEFECT 14 (vertices=37, convex hull=66, v0=34138) After retessellation of defect 14 (v0=34138), euler #=-61 (121314,362036,240661) : difference with theory (-60) = 1 CORRECTING DEFECT 15 (vertices=95, convex hull=114, v0=35941) After retessellation of defect 15 (v0=35941), euler #=-60 (121350,362195,240785) : difference with theory (-59) = 1 CORRECTING DEFECT 16 (vertices=24, convex hull=60, v0=42207) After retessellation of defect 16 (v0=42207), euler #=-59 (121361,362249,240829) : difference with theory (-58) = 1 CORRECTING DEFECT 17 (vertices=91, convex hull=112, v0=42629) After retessellation of defect 17 (v0=42629), euler #=-58 (121423,362491,241010) : difference with theory (-57) = 1 CORRECTING DEFECT 18 (vertices=14, convex hull=25, v0=42773) After retessellation of defect 18 (v0=42773), euler #=-57 (121425,362507,241025) : difference with theory (-56) = 1 CORRECTING DEFECT 19 (vertices=73, convex hull=88, v0=46442) After retessellation of defect 19 (v0=46442), euler #=-56 (121451,362623,241116) : difference with theory (-55) = 1 CORRECTING DEFECT 20 (vertices=131, convex hull=160, v0=47640) After retessellation of defect 20 (v0=47640), euler #=-55 (121465,362739,241219) : difference with theory (-54) = 1 CORRECTING DEFECT 21 (vertices=67, convex hull=88, v0=47807) After retessellation of defect 21 (v0=47807), euler #=-54 (121495,362867,241318) : difference with theory (-53) = 1 CORRECTING DEFECT 22 (vertices=25, convex hull=57, v0=48026) After retessellation of defect 22 (v0=48026), euler #=-53 (121509,362930,241368) : difference with theory (-52) = 1 CORRECTING DEFECT 23 (vertices=49, convex hull=63, v0=49106) After retessellation of defect 23 (v0=49106), euler #=-52 (121531,363023,241440) : difference with theory (-51) = 1 CORRECTING DEFECT 24 (vertices=32, convex hull=72, v0=51000) After retessellation of defect 24 (v0=51000), euler #=-51 (121543,363086,241492) : difference with theory (-50) = 1 CORRECTING DEFECT 25 (vertices=143, convex hull=127, v0=54823) After retessellation of defect 25 (v0=54823), euler #=-50 (121556,363177,241571) : difference with theory (-49) = 1 CORRECTING DEFECT 26 (vertices=24, convex hull=43, v0=56715) After retessellation of defect 26 (v0=56715), euler #=-49 (121570,363236,241617) : difference with theory (-48) = 1 CORRECTING DEFECT 27 (vertices=34, convex hull=28, v0=58810) After retessellation of defect 27 (v0=58810), euler #=-48 (121574,363257,241635) : difference with theory (-47) = 1 CORRECTING DEFECT 28 (vertices=33, convex hull=54, v0=62226) After retessellation of defect 28 (v0=62226), euler #=-47 (121592,363329,241690) : difference with theory (-46) = 1 CORRECTING DEFECT 29 (vertices=113, convex hull=65, v0=63856) After retessellation of defect 29 (v0=63856), euler #=-46 (121601,363389,241742) : difference with theory (-45) = 1 CORRECTING DEFECT 30 (vertices=23, convex hull=37, v0=64810) After retessellation of defect 30 (v0=64810), euler #=-45 (121615,363445,241785) : difference with theory (-44) = 1 CORRECTING DEFECT 31 (vertices=23, convex hull=64, v0=66472) After retessellation of defect 31 (v0=66472), euler #=-44 (121624,363494,241826) : difference with theory (-43) = 1 CORRECTING DEFECT 32 (vertices=27, convex hull=48, v0=72303) After retessellation of defect 32 (v0=72303), euler #=-43 (121633,363538,241862) : difference with theory (-42) = 1 CORRECTING DEFECT 33 (vertices=48, convex hull=89, v0=74120) After retessellation of defect 33 (v0=74120), euler #=-42 (121651,363624,241931) : difference with theory (-41) = 1 CORRECTING DEFECT 34 (vertices=38, convex hull=83, v0=78234) After retessellation of defect 34 (v0=78234), euler #=-41 (121677,363735,242017) : difference with theory (-40) = 1 CORRECTING DEFECT 35 (vertices=25, convex hull=68, v0=80725) After retessellation of defect 35 (v0=80725), euler #=-40 (121693,363808,242075) : difference with theory (-39) = 1 CORRECTING DEFECT 36 (vertices=54, convex hull=35, v0=84169) After retessellation of defect 36 (v0=84169), euler #=-39 (121699,363836,242098) : difference with theory (-38) = 1 CORRECTING DEFECT 37 (vertices=54, convex hull=38, v0=84418) After retessellation of defect 37 (v0=84418), euler #=-38 (121707,363873,242128) : difference with theory (-37) = 1 CORRECTING DEFECT 38 (vertices=79, convex hull=96, v0=84713) After retessellation of defect 38 (v0=84713), euler #=-37 (121749,364046,242260) : difference with theory (-36) = 1 CORRECTING DEFECT 39 (vertices=32, convex hull=69, v0=85670) After retessellation of defect 39 (v0=85670), euler #=-36 (121765,364120,242319) : difference with theory (-35) = 1 CORRECTING DEFECT 40 (vertices=28, convex hull=54, v0=87898) After retessellation of defect 40 (v0=87898), euler #=-35 (121776,364172,242361) : difference with theory (-34) = 1 CORRECTING DEFECT 41 (vertices=31, convex hull=26, v0=89552) After retessellation of defect 41 (v0=89552), euler #=-34 (121779,364186,242373) : difference with theory (-33) = 1 CORRECTING DEFECT 42 (vertices=141, convex hull=64, v0=89881) After retessellation of defect 42 (v0=89881), euler #=-33 (121794,364258,242431) : difference with theory (-32) = 1 CORRECTING DEFECT 43 (vertices=102, convex hull=63, v0=90463) After retessellation of defect 43 (v0=90463), euler #=-32 (121823,364370,242515) : difference with theory (-31) = 1 CORRECTING DEFECT 44 (vertices=46, convex hull=58, v0=90482) After retessellation of defect 44 (v0=90482), euler #=-31 (121836,364438,242571) : difference with theory (-30) = 1 CORRECTING DEFECT 45 (vertices=227, convex hull=209, v0=91794) After retessellation of defect 45 (v0=91794), euler #=-29 (121921,364794,242844) : difference with theory (-29) = 0 CORRECTING DEFECT 46 (vertices=42, convex hull=39, v0=94064) After retessellation of defect 46 (v0=94064), euler #=-28 (121924,364815,242863) : difference with theory (-28) = 0 CORRECTING DEFECT 47 (vertices=35, convex hull=65, v0=94773) After retessellation of defect 47 (v0=94773), euler #=-27 (121942,364895,242926) : difference with theory (-27) = 0 CORRECTING DEFECT 48 (vertices=68, convex hull=39, v0=94823) After retessellation of defect 48 (v0=94823), euler #=-26 (121947,364924,242951) : difference with theory (-26) = 0 CORRECTING DEFECT 49 (vertices=68, convex hull=94, v0=95031) After retessellation of defect 49 (v0=95031), euler #=-25 (121990,365091,243076) : difference with theory (-25) = 0 CORRECTING DEFECT 50 (vertices=83, convex hull=104, v0=95407) After retessellation of defect 50 (v0=95407), euler #=-23 (122018,365225,243184) : difference with theory (-24) = -1 CORRECTING DEFECT 51 (vertices=56, convex hull=41, v0=96604) After retessellation of defect 51 (v0=96604), euler #=-22 (122025,365264,243217) : difference with theory (-23) = -1 CORRECTING DEFECT 52 (vertices=44, convex hull=64, v0=97308) After retessellation of defect 52 (v0=97308), euler #=-21 (122046,365352,243285) : difference with theory (-22) = -1 CORRECTING DEFECT 53 (vertices=8, convex hull=25, v0=98967) After retessellation of defect 53 (v0=98967), euler #=-20 (122051,365374,243303) : difference with theory (-21) = -1 CORRECTING DEFECT 54 (vertices=442, convex hull=177, v0=99115) After retessellation of defect 54 (v0=99115), euler #=-19 (122096,365584,243469) : difference with theory (-20) = -1 CORRECTING DEFECT 55 (vertices=40, convex hull=80, v0=99339) After retessellation of defect 55 (v0=99339), euler #=-18 (122111,365665,243536) : difference with theory (-19) = -1 CORRECTING DEFECT 56 (vertices=162, convex hull=142, v0=99876) After retessellation of defect 56 (v0=99876), euler #=-17 (122122,365763,243624) : difference with theory (-18) = -1 CORRECTING DEFECT 57 (vertices=23, convex hull=28, v0=102191) After retessellation of defect 57 (v0=102191), euler #=-16 (122125,365781,243640) : difference with theory (-17) = -1 CORRECTING DEFECT 58 (vertices=18, convex hull=27, v0=102323) After retessellation of defect 58 (v0=102323), euler #=-16 (122127,365799,243656) : difference with theory (-16) = 0 CORRECTING DEFECT 59 (vertices=118, convex hull=178, v0=104945) After retessellation of defect 59 (v0=104945), euler #=-15 (122178,366041,243848) : difference with theory (-15) = 0 CORRECTING DEFECT 60 (vertices=6, convex hull=24, v0=108613) After retessellation of defect 60 (v0=108613), euler #=-14 (122179,366050,243857) : difference with theory (-14) = 0 CORRECTING DEFECT 61 (vertices=25, convex hull=44, v0=108879) After retessellation of defect 61 (v0=108879), euler #=-13 (122188,366093,243892) : difference with theory (-13) = 0 CORRECTING DEFECT 62 (vertices=38, convex hull=64, v0=109941) After retessellation of defect 62 (v0=109941), euler #=-12 (122205,366173,243956) : difference with theory (-12) = 0 CORRECTING DEFECT 63 (vertices=80, convex hull=143, v0=111899) After retessellation of defect 63 (v0=111899), euler #=-11 (122255,366390,244124) : difference with theory (-11) = 0 CORRECTING DEFECT 64 (vertices=33, convex hull=70, v0=112258) After retessellation of defect 64 (v0=112258), euler #=-10 (122266,366446,244170) : difference with theory (-10) = 0 CORRECTING DEFECT 65 (vertices=39, convex hull=63, v0=113051) After retessellation of defect 65 (v0=113051), euler #=-9 (122286,366529,244234) : difference with theory (-9) = 0 CORRECTING DEFECT 66 (vertices=34, convex hull=66, v0=114479) After retessellation of defect 66 (v0=114479), euler #=-8 (122301,366601,244292) : difference with theory (-8) = 0 CORRECTING DEFECT 67 (vertices=17, convex hull=25, v0=115665) After retessellation of defect 67 (v0=115665), euler #=-7 (122304,366616,244305) : difference with theory (-7) = 0 CORRECTING DEFECT 68 (vertices=74, convex hull=103, v0=115828) After retessellation of defect 68 (v0=115828), euler #=-6 (122340,366772,244426) : difference with theory (-6) = 0 CORRECTING DEFECT 69 (vertices=71, convex hull=84, v0=117566) After retessellation of defect 69 (v0=117566), euler #=-5 (122376,366916,244535) : difference with theory (-5) = 0 CORRECTING DEFECT 70 (vertices=44, convex hull=72, v0=118377) After retessellation of defect 70 (v0=118377), euler #=-4 (122399,367009,244606) : difference with theory (-4) = 0 CORRECTING DEFECT 71 (vertices=30, convex hull=74, v0=120957) After retessellation of defect 71 (v0=120957), euler #=-3 (122412,367075,244660) : difference with theory (-3) = 0 CORRECTING DEFECT 72 (vertices=52, convex hull=73, v0=121460) After retessellation of defect 72 (v0=121460), euler #=-2 (122426,367150,244722) : difference with theory (-2) = 0 CORRECTING DEFECT 73 (vertices=111, convex hull=81, v0=121935) After retessellation of defect 73 (v0=121935), euler #=-1 (122454,367270,244815) : difference with theory (-1) = 0 CORRECTING DEFECT 74 (vertices=27, convex hull=60, v0=124499) After retessellation of defect 74 (v0=124499), euler #=0 (122465,367327,244862) : difference with theory (0) = 0 CORRECTING DEFECT 75 (vertices=29, convex hull=68, v0=124588) After retessellation of defect 75 (v0=124588), euler #=1 (122474,367382,244909) : difference with theory (1) = 0 CORRECTING DEFECT 76 (vertices=56, convex hull=81, v0=125408) After retessellation of defect 76 (v0=125408), euler #=2 (122501,367497,244998) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.07-->13.10) (max @ vno 95106 --> 105711) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.07-->13.10) (max @ vno 95106 --> 105711) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 243 mutations (33.8%), 476 crossovers (66.2%), 434 vertices were eliminated building final representation... 3935 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=122501, nf=244998, ne=367497, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 52.8 minutes 0 defective edges removing intersecting faces 000: 392 intersecting 001: 12 intersecting mris_fix_topology utimesec 3164.428933 mris_fix_topology stimesec 0.380942 mris_fix_topology ru_maxrss 396600 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 52621 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 52 mris_fix_topology ru_nivcsw 4923 FSRUNTIME@ mris_fix_topology rh 0.8793 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 123245 - 369729 + 246486 = 2 --> 0 holes F =2V-4: 246486 = 246490-4 (0) 2E=3F: 739458 = 739458 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 122501 - 367497 + 244998 = 2 --> 0 holes F =2V-4: 244998 = 245002-4 (0) 2E=3F: 734994 = 734994 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 72 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 36 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jul 6 22:36:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 22930 bright wm thresholded. 1582 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... computing class statistics... border white: 245706 voxels (1.46%) border gray 269674 voxels (1.61%) WM (94.0): 95.3 +- 7.2 [70.0 --> 110.0] GM (75.0) : 72.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.3 (was 70) setting MAX_BORDER_WHITE to 103.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 48.5 (was 40) setting MAX_GRAY to 88.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->4.14) (max @ vno 88683 --> 95207) face area 0.27 +- 0.13 (0.00-->3.38) mean absolute distance = 0.81 +- 1.07 4325 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=96+-6.1, GM=74+-12.2 mean inside = 91.2, mean outside = 76.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.1, 266 (266) missing vertices, mean dist 0.0 [0.9 (%43.1)->0.7 (%56.9))] %39 local maxima, %55 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 0.89 +- 0.26 (0.07-->4.43) (max @ vno 88683 --> 95207) face area 0.27 +- 0.14 (0.00-->3.66) mean absolute distance = 0.61 +- 0.94 6462 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2046797.4, rms=8.067 001: dt: 0.5000, sse=1255776.2, rms=5.755 (28.664%) 002: dt: 0.5000, sse=944171.1, rms=4.459 (22.521%) 003: dt: 0.5000, sse=816683.1, rms=3.820 (14.319%) 004: dt: 0.5000, sse=760212.3, rms=3.474 (9.055%) 005: dt: 0.5000, sse=719381.7, rms=3.221 (7.299%) 006: dt: 0.5000, sse=689809.1, rms=2.982 (7.421%) 007: dt: 0.5000, sse=662981.6, rms=2.819 (5.471%) 008: dt: 0.5000, sse=650938.7, rms=2.679 (4.961%) 009: dt: 0.5000, sse=632692.2, rms=2.582 (3.604%) rms = 2.55, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=632231.1, rms=2.551 (1.210%) 011: dt: 0.2500, sse=556101.4, rms=1.715 (32.761%) 012: dt: 0.2500, sse=544532.6, rms=1.548 (9.749%) rms = 1.53, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=542166.8, rms=1.525 (1.466%) 014: dt: 0.1250, sse=536924.2, rms=1.456 (4.560%) rms = 1.44, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=536347.5, rms=1.445 (0.778%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.2, 170 (71) missing vertices, mean dist -0.4 [0.8 (%60.1)->0.3 (%39.9))] %50 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.88 +- 0.26 (0.08-->4.56) (max @ vno 81852 --> 80916) face area 0.33 +- 0.17 (0.00-->4.41) mean absolute distance = 0.51 +- 0.63 4426 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=935697.1, rms=3.845 016: dt: 0.5000, sse=761803.3, rms=2.706 (29.621%) 017: dt: 0.5000, sse=712572.5, rms=2.306 (14.791%) rms = 2.32, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=679798.5, rms=1.986 (13.881%) 019: dt: 0.2500, sse=668583.9, rms=1.804 (9.161%) 020: dt: 0.2500, sse=664625.4, rms=1.733 (3.923%) 021: dt: 0.2500, sse=654933.0, rms=1.656 (4.443%) 022: dt: 0.2500, sse=651262.2, rms=1.582 (4.450%) 023: dt: 0.2500, sse=649756.2, rms=1.516 (4.180%) rms = 1.48, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=642525.0, rms=1.479 (2.456%) 025: dt: 0.1250, sse=645114.5, rms=1.392 (5.861%) rms = 1.37, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=634686.3, rms=1.370 (1.610%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=88.1, 164 (44) missing vertices, mean dist -0.3 [0.6 (%61.7)->0.3 (%38.3))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.87 +- 0.26 (0.04-->4.47) (max @ vno 81852 --> 80916) face area 0.32 +- 0.16 (0.00-->4.25) mean absolute distance = 0.41 +- 0.49 4008 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=822253.6, rms=3.252 027: dt: 0.5000, sse=708243.5, rms=2.146 (34.019%) 028: dt: 0.5000, sse=674920.9, rms=1.893 (11.769%) rms = 2.02, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=632624.6, rms=1.521 (19.636%) 030: dt: 0.2500, sse=626999.3, rms=1.389 (8.696%) rms = 1.39, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=635074.1, rms=1.388 (0.113%) 032: dt: 0.1250, sse=619105.2, rms=1.284 (7.447%) rms = 1.27, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=619395.2, rms=1.268 (1.237%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.0, 175 (27) missing vertices, mean dist -0.1 [0.5 (%56.7)->0.3 (%43.3))] %72 local maxima, %23 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/AD01/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=665738.2, rms=1.981 034: dt: 0.5000, sse=639183.9, rms=1.476 (25.473%) rms = 1.69, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=609231.8, rms=1.170 (20.769%) rms = 1.14, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=612415.6, rms=1.143 (2.294%) 037: dt: 0.1250, sse=599139.0, rms=1.034 (9.527%) rms = 1.01, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=589788.2, rms=1.009 (2.400%) positioning took 0.6 minutes generating cortex label... 11 non-cortical segments detected only using segment with 7478 vertices erasing segment 1 (vno[0] = 90415) erasing segment 2 (vno[0] = 91282) erasing segment 3 (vno[0] = 91307) erasing segment 4 (vno[0] = 93243) erasing segment 5 (vno[0] = 94072) erasing segment 6 (vno[0] = 94332) erasing segment 7 (vno[0] = 94894) erasing segment 8 (vno[0] = 95767) erasing segment 9 (vno[0] = 96661) erasing segment 10 (vno[0] = 96667) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.area vertex spacing 0.87 +- 0.27 (0.03-->4.52) (max @ vno 80916 --> 81852) face area 0.32 +- 0.16 (0.00-->4.02) refinement took 5.4 minutes #-------------------------------------------- #@# Make White Surf rh Wed Jul 6 22:41:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 22930 bright wm thresholded. 1582 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... computing class statistics... border white: 245706 voxels (1.46%) border gray 269674 voxels (1.61%) WM (94.0): 95.3 +- 7.2 [70.0 --> 110.0] GM (75.0) : 72.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 103.2 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 50.5 (was 40) setting MAX_GRAY to 88.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->5.75) (max @ vno 95093 --> 95106) face area 0.27 +- 0.13 (0.00-->4.79) mean absolute distance = 0.80 +- 1.03 3866 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=96+-6.1, GM=76+-9.6 mean inside = 91.6, mean outside = 78.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.3, 101 (101) missing vertices, mean dist 0.1 [0.9 (%40.1)->0.8 (%59.9))] %42 local maxima, %53 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.26 (0.09-->5.53) (max @ vno 95094 --> 94160) face area 0.27 +- 0.14 (0.00-->4.26) mean absolute distance = 0.57 +- 0.89 5706 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1731780.6, rms=7.212 001: dt: 0.5000, sse=1063770.6, rms=5.033 (30.214%) 002: dt: 0.5000, sse=789118.0, rms=3.683 (26.817%) 003: dt: 0.5000, sse=670305.2, rms=2.935 (20.325%) 004: dt: 0.5000, sse=627176.8, rms=2.598 (11.478%) 005: dt: 0.5000, sse=612920.9, rms=2.451 (5.673%) 006: dt: 0.5000, sse=604064.2, rms=2.389 (2.508%) rms = 2.36, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=599802.8, rms=2.356 (1.375%) 008: dt: 0.2500, sse=542506.5, rms=1.639 (30.446%) 009: dt: 0.2500, sse=534673.6, rms=1.495 (8.757%) rms = 1.47, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=530623.1, rms=1.467 (1.898%) 011: dt: 0.1250, sse=526572.2, rms=1.408 (4.002%) rms = 1.40, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=525151.9, rms=1.395 (0.931%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.5, 92 (31) missing vertices, mean dist -0.4 [0.8 (%62.2)->0.3 (%37.8))] %53 local maxima, %42 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 0.87 +- 0.26 (0.01-->7.42) (max @ vno 95093 --> 94160) face area 0.33 +- 0.17 (0.00-->5.58) mean absolute distance = 0.46 +- 0.58 4691 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=897951.9, rms=3.688 013: dt: 0.5000, sse=738848.5, rms=2.576 (30.139%) 014: dt: 0.5000, sse=690480.4, rms=2.188 (15.078%) rms = 2.16, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=688238.0, rms=2.160 (1.278%) 016: dt: 0.2500, sse=651244.1, rms=1.647 (23.761%) 017: dt: 0.2500, sse=639691.6, rms=1.539 (6.548%) 018: dt: 0.2500, sse=635316.1, rms=1.481 (3.789%) 019: dt: 0.2500, sse=632110.8, rms=1.426 (3.692%) rms = 1.39, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=629164.4, rms=1.387 (2.703%) 021: dt: 0.1250, sse=623145.0, rms=1.315 (5.230%) rms = 1.30, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=626967.2, rms=1.296 (1.460%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=88.5, 114 (20) missing vertices, mean dist -0.3 [0.6 (%64.1)->0.3 (%35.9))] %67 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.87 +- 0.26 (0.05-->8.02) (max @ vno 95093 --> 94160) face area 0.32 +- 0.17 (0.00-->6.67) mean absolute distance = 0.37 +- 0.45 3416 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=801319.1, rms=3.150 023: dt: 0.5000, sse=680698.9, rms=2.023 (35.760%) 024: dt: 0.5000, sse=647342.7, rms=1.797 (11.215%) rms = 1.89, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=615896.7, rms=1.445 (19.557%) 026: dt: 0.2500, sse=613202.0, rms=1.320 (8.634%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.28, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=607999.3, rms=1.281 (2.966%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.4, 143 (15) missing vertices, mean dist -0.1 [0.4 (%57.5)->0.3 (%42.5))] %76 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/AD01/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=645378.5, rms=1.872 028: dt: 0.5000, sse=622999.4, rms=1.457 (22.185%) rms = 1.64, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=596892.3, rms=1.149 (21.137%) rms = 1.14, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=596723.3, rms=1.143 (0.484%) 031: dt: 0.1250, sse=590816.2, rms=1.003 (12.293%) rms = 0.97, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=582420.2, rms=0.971 (3.130%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7548 vertices erasing segment 1 (vno[0] = 48916) erasing segment 2 (vno[0] = 52006) erasing segment 3 (vno[0] = 52020) erasing segment 4 (vno[0] = 90525) erasing segment 5 (vno[0] = 91414) erasing segment 6 (vno[0] = 91445) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label... writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.area vertex spacing 0.87 +- 0.27 (0.04-->8.42) (max @ vno 94160 --> 95093) face area 0.32 +- 0.17 (0.00-->7.29) refinement took 4.7 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jul 6 22:46:12 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Jul 6 22:46:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Jul 6 22:46:23 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.7 mm, total surface area = 69692 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.183 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 46.999854 mris_inflate stimesec 0.053991 mris_inflate ru_maxrss 159600 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 21538 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 50 mris_inflate ru_nivcsw 71 #-------------------------------------------- #@# Inflation2 rh Wed Jul 6 22:47:10 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.6 mm, total surface area = 69143 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.187 (target=0.015) step 005: RMS=0.132 (target=0.015) step 010: RMS=0.101 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. inflation took 0.8 minutes mris_inflate utimesec 46.637909 mris_inflate stimesec 0.087986 mris_inflate ru_maxrss 158780 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20820 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 68 #-------------------------------------------- #@# Curv .H and .K lh Wed Jul 6 22:47:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_curvature -w lh.white total integrated curvature = 16.544*4pi (207.897) --> -16 handles ICI = 232.3, FI = 1681.7, variation=28946.909 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 139 vertices thresholded to be in k1 ~ [-1.06 0.82], k2 ~ [-0.21 0.06] total integrated curvature = 0.497*4pi (6.247) --> 1 handles ICI = 1.4, FI = 8.6, variation=148.453 111 vertices thresholded to be in [-0.04 0.04] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 110 vertices thresholded to be in [-0.43 0.31] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.025 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Jul 6 22:49:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_curvature -w rh.white total integrated curvature = 19.250*4pi (241.905) --> -18 handles ICI = 241.1, FI = 1710.1, variation=29599.242 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 120 vertices thresholded to be in k1 ~ [-0.38 1.09], k2 ~ [-0.26 0.08] total integrated curvature = 0.486*4pi (6.108) --> 1 handles ICI = 1.3, FI = 7.9, variation=137.072 99 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 90 vertices thresholded to be in [-0.18 0.33] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Wed Jul 6 22:50:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm AD01 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 [ AD01/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 [ 283 ] Gb_filter = 0 WARN: S lookup min: -0.112872 WARN: S explicit min: 0.000000 vertex = 4 #----------------------------------------- #@# Curvature Stats rh Wed Jul 6 22:50:48 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm AD01 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 [ AD01/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 [ 286 ] Gb_filter = 0 WARN: S lookup min: -0.112285 WARN: S explicit min: 0.000000 vertex = 621 #-------------------------------------------- #@# Sphere lh Wed Jul 6 22:50:52 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl 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 0.349... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.83 pass 1: epoch 2 of 3 starting distance error %19.80 unfolding complete - removing small folds... starting distance error %19.72 removing remaining folds... final distance error %19.74 MRISunfold() return, current seed 1234 -01: dt=0.0000, 399 negative triangles 170: dt=0.9900, 399 negative triangles 171: dt=0.9900, 237 negative triangles 172: dt=0.9900, 210 negative triangles 173: dt=0.9900, 172 negative triangles 174: dt=0.9900, 145 negative triangles 175: dt=0.9900, 123 negative triangles 176: dt=0.9900, 135 negative triangles 177: dt=0.9900, 110 negative triangles 178: dt=0.9900, 105 negative triangles 179: dt=0.9900, 85 negative triangles 180: dt=0.9900, 91 negative triangles 181: dt=0.9900, 77 negative triangles 182: dt=0.9900, 73 negative triangles 183: dt=0.9900, 69 negative triangles 184: dt=0.9900, 77 negative triangles 185: dt=0.9900, 70 negative triangles 186: dt=0.9900, 56 negative triangles 187: dt=0.9900, 60 negative triangles 188: dt=0.9900, 59 negative triangles 189: dt=0.9900, 63 negative triangles 190: dt=0.9900, 56 negative triangles 191: dt=0.9900, 56 negative triangles 192: dt=0.9900, 50 negative triangles 193: dt=0.9900, 51 negative triangles 194: dt=0.9900, 55 negative triangles 195: dt=0.9900, 49 negative triangles 196: dt=0.9900, 48 negative triangles 197: dt=0.9900, 52 negative triangles 198: dt=0.9900, 47 negative triangles 199: dt=0.9900, 51 negative triangles 200: dt=0.9900, 47 negative triangles 201: dt=0.9900, 45 negative triangles 202: dt=0.9900, 50 negative triangles 203: dt=0.9900, 42 negative triangles 204: dt=0.9900, 44 negative triangles 205: dt=0.9900, 38 negative triangles 206: dt=0.9900, 39 negative triangles 207: dt=0.9900, 36 negative triangles 208: dt=0.9900, 35 negative triangles 209: dt=0.9900, 36 negative triangles 210: dt=0.9900, 35 negative triangles 211: dt=0.9900, 34 negative triangles 212: dt=0.9900, 28 negative triangles 213: dt=0.9900, 37 negative triangles 214: dt=0.9900, 30 negative triangles 215: dt=0.9900, 27 negative triangles 216: dt=0.9900, 34 negative triangles 217: dt=0.9900, 29 negative triangles 218: dt=0.9900, 26 negative triangles 219: dt=0.9900, 26 negative triangles 220: dt=0.9900, 26 negative triangles 221: dt=0.9900, 25 negative triangles 222: dt=0.9900, 26 negative triangles 223: dt=0.9900, 23 negative triangles 224: dt=0.9900, 25 negative triangles 225: dt=0.9900, 25 negative triangles 226: dt=0.9900, 24 negative triangles 227: dt=0.9900, 20 negative triangles 228: dt=0.9900, 21 negative triangles 229: dt=0.9900, 22 negative triangles 230: dt=0.9900, 24 negative triangles 231: dt=0.9900, 22 negative triangles 232: dt=0.9900, 21 negative triangles 233: dt=0.9900, 19 negative triangles 234: dt=0.9900, 21 negative triangles 235: dt=0.9900, 25 negative triangles 236: dt=0.9900, 22 negative triangles 237: dt=0.9900, 22 negative triangles 238: dt=0.9900, 17 negative triangles 239: dt=0.9900, 18 negative triangles 240: dt=0.9900, 21 negative triangles 241: dt=0.9900, 22 negative triangles 242: dt=0.9900, 17 negative triangles 243: dt=0.9900, 19 negative triangles 244: dt=0.9900, 19 negative triangles 245: dt=0.9900, 19 negative triangles 246: dt=0.9900, 21 negative triangles 247: dt=0.9900, 16 negative triangles 248: dt=0.9900, 15 negative triangles 249: dt=0.9900, 17 negative triangles 250: dt=0.9900, 14 negative triangles 251: dt=0.9900, 17 negative triangles 252: dt=0.9900, 17 negative triangles 253: dt=0.9900, 15 negative triangles 254: dt=0.9900, 16 negative triangles 255: dt=0.9900, 8 negative triangles 256: dt=0.9900, 14 negative triangles 257: dt=0.9900, 12 negative triangles 258: dt=0.9900, 11 negative triangles 259: dt=0.9900, 11 negative triangles 260: dt=0.9900, 14 negative triangles 261: dt=0.9900, 8 negative triangles 262: dt=0.9900, 13 negative triangles 263: dt=0.9900, 10 negative triangles 264: dt=0.9900, 10 negative triangles 265: dt=0.9405, 9 negative triangles 266: dt=0.9405, 11 negative triangles 267: dt=0.9405, 9 negative triangles 268: dt=0.9405, 9 negative triangles 269: dt=0.9405, 7 negative triangles 270: dt=0.9405, 6 negative triangles 271: dt=0.9405, 6 negative triangles 272: dt=0.9405, 3 negative triangles 273: dt=0.9405, 2 negative triangles 274: dt=0.9405, 2 negative triangles 275: dt=0.9405, 4 negative triangles 276: dt=0.9405, 5 negative triangles 277: dt=0.9405, 4 negative triangles 278: dt=0.9405, 3 negative triangles 279: dt=0.9405, 5 negative triangles 280: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.97 hours mris_sphere utimesec 3488.242706 mris_sphere stimesec 0.292955 mris_sphere ru_maxrss 219224 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 36050 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 51 mris_sphere ru_nivcsw 4340 FSRUNTIME@ mris_sphere 0.9692 hours 1 threads #-------------------------------------------- #@# Sphere rh Wed Jul 6 23:49:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl 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 0.350... 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 %20.28 pass 1: epoch 2 of 3 starting distance error %20.24 unfolding complete - removing small folds... starting distance error %20.11 removing remaining folds... final distance error %20.13 MRISunfold() return, current seed 1234 -01: dt=0.0000, 327 negative triangles 205: dt=0.9900, 327 negative triangles 206: dt=0.9900, 156 negative triangles 207: dt=0.9900, 131 negative triangles 208: dt=0.9900, 113 negative triangles 209: dt=0.9900, 89 negative triangles 210: dt=0.9900, 72 negative triangles 211: dt=0.9900, 78 negative triangles 212: dt=0.9900, 61 negative triangles 213: dt=0.9900, 49 negative triangles 214: dt=0.9900, 49 negative triangles 215: dt=0.9900, 49 negative triangles 216: dt=0.9900, 41 negative triangles 217: dt=0.9900, 46 negative triangles 218: dt=0.9900, 37 negative triangles 219: dt=0.9900, 37 negative triangles 220: dt=0.9900, 32 negative triangles 221: dt=0.9900, 37 negative triangles 222: dt=0.9900, 40 negative triangles 223: dt=0.9900, 28 negative triangles 224: dt=0.9900, 23 negative triangles 225: dt=0.9900, 18 negative triangles 226: dt=0.9900, 24 negative triangles 227: dt=0.9900, 22 negative triangles 228: dt=0.9900, 17 negative triangles 229: dt=0.9900, 20 negative triangles 230: dt=0.9900, 19 negative triangles 231: dt=0.9900, 13 negative triangles 232: dt=0.9900, 8 negative triangles 233: dt=0.9900, 6 negative triangles 234: dt=0.9900, 10 negative triangles 235: dt=0.9900, 6 negative triangles 236: dt=0.9900, 5 negative triangles 237: dt=0.9900, 4 negative triangles 238: dt=0.9900, 5 negative triangles 239: dt=0.9900, 6 negative triangles 240: dt=0.9900, 6 negative triangles 241: dt=0.9900, 3 negative triangles 242: dt=0.9900, 3 negative triangles 243: dt=0.9900, 2 negative triangles 244: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.99 hours mris_sphere utimesec 3580.748643 mris_sphere stimesec 0.373943 mris_sphere ru_maxrss 218088 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 36295 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 55 mris_sphere ru_nivcsw 4583 FSRUNTIME@ mris_sphere 0.9950 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Thu Jul 7 00:48:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl 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 = 5.226 curvature mean = 0.026, std = 0.816 curvature mean = 0.025, std = 0.872 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 301971.5, tmin=1.2626 d=32.00 min @ (0.00, 8.00, 0.00) sse = 262861.2, tmin=2.5522 d=16.00 min @ (0.00, 0.00, 4.00) sse = 252332.0, tmin=3.8457 d=8.00 min @ (2.00, 0.00, 0.00) sse = 246878.9, tmin=5.1489 d=4.00 min @ (0.00, 0.00, -1.00) sse = 245782.6, tmin=6.4570 d=2.00 min @ (0.00, -0.50, 0.00) sse = 245676.4, tmin=7.7671 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 245590.1, tmin=9.0741 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 10.38 min curvature mean = -0.018, std = 0.840 curvature mean = 0.007, std = 0.951 curvature mean = -0.022, std = 0.851 curvature mean = 0.002, std = 0.981 curvature mean = -0.023, std = 0.855 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.038, std = 0.336 curvature mean = 0.033, std = 0.246 curvature mean = 0.064, std = 0.318 curvature mean = 0.031, std = 0.305 curvature mean = 0.037, std = 0.482 curvature mean = 0.030, std = 0.331 curvature mean = 0.023, std = 0.604 curvature mean = 0.030, std = 0.341 curvature mean = 0.010, std = 0.718 MRISregister() return, current seed 0 -01: dt=0.0000, 173 negative triangles 110: dt=0.9900, 173 negative triangles expanding nbhd size to 1 111: dt=0.9900, 210 negative triangles 112: dt=0.9900, 181 negative triangles 113: dt=0.9900, 169 negative triangles 114: dt=0.9900, 167 negative triangles 115: dt=0.9900, 156 negative triangles 116: dt=0.9900, 157 negative triangles 117: dt=0.9900, 146 negative triangles 118: dt=0.9900, 139 negative triangles 119: dt=0.9900, 130 negative triangles 120: dt=0.9900, 125 negative triangles 121: dt=0.9900, 123 negative triangles 122: dt=0.9900, 116 negative triangles 123: dt=0.9900, 113 negative triangles 124: dt=0.9900, 104 negative triangles 125: dt=0.9900, 105 negative triangles 126: dt=0.9900, 93 negative triangles 127: dt=0.9900, 96 negative triangles 128: dt=0.9900, 83 negative triangles 129: dt=0.9900, 82 negative triangles 130: dt=0.9900, 80 negative triangles 131: dt=0.9900, 76 negative triangles 132: dt=0.9900, 70 negative triangles 133: dt=0.9900, 76 negative triangles 134: dt=0.9900, 66 negative triangles 135: dt=0.9900, 69 negative triangles 136: dt=0.9900, 64 negative triangles 137: dt=0.9900, 67 negative triangles 138: dt=0.9900, 62 negative triangles 139: dt=0.9900, 66 negative triangles 140: dt=0.9900, 59 negative triangles 141: dt=0.9900, 55 negative triangles 142: dt=0.9900, 50 negative triangles 143: dt=0.9900, 52 negative triangles 144: dt=0.9900, 49 negative triangles 145: dt=0.9900, 50 negative triangles 146: dt=0.9900, 47 negative triangles 147: dt=0.9900, 43 negative triangles 148: dt=0.9900, 45 negative triangles 149: dt=0.9900, 47 negative triangles 150: dt=0.9900, 46 negative triangles 151: dt=0.9900, 39 negative triangles 152: dt=0.9900, 38 negative triangles 153: dt=0.9900, 40 negative triangles 154: dt=0.9900, 36 negative triangles 155: dt=0.9900, 34 negative triangles 156: dt=0.9900, 33 negative triangles 157: dt=0.9900, 37 negative triangles 158: dt=0.9900, 35 negative triangles 159: dt=0.9900, 32 negative triangles 160: dt=0.9900, 31 negative triangles 161: dt=0.9900, 30 negative triangles 162: dt=0.9900, 30 negative triangles 163: dt=0.9900, 29 negative triangles 164: dt=0.9900, 28 negative triangles 165: dt=0.9900, 26 negative triangles 166: dt=0.9900, 23 negative triangles 167: dt=0.9900, 20 negative triangles 168: dt=0.9900, 16 negative triangles 169: dt=0.9900, 17 negative triangles 170: dt=0.9900, 15 negative triangles 171: dt=0.9900, 13 negative triangles 172: dt=0.9900, 13 negative triangles 173: dt=0.9900, 11 negative triangles 174: dt=0.9900, 11 negative triangles 175: dt=0.9900, 11 negative triangles 176: dt=0.9900, 11 negative triangles 177: dt=0.9900, 9 negative triangles 178: dt=0.9900, 8 negative triangles 179: dt=0.9900, 7 negative triangles 180: dt=0.9900, 8 negative triangles 181: dt=0.9900, 8 negative triangles 182: dt=0.9900, 7 negative triangles 183: dt=0.9900, 7 negative triangles 184: dt=0.9900, 7 negative triangles 185: dt=0.9900, 6 negative triangles 186: dt=0.9900, 6 negative triangles 187: dt=0.9900, 6 negative triangles 188: dt=0.9900, 5 negative triangles 189: dt=0.9900, 4 negative triangles 190: dt=0.9900, 5 negative triangles 191: dt=0.9900, 3 negative triangles 192: dt=0.9900, 3 negative triangles 193: dt=0.9900, 4 negative triangles 194: dt=0.9900, 3 negative triangles 195: dt=0.9900, 2 negative triangles 196: dt=0.9900, 4 negative triangles 197: dt=0.9900, 2 negative triangles 198: dt=0.9900, 3 negative triangles 199: dt=0.9900, 2 negative triangles 200: dt=0.9900, 3 negative triangles 201: dt=0.9900, 3 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 3 negative triangles 204: dt=0.9900, 2 negative triangles 205: dt=0.9405, 4 negative triangles 206: dt=0.9405, 1 negative triangles 207: dt=0.9405, 1 negative triangles 208: dt=0.9405, 2 negative triangles 209: dt=0.9405, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.76 hours mris_register utimesec 6345.321364 mris_register stimesec 0.585910 mris_register ru_maxrss 211800 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 27811 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 128 mris_register ru_nivcsw 6927 FSRUNTIME@ mris_register 1.7632 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Jul 7 02:34:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/scripts cmdline mris_register -curv -rusage /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.781 2016/06/13 21:20:50 fischl 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 = 5.192 curvature mean = 0.019, std = 0.819 curvature mean = 0.027, std = 0.870 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 303967.5, tmin=1.2772 d=32.00 min @ (8.00, 8.00, 8.00) sse = 266691.4, tmin=2.5774 d=16.00 min @ (0.00, -4.00, 0.00) sse = 254994.8, tmin=3.9115 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 251445.0, tmin=5.2189 d=4.00 min @ (1.00, 0.00, 1.00) sse = 250881.2, tmin=6.5119 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 250790.8, tmin=7.8066 d=1.00 min @ (0.00, 0.00, -0.25) sse = 250724.9, tmin=9.1082 d=0.50 min @ (0.12, -0.12, 0.12) sse = 250709.6, tmin=10.4080 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 10.41 min curvature mean = -0.023, std = 0.833 curvature mean = 0.009, std = 0.951 curvature mean = -0.026, std = 0.844 curvature mean = 0.003, std = 0.980 curvature mean = -0.028, std = 0.845 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.044, std = 0.344 curvature mean = 0.029, std = 0.239 curvature mean = 0.080, std = 0.313 curvature mean = 0.025, std = 0.299 curvature mean = 0.048, std = 0.476 curvature mean = 0.024, std = 0.326 curvature mean = 0.029, std = 0.603 curvature mean = 0.024, std = 0.337 curvature mean = 0.012, std = 0.713 MRISregister() return, current seed 0 -01: dt=0.0000, 50 negative triangles 110: dt=0.9900, 50 negative triangles expanding nbhd size to 1 111: dt=0.9900, 78 negative triangles 112: dt=0.9900, 54 negative triangles 113: dt=0.9900, 53 negative triangles 114: dt=0.9900, 48 negative triangles 115: dt=0.9900, 49 negative triangles 116: dt=0.9900, 40 negative triangles 117: dt=0.9900, 40 negative triangles 118: dt=0.9900, 32 negative triangles 119: dt=0.9900, 30 negative triangles 120: dt=0.9900, 25 negative triangles 121: dt=0.9900, 26 negative triangles 122: dt=0.9900, 23 negative triangles 123: dt=0.9900, 23 negative triangles 124: dt=0.9900, 22 negative triangles 125: dt=0.9900, 22 negative triangles 126: dt=0.9900, 13 negative triangles 127: dt=0.9900, 17 negative triangles 128: dt=0.9900, 12 negative triangles 129: dt=0.9900, 11 negative triangles 130: dt=0.9900, 10 negative triangles 131: dt=0.9900, 5 negative triangles 132: dt=0.9900, 6 negative triangles 133: dt=0.9900, 10 negative triangles 134: dt=0.9900, 7 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 5 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 3 negative triangles 139: dt=0.9900, 4 negative triangles 140: dt=0.9900, 4 negative triangles 141: dt=0.9900, 3 negative triangles 142: dt=0.9900, 3 negative triangles 143: dt=0.9900, 3 negative triangles 144: dt=0.9900, 4 negative triangles 145: dt=0.9900, 1 negative triangles 146: dt=0.9900, 1 negative triangles 147: dt=0.9900, 1 negative triangles 148: dt=0.9900, 1 negative triangles 149: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.26 hours mris_register utimesec 4548.845470 mris_register stimesec 0.478927 mris_register ru_maxrss 213560 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 29784 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 66 mris_register ru_nivcsw 28130 FSRUNTIME@ mris_register 1.2641 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Jul 7 03:50:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Thu Jul 7 03:50:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Thu Jul 7 03:50:26 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Thu Jul 7 03:50:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 Thu Jul 7 03:50:30 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 1168 labels changed using aseg relabeling using gibbs priors... 000: 2762 changed, 123245 examined... 001: 642 changed, 11795 examined... 002: 174 changed, 3583 examined... 003: 63 changed, 1022 examined... 004: 21 changed, 347 examined... 005: 6 changed, 138 examined... 006: 2 changed, 43 examined... 007: 0 changed, 14 examined... 260 labels changed using aseg 000: 129 total segments, 89 labels (379 vertices) changed 001: 44 total segments, 6 labels (13 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 7 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2086 vertices marked for relabeling... 2086 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Jul 7 03:50:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 780 labels changed using aseg relabeling using gibbs priors... 000: 2688 changed, 122501 examined... 001: 643 changed, 11501 examined... 002: 125 changed, 3625 examined... 003: 34 changed, 770 examined... 004: 15 changed, 208 examined... 005: 7 changed, 84 examined... 006: 3 changed, 38 examined... 007: 4 changed, 19 examined... 008: 0 changed, 21 examined... 176 labels changed using aseg 000: 105 total segments, 65 labels (361 vertices) changed 001: 43 total segments, 3 labels (13 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 13 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1342 vertices marked for relabeling... 1342 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Jul 7 03:50:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 22930 bright wm thresholded. 1582 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... computing class statistics... border white: 245706 voxels (1.46%) border gray 269674 voxels (1.61%) WM (94.0): 95.3 +- 7.2 [70.0 --> 110.0] GM (75.0) : 72.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.3 (was 70) setting MAX_BORDER_WHITE to 103.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 48.5 (was 40) setting MAX_GRAY to 88.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.8 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-6.1, GM=74+-12.2 mean inside = 91.2, mean outside = 76.7 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... deleting segment 1 with 74 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=59.2, 326 (326) missing vertices, mean dist 2.0 [0.0 (%0.0)->2.8 (%100.0))] %19 local maxima, %51 large gradients and %25 min vals, 107 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=22444754.0, rms=30.566 001: dt: 0.0500, sse=20517348.0, rms=29.189 (4.503%) 002: dt: 0.0500, sse=19190018.0, rms=28.202 (3.382%) 003: dt: 0.0500, sse=18155600.0, rms=27.408 (2.816%) 004: dt: 0.0500, sse=17297040.0, rms=26.731 (2.471%) 005: dt: 0.0500, sse=16553030.0, rms=26.129 (2.249%) 006: dt: 0.0500, sse=15888767.0, rms=25.581 (2.100%) 007: dt: 0.0500, sse=15283759.0, rms=25.071 (1.994%) 008: dt: 0.0500, sse=14723461.0, rms=24.589 (1.922%) 009: dt: 0.0500, sse=14198393.0, rms=24.128 (1.873%) 010: dt: 0.0500, sse=13702866.0, rms=23.685 (1.835%) positioning took 0.9 minutes mean border=58.9, 182 (139) missing vertices, mean dist 1.6 [0.1 (%0.1)->2.2 (%99.9))] %19 local maxima, %52 large gradients and %24 min vals, 110 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=14707206.0, rms=24.559 011: dt: 0.0500, sse=14230001.0, rms=24.141 (1.702%) 012: dt: 0.0500, sse=13774500.0, rms=23.736 (1.681%) 013: dt: 0.0500, sse=13338537.0, rms=23.340 (1.665%) 014: dt: 0.0500, sse=12920264.0, rms=22.955 (1.652%) 015: dt: 0.0500, sse=12519345.0, rms=22.579 (1.637%) 016: dt: 0.0500, sse=12134703.0, rms=22.213 (1.623%) 017: dt: 0.0500, sse=11766123.0, rms=21.856 (1.607%) 018: dt: 0.0500, sse=11412652.0, rms=21.508 (1.592%) 019: dt: 0.0500, sse=11073408.0, rms=21.168 (1.578%) 020: dt: 0.0500, sse=10747522.0, rms=20.837 (1.565%) positioning took 0.9 minutes mean border=58.7, 170 (94) missing vertices, mean dist 1.4 [0.1 (%1.4)->1.8 (%98.6))] %19 local maxima, %52 large gradients and %24 min vals, 97 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=10872494.0, rms=20.965 021: dt: 0.0500, sse=10544954.0, rms=20.629 (1.603%) 022: dt: 0.0500, sse=10231241.0, rms=20.302 (1.586%) 023: dt: 0.0500, sse=9926927.0, rms=19.979 (1.589%) 024: dt: 0.0500, sse=9637016.0, rms=19.667 (1.563%) 025: dt: 0.0500, sse=9361124.0, rms=19.365 (1.535%) 026: dt: 0.0500, sse=9097839.0, rms=19.072 (1.511%) 027: dt: 0.0500, sse=8844257.0, rms=18.786 (1.501%) 028: dt: 0.0500, sse=8596620.0, rms=18.502 (1.511%) 029: dt: 0.0500, sse=8354540.0, rms=18.221 (1.523%) 030: dt: 0.0500, sse=8117866.5, rms=17.941 (1.536%) positioning took 0.9 minutes mean border=58.5, 209 (79) missing vertices, mean dist 1.1 [0.1 (%12.0)->1.7 (%88.0))] %20 local maxima, %52 large gradients and %23 min vals, 92 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8248338.0, rms=18.093 031: dt: 0.5000, sse=6489930.5, rms=15.887 (12.196%) 032: dt: 0.5000, sse=5131078.0, rms=13.937 (12.271%) 033: dt: 0.5000, sse=4031184.0, rms=12.141 (12.886%) 034: dt: 0.5000, sse=3181649.2, rms=10.536 (13.225%) 035: dt: 0.5000, sse=2564481.2, rms=9.203 (12.645%) 036: dt: 0.5000, sse=2163905.0, rms=8.214 (10.754%) 037: dt: 0.5000, sse=1901639.5, rms=7.503 (8.648%) 038: dt: 0.5000, sse=1745718.6, rms=7.035 (6.235%) 039: dt: 0.5000, sse=1639300.1, rms=6.706 (4.685%) 040: dt: 0.5000, sse=1576436.0, rms=6.495 (3.151%) 041: dt: 0.5000, sse=1520506.0, rms=6.310 (2.846%) 042: dt: 0.5000, sse=1488976.2, rms=6.194 (1.836%) 043: dt: 0.5000, sse=1454490.9, rms=6.075 (1.916%) 044: dt: 0.5000, sse=1436471.2, rms=6.005 (1.160%) 045: dt: 0.5000, sse=1414328.8, rms=5.928 (1.286%) rms = 5.88, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1403895.8, rms=5.883 (0.748%) 047: dt: 0.2500, sse=1236027.2, rms=5.188 (11.817%) 048: dt: 0.2500, sse=1195156.6, rms=5.012 (3.388%) rms = 4.99, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1191346.8, rms=4.990 (0.437%) 050: dt: 0.1250, sse=1168688.6, rms=4.885 (2.120%) rms = 4.87, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1165714.9, rms=4.870 (0.291%) positioning took 2.1 minutes mean border=57.6, 1509 (30) missing vertices, mean dist 0.2 [0.2 (%50.2)->0.7 (%49.8))] %30 local maxima, %45 large gradients and %19 min vals, 75 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=1290714.2, rms=5.010 052: dt: 0.5000, sse=1239537.0, rms=4.803 (4.141%) rms = 4.92, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1104643.5, rms=4.125 (14.122%) 054: dt: 0.2500, sse=1048985.0, rms=3.814 (7.532%) 055: dt: 0.2500, sse=1025833.4, rms=3.680 (3.513%) 056: dt: 0.2500, sse=1013746.5, rms=3.610 (1.890%) 057: dt: 0.2500, sse=1003356.4, rms=3.551 (1.645%) rms = 3.51, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=996449.4, rms=3.510 (1.147%) 059: dt: 0.1250, sse=976376.2, rms=3.376 (3.827%) rms = 3.34, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=971178.8, rms=3.343 (0.971%) positioning took 0.9 minutes mean border=57.2, 1819 (24) missing vertices, mean dist 0.1 [0.1 (%59.3)->0.5 (%40.7))] %42 local maxima, %35 large gradients and %17 min vals, 90 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=1001952.2, rms=3.620 rms = 3.95, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=968513.7, rms=3.416 (5.625%) 062: dt: 0.2500, sse=955675.8, rms=3.342 (2.164%) rms = 3.33, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=952116.3, rms=3.327 (0.462%) 064: dt: 0.1250, sse=939320.6, rms=3.237 (2.714%) rms = 3.21, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=935435.1, rms=3.212 (0.763%) positioning took 0.6 minutes mean border=56.6, 3001 (21) missing vertices, mean dist 0.1 [0.1 (%55.3)->0.4 (%44.7))] %47 local maxima, %29 large gradients and %17 min vals, 100 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/AD01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=963975.9, rms=3.396 rms = 3.71, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=936331.9, rms=3.215 (5.317%) 067: dt: 0.2500, sse=919217.6, rms=3.110 (3.264%) rms = 3.06, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=911267.1, rms=3.062 (1.540%) 069: dt: 0.1250, sse=897387.2, rms=2.959 (3.367%) rms = 2.92, time step reduction 3 of 3 to 0.062... 070: dt: 0.1250, sse=891745.1, rms=2.921 (1.309%) positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.area.pial vertex spacing 0.93 +- 0.39 (0.05-->5.66) (max @ vno 83830 --> 80888) face area 0.35 +- 0.27 (0.00-->7.68) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123245 vertices processed 25000 of 123245 vertices processed 50000 of 123245 vertices processed 75000 of 123245 vertices processed 100000 of 123245 vertices processed 0 of 123245 vertices processed 25000 of 123245 vertices processed 50000 of 123245 vertices processed 75000 of 123245 vertices processed 100000 of 123245 vertices processed thickness calculation complete, 569:929 truncations. 33625 vertices at 0 distance 86550 vertices at 1 distance 65779 vertices at 2 distance 30183 vertices at 3 distance 11715 vertices at 4 distance 4197 vertices at 5 distance 1479 vertices at 6 distance 614 vertices at 7 distance 298 vertices at 8 distance 127 vertices at 9 distance 75 vertices at 10 distance 52 vertices at 11 distance 28 vertices at 12 distance 28 vertices at 13 distance 28 vertices at 14 distance 19 vertices at 15 distance 19 vertices at 16 distance 15 vertices at 17 distance 9 vertices at 18 distance 7 vertices at 19 distance 11 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.thickness positioning took 9.2 minutes #-------------------------------------------- #@# Make Pial Surf rh Thu Jul 7 04:00:09 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs AD01 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 1.781 2016/06/13 21:20:50 fischl Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 22930 bright wm thresholded. 1582 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... computing class statistics... border white: 245706 voxels (1.46%) border gray 269674 voxels (1.61%) WM (94.0): 95.3 +- 7.2 [70.0 --> 110.0] GM (75.0) : 72.5 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 103.2 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 50.5 (was 40) setting MAX_GRAY to 88.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.8 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-6.1, GM=76+-9.6 mean inside = 91.6, mean outside = 78.2 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 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=60.8, 193 (193) missing vertices, mean dist 2.1 [0.2 (%0.0)->2.9 (%100.0))] %20 local maxima, %48 large gradients and %27 min vals, 142 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=20587758.0, rms=29.352 001: dt: 0.0500, sse=18811914.0, rms=28.022 (4.533%) 002: dt: 0.0500, sse=17600498.0, rms=27.076 (3.373%) 003: dt: 0.0500, sse=16664007.0, rms=26.322 (2.785%) 004: dt: 0.0500, sse=15891763.0, rms=25.684 (2.426%) 005: dt: 0.0500, sse=15226268.0, rms=25.120 (2.194%) 006: dt: 0.0500, sse=14637081.0, rms=24.611 (2.029%) 007: dt: 0.0500, sse=14103310.0, rms=24.139 (1.914%) 008: dt: 0.0500, sse=13612040.0, rms=23.698 (1.831%) 009: dt: 0.0500, sse=13153548.0, rms=23.278 (1.772%) 010: dt: 0.0500, sse=12722095.0, rms=22.875 (1.728%) positioning took 0.9 minutes mean border=60.5, 130 (73) missing vertices, mean dist 1.7 [0.1 (%0.1)->2.3 (%99.9))] %21 local maxima, %49 large gradients and %25 min vals, 128 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=13692823.0, rms=23.763 011: dt: 0.0500, sse=13279380.0, rms=23.386 (1.587%) 012: dt: 0.0500, sse=12885910.0, rms=23.021 (1.559%) 013: dt: 0.0500, sse=12509759.0, rms=22.667 (1.538%) 014: dt: 0.0500, sse=12150033.0, rms=22.323 (1.517%) 015: dt: 0.0500, sse=11804999.0, rms=21.988 (1.500%) 016: dt: 0.0500, sse=11474548.0, rms=21.663 (1.481%) 017: dt: 0.0500, sse=11157025.0, rms=21.345 (1.466%) 018: dt: 0.0500, sse=10852040.0, rms=21.035 (1.451%) 019: dt: 0.0500, sse=10558809.0, rms=20.733 (1.436%) 020: dt: 0.0500, sse=10276972.0, rms=20.438 (1.421%) positioning took 0.9 minutes mean border=60.3, 154 (56) missing vertices, mean dist 1.4 [0.1 (%1.2)->1.9 (%98.8))] %21 local maxima, %49 large gradients and %25 min vals, 112 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=10390610.0, rms=20.561 021: dt: 0.0500, sse=10108037.0, rms=20.263 (1.449%) 022: dt: 0.0500, sse=9837333.0, rms=19.974 (1.429%) 023: dt: 0.0500, sse=9573887.0, rms=19.687 (1.432%) 024: dt: 0.0500, sse=9321550.0, rms=19.410 (1.412%) 025: dt: 0.0500, sse=9080003.0, rms=19.140 (1.391%) 026: dt: 0.0500, sse=8847766.0, rms=18.876 (1.375%) 027: dt: 0.0500, sse=8622841.0, rms=18.618 (1.369%) 028: dt: 0.0500, sse=8402996.0, rms=18.362 (1.376%) 029: dt: 0.0500, sse=8187670.5, rms=18.107 (1.386%) 030: dt: 0.0500, sse=7976459.5, rms=17.854 (1.399%) positioning took 0.9 minutes mean border=60.2, 199 (48) missing vertices, mean dist 1.2 [0.1 (%9.7)->1.7 (%90.3))] %21 local maxima, %50 large gradients and %24 min vals, 129 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=8105210.0, rms=18.008 031: dt: 0.5000, sse=6496369.0, rms=15.971 (11.311%) 032: dt: 0.5000, sse=5197998.5, rms=14.108 (11.665%) 033: dt: 0.5000, sse=4130972.8, rms=12.374 (12.289%) 034: dt: 0.5000, sse=3285310.8, rms=10.795 (12.759%) 035: dt: 0.5000, sse=2659879.0, rms=9.465 (12.321%) 036: dt: 0.5000, sse=2212790.2, rms=8.378 (11.485%) 037: dt: 0.5000, sse=1903197.5, rms=7.538 (10.024%) 038: dt: 0.5000, sse=1693608.8, rms=6.905 (8.405%) 039: dt: 0.5000, sse=1552265.8, rms=6.448 (6.616%) 040: dt: 0.5000, sse=1461795.4, rms=6.128 (4.956%) 041: dt: 0.5000, sse=1399406.6, rms=5.906 (3.624%) 042: dt: 0.5000, sse=1358372.5, rms=5.745 (2.730%) 043: dt: 0.5000, sse=1329328.4, rms=5.637 (1.873%) 044: dt: 0.5000, sse=1304850.4, rms=5.536 (1.796%) 045: dt: 0.5000, sse=1285633.1, rms=5.464 (1.295%) 046: dt: 0.5000, sse=1272653.5, rms=5.405 (1.087%) rms = 5.36, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1261399.2, rms=5.364 (0.767%) 048: dt: 0.2500, sse=1121628.5, rms=4.704 (12.304%) 049: dt: 0.2500, sse=1083315.0, rms=4.523 (3.845%) rms = 4.52, time step reduction 2 of 3 to 0.125... 050: dt: 0.2500, sse=1084057.5, rms=4.519 (0.081%) 051: dt: 0.1250, sse=1064362.0, rms=4.416 (2.276%) rms = 4.40, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1061463.4, rms=4.401 (0.343%) positioning took 2.2 minutes mean border=59.1, 1286 (15) missing vertices, mean dist 0.2 [0.2 (%48.5)->0.6 (%51.5))] %34 local maxima, %40 large gradients and %20 min vals, 93 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=1239585.6, rms=4.750 053: dt: 0.5000, sse=1161250.0, rms=4.394 (7.502%) rms = 4.38, time step reduction 1 of 3 to 0.250... 054: dt: 0.5000, sse=1151316.9, rms=4.380 (0.306%) 055: dt: 0.2500, sse=986034.7, rms=3.384 (22.754%) 056: dt: 0.2500, sse=947357.4, rms=3.121 (7.754%) 057: dt: 0.2500, sse=935111.6, rms=3.030 (2.942%) 058: dt: 0.2500, sse=925478.4, rms=2.962 (2.231%) rms = 2.92, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=920231.9, rms=2.924 (1.288%) 060: dt: 0.1250, sse=902695.7, rms=2.780 (4.913%) rms = 2.74, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=897898.0, rms=2.742 (1.375%) positioning took 0.9 minutes mean border=58.6, 1372 (13) missing vertices, mean dist 0.1 [0.1 (%55.6)->0.4 (%44.4))] %46 local maxima, %30 large gradients and %18 min vals, 102 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=938977.8, rms=3.162 rms = 3.55, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=899569.1, rms=2.877 (8.993%) 063: dt: 0.2500, sse=885075.1, rms=2.772 (3.678%) rms = 2.75, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=881571.2, rms=2.753 (0.664%) 065: dt: 0.1250, sse=869492.7, rms=2.649 (3.795%) rms = 2.61, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=864840.5, rms=2.612 (1.387%) positioning took 0.6 minutes mean border=58.0, 2440 (12) missing vertices, mean dist 0.1 [0.1 (%53.4)->0.3 (%46.6))] %51 local maxima, %25 large gradients and %17 min vals, 119 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/AD01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=891707.9, rms=2.836 rms = 3.25, time step reduction 1 of 3 to 0.250... 067: dt: 0.2500, sse=868044.9, rms=2.645 (6.724%) 068: dt: 0.2500, sse=858797.1, rms=2.580 (2.482%) rms = 2.57, time step reduction 2 of 3 to 0.125... 069: dt: 0.2500, sse=856220.3, rms=2.568 (0.452%) 070: dt: 0.1250, sse=845787.8, rms=2.473 (3.693%) rms = 2.44, time step reduction 3 of 3 to 0.062... 071: dt: 0.1250, sse=841290.5, rms=2.437 (1.466%) positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.area.pial vertex spacing 0.93 +- 0.40 (0.08-->7.72) (max @ vno 53068 --> 121545) face area 0.35 +- 0.28 (0.00-->9.46) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 122501 vertices processed 25000 of 122501 vertices processed 50000 of 122501 vertices processed 75000 of 122501 vertices processed 100000 of 122501 vertices processed 0 of 122501 vertices processed 25000 of 122501 vertices processed 50000 of 122501 vertices processed 75000 of 122501 vertices processed 100000 of 122501 vertices processed thickness calculation complete, 657:1356 truncations. 28705 vertices at 0 distance 79697 vertices at 1 distance 68965 vertices at 2 distance 33469 vertices at 3 distance 13585 vertices at 4 distance 4974 vertices at 5 distance 1902 vertices at 6 distance 798 vertices at 7 distance 318 vertices at 8 distance 149 vertices at 9 distance 85 vertices at 10 distance 57 vertices at 11 distance 33 vertices at 12 distance 26 vertices at 13 distance 12 vertices at 14 distance 23 vertices at 15 distance 17 vertices at 16 distance 17 vertices at 17 distance 18 vertices at 18 distance 20 vertices at 19 distance 18 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.thickness positioning took 9.2 minutes #-------------------------------------------- #@# Surf Volume lh Thu Jul 7 04:09:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 lh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label Total face volume 175170 Total vertex volume 171122 (mask=0) #@# AD01 lh 171122 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Jul 7 04:09:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 rh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.volume masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label Total face volume 184815 Total vertex volume 180803 (mask=0) #@# AD01 rh 180803 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Jul 7 04:09:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 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 = 11 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Jul 7 04:17:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 900 634 1173 1.996 0.442 0.081 0.013 4 0.5 bankssts 816 539 1588 3.539 0.791 0.147 0.032 17 0.9 caudalanteriorcingulate 3237 2019 3783 1.952 0.484 0.132 0.041 35 6.0 caudalmiddlefrontal 2259 1382 3067 2.094 0.564 0.146 0.049 33 4.2 cuneus 519 347 1686 3.544 0.758 0.121 0.044 7 0.7 entorhinal 3970 2682 7070 2.370 0.747 0.159 0.061 73 10.5 fusiform 4549 2797 5303 1.794 0.452 0.141 0.045 74 8.4 inferiorparietal 4159 2789 9003 2.545 0.920 0.162 0.063 89 11.2 inferiortemporal 1670 963 1848 1.913 0.677 0.116 0.036 24 2.3 isthmuscingulate 8033 4953 11335 2.185 0.639 0.141 0.050 116 17.0 lateraloccipital 3882 2527 6662 2.557 0.746 0.149 0.059 65 10.3 lateralorbitofrontal 4839 3189 6206 1.910 0.625 0.148 0.048 68 9.4 lingual 2827 1777 4753 2.559 0.889 0.129 0.050 39 5.6 medialorbitofrontal 3294 2052 6391 2.485 0.824 0.137 0.051 59 6.2 middletemporal 714 488 1573 2.673 0.960 0.110 0.027 8 0.6 parahippocampal 1815 1121 3101 2.705 0.723 0.123 0.039 26 3.2 paracentral 2644 1550 3620 2.270 0.609 0.123 0.048 31 5.1 parsopercularis 1164 674 2121 2.507 0.754 0.137 0.056 19 2.9 parsorbitalis 2197 1393 3266 2.257 0.554 0.136 0.060 41 5.7 parstriangularis 1952 1292 1998 1.732 0.467 0.151 0.046 28 3.6 pericalcarine 5530 3378 7057 1.948 0.613 0.123 0.039 59 9.5 postcentral 1381 848 2129 2.501 0.690 0.132 0.046 21 2.6 posteriorcingulate 7672 5005 10761 2.132 0.681 0.131 0.043 85 15.3 precentral 4054 2526 4817 1.822 0.548 0.124 0.040 56 6.5 precuneus 1210 758 2683 3.275 1.127 0.125 0.046 18 2.1 rostralanteriorcingulate 8020 4897 10693 2.099 0.552 0.141 0.048 115 16.0 rostralmiddlefrontal 10666 6753 16498 2.372 0.679 0.135 0.045 132 20.8 superiorfrontal 6694 4130 7903 1.861 0.494 0.130 0.041 77 11.6 superiorparietal 5128 3276 8156 2.272 0.636 0.121 0.041 70 8.2 superiortemporal 3865 2311 4983 2.093 0.628 0.123 0.044 46 6.8 supramarginal 395 232 820 2.429 0.616 0.166 0.068 9 1.0 frontalpole 789 547 2219 3.140 0.812 0.156 0.064 12 2.1 temporalpole 690 368 1008 2.428 0.376 0.110 0.033 6 0.9 transversetemporal 3861 2369 5848 2.736 0.752 0.128 0.054 50 8.6 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 AD01 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 900 556 1173 1.996 0.442 0.073 0.013 7 0.5 bankssts 816 502 1588 3.539 0.791 0.123 0.037 69 0.9 caudalanteriorcingulate 3237 1937 3783 1.952 0.484 0.102 0.023 35 3.2 caudalmiddlefrontal 2259 1551 3067 2.094 0.564 0.126 0.033 36 3.3 cuneus 519 573 1686 3.544 0.758 0.162 0.039 7 1.0 entorhinal 3970 3144 7070 2.370 0.747 0.144 0.043 84 8.1 fusiform 4549 3152 5303 1.794 0.452 0.129 0.028 52 5.3 inferiorparietal 4159 3721 9003 2.545 0.920 0.162 0.049 87 10.4 inferiortemporal 1670 1065 1848 1.913 0.677 0.134 0.037 51 2.6 isthmuscingulate 8033 5591 11335 2.185 0.639 0.125 0.033 191 11.7 lateraloccipital 3882 2645 6662 2.557 0.746 0.127 0.038 80 6.2 lateralorbitofrontal 4839 3525 6206 1.910 0.625 0.135 0.035 93 7.2 lingual 2827 1981 4753 2.559 0.889 0.132 0.037 43 4.3 medialorbitofrontal 3294 2703 6391 2.485 0.824 0.145 0.034 60 4.8 middletemporal 714 663 1573 2.673 0.960 0.160 0.039 16 1.1 parahippocampal 1815 1241 3101 2.705 0.723 0.098 0.023 19 1.8 paracentral 2644 1658 3620 2.270 0.609 0.101 0.022 21 2.4 parsopercularis 1164 976 2121 2.507 0.754 0.152 0.047 22 2.3 parsorbitalis 2197 1465 3266 2.257 0.554 0.123 0.027 32 2.4 parstriangularis 1952 1076 1998 1.732 0.467 0.117 0.034 42 2.8 pericalcarine 5530 3948 7057 1.948 0.613 0.110 0.025 45 5.9 postcentral 1381 880 2129 2.501 0.690 0.130 0.039 32 2.2 posteriorcingulate 7672 5332 10761 2.132 0.681 0.112 0.034 134 13.1 precentral 4054 2811 4817 1.822 0.548 0.121 0.026 46 4.4 precuneus 1210 921 2683 3.275 1.127 0.125 0.023 19 1.2 rostralanteriorcingulate 8020 5347 10693 2.099 0.552 0.129 0.035 213 13.2 rostralmiddlefrontal 10666 7278 16498 2.372 0.679 0.115 0.031 179 13.6 superiorfrontal 6694 4421 7903 1.861 0.494 0.119 0.028 75 7.7 superiorparietal 5128 3701 8156 2.272 0.636 0.118 0.026 64 5.4 superiortemporal 3865 2514 4983 2.093 0.628 0.108 0.024 34 3.9 supramarginal 395 397 820 2.429 0.616 0.197 0.035 5 0.7 frontalpole 789 855 2219 3.140 0.812 0.157 0.029 8 1.0 temporalpole 690 451 1008 2.428 0.376 0.089 0.017 4 0.4 transversetemporal 3861 1909 5848 2.736 0.752 0.100 0.037 119 4.5 insula #----------------------------------------- #@# Parcellation Stats rh Thu Jul 7 04:18:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 743 492 1084 2.299 0.768 0.130 0.047 10 1.4 bankssts 753 519 1516 3.097 0.753 0.157 0.035 16 0.9 caudalanteriorcingulate 3475 2085 4756 2.254 0.548 0.128 0.050 41 8.1 caudalmiddlefrontal 2028 1217 2553 2.062 0.662 0.144 0.055 33 4.7 cuneus 534 348 1856 3.452 0.962 0.129 0.074 11 1.4 entorhinal 3845 2585 7660 2.565 0.812 0.150 0.055 67 8.8 fusiform 4992 3109 7222 2.102 0.605 0.137 0.050 72 9.5 inferiorparietal 3518 2346 6669 2.532 0.930 0.148 0.052 57 7.6 inferiortemporal 1223 779 1734 2.078 0.760 0.137 0.059 20 2.8 isthmuscingulate 7201 4591 11625 2.397 0.669 0.149 0.054 105 15.7 lateraloccipital 3885 2504 6866 2.559 0.951 0.146 0.053 58 8.7 lateralorbitofrontal 4448 2946 6264 2.018 0.599 0.144 0.053 62 10.0 lingual 2536 1640 4389 2.406 0.788 0.131 0.038 37 3.5 medialorbitofrontal 3713 2400 7535 2.423 0.753 0.138 0.056 65 9.1 middletemporal 811 552 1615 2.558 0.798 0.104 0.031 8 0.8 parahippocampal 2350 1345 3306 2.425 0.651 0.116 0.037 25 3.6 paracentral 2525 1522 3918 2.359 0.603 0.129 0.060 35 6.3 parsopercularis 1234 740 2383 2.525 0.658 0.155 0.070 28 3.4 parsorbitalis 1997 1237 3052 2.384 0.593 0.136 0.060 37 4.3 parstriangularis 1820 1192 1785 1.732 0.479 0.142 0.043 23 3.1 pericalcarine 5195 3168 6600 1.971 0.719 0.120 0.036 60 8.0 postcentral 1316 909 2547 2.832 0.767 0.160 0.043 25 2.2 posteriorcingulate 7595 4859 10951 2.310 0.731 0.131 0.040 79 13.6 precentral 4822 3002 6248 1.987 0.565 0.123 0.040 61 8.0 precuneus 689 421 1905 3.711 0.532 0.132 0.048 10 1.3 rostralanteriorcingulate 8628 5197 12184 2.236 0.556 0.138 0.055 125 19.8 rostralmiddlefrontal 10975 6690 16841 2.478 0.675 0.140 0.052 164 24.4 superiorfrontal 8024 4732 11177 2.152 0.564 0.134 0.050 115 16.5 superiorparietal 4393 2875 7199 2.272 0.592 0.117 0.037 49 6.3 superiortemporal 4449 2732 6768 2.376 0.634 0.127 0.041 53 7.4 supramarginal 581 378 1111 2.359 0.791 0.186 0.078 14 2.0 frontalpole 548 369 2359 3.785 0.813 0.154 0.064 11 1.3 temporalpole 509 270 777 2.273 0.438 0.113 0.039 6 0.7 transversetemporal 3086 2014 6350 3.178 0.934 0.123 0.048 42 6.4 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 AD01 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 743 435 1084 2.299 0.768 0.125 0.083 60 0.9 bankssts 753 516 1516 3.097 0.753 0.186 0.043 59 1.6 caudalanteriorcingulate 3475 2114 4756 2.254 0.548 0.101 0.029 49 4.4 caudalmiddlefrontal 2028 1374 2553 2.062 0.662 0.126 0.032 28 3.1 cuneus 534 613 1856 3.452 0.962 0.185 0.042 9 1.0 entorhinal 3845 3067 7660 2.565 0.812 0.139 0.038 60 6.6 fusiform 4992 3583 7222 2.102 0.605 0.131 0.030 62 6.2 inferiorparietal 3518 2795 6669 2.532 0.930 0.149 0.040 56 6.3 inferiortemporal 1223 888 1734 2.078 0.760 0.143 0.044 21 2.1 isthmuscingulate 7201 5103 11625 2.397 0.669 0.124 0.031 114 9.9 lateraloccipital 3885 2747 6866 2.559 0.951 0.146 0.043 68 7.3 lateralorbitofrontal 4448 3312 6264 2.018 0.599 0.138 0.035 74 7.4 lingual 2536 1885 4389 2.406 0.788 0.137 0.030 42 3.0 medialorbitofrontal 3713 3454 7535 2.423 0.753 0.147 0.036 45 6.3 middletemporal 811 704 1615 2.558 0.798 0.135 0.030 7 1.1 parahippocampal 2350 1433 3306 2.425 0.651 0.098 0.024 26 2.4 paracentral 2525 1752 3918 2.359 0.603 0.124 0.029 27 3.2 parsopercularis 1234 1049 2383 2.525 0.658 0.154 0.036 31 2.0 parsorbitalis 1997 1262 3052 2.384 0.593 0.125 0.037 34 3.1 parstriangularis 1820 955 1785 1.732 0.479 0.113 0.032 35 2.4 pericalcarine 5195 3511 6600 1.971 0.719 0.106 0.022 52 4.9 postcentral 1316 947 2547 2.832 0.767 0.157 0.035 53 1.7 posteriorcingulate 7595 4803 10951 2.310 0.731 0.098 0.023 105 7.3 precentral 4822 3284 6248 1.987 0.565 0.116 0.025 48 4.9 precuneus 689 602 1905 3.711 0.532 0.143 0.024 7 0.7 rostralanteriorcingulate 8628 5654 12184 2.236 0.556 0.126 0.033 115 12.5 rostralmiddlefrontal 10975 6954 16841 2.478 0.675 0.110 0.034 185 16.2 superiorfrontal 8024 5576 11177 2.152 0.564 0.124 0.031 98 10.2 superiorparietal 4393 3354 7199 2.272 0.592 0.118 0.024 70 4.8 superiortemporal 4449 2880 6768 2.376 0.634 0.115 0.027 49 4.9 supramarginal 581 505 1111 2.359 0.791 0.171 0.041 14 1.1 frontalpole 548 735 2359 3.785 0.813 0.207 0.037 8 1.0 temporalpole 509 375 777 2.273 0.438 0.096 0.015 2 0.2 transversetemporal 3086 1746 6350 3.178 0.934 0.116 0.039 55 5.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Jul 7 04:19:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 34 labels changed using aseg relabeling using gibbs priors... 000: 7931 changed, 123245 examined... 001: 1896 changed, 31728 examined... 002: 583 changed, 10053 examined... 003: 247 changed, 3313 examined... 004: 111 changed, 1394 examined... 005: 44 changed, 624 examined... 006: 14 changed, 255 examined... 007: 8 changed, 74 examined... 008: 4 changed, 52 examined... 009: 2 changed, 27 examined... 010: 0 changed, 8 examined... 3 labels changed using aseg 000: 247 total segments, 159 labels (2019 vertices) changed 001: 92 total segments, 4 labels (19 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 46 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1510 vertices marked for relabeling... 1510 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Jul 7 04:20:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 49 labels changed using aseg relabeling using gibbs priors... 000: 8182 changed, 122501 examined... 001: 1927 changed, 32060 examined... 002: 575 changed, 10100 examined... 003: 237 changed, 3191 examined... 004: 111 changed, 1403 examined... 005: 62 changed, 620 examined... 006: 41 changed, 337 examined... 007: 20 changed, 227 examined... 008: 6 changed, 107 examined... 009: 5 changed, 38 examined... 010: 4 changed, 31 examined... 011: 3 changed, 26 examined... 012: 3 changed, 16 examined... 013: 1 changed, 15 examined... 014: 0 changed, 6 examined... 15 labels changed using aseg 000: 258 total segments, 172 labels (1982 vertices) changed 001: 90 total segments, 4 labels (19 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 942 vertices marked for relabeling... 942 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Jul 7 04:20:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 1202 765 1862 2.326 0.559 0.145 0.048 18 2.3 G&S_frontomargin 2121 1299 3097 2.157 0.657 0.145 0.052 35 4.3 G&S_occipital_inf 1293 773 2101 2.363 0.816 0.127 0.037 13 2.0 G&S_paracentral 1444 879 2502 2.472 0.593 0.135 0.049 22 2.7 G&S_subcentral 703 424 1310 2.315 0.529 0.163 0.065 16 1.6 G&S_transv_frontopol 1898 1284 4079 3.112 0.789 0.141 0.048 29 3.5 G&S_cingul-Ant 1202 800 2151 2.958 0.588 0.136 0.029 15 1.5 G&S_cingul-Mid-Ant 1144 744 1860 2.643 0.515 0.138 0.042 14 2.0 G&S_cingul-Mid-Post 435 218 741 2.373 0.506 0.117 0.042 6 0.8 G_cingul-Post-dorsal 425 243 606 2.102 0.521 0.131 0.046 6 0.7 G_cingul-Post-ventral 2272 1371 3322 2.103 0.575 0.147 0.052 34 4.7 G_cuneus 1509 803 2306 2.361 0.602 0.129 0.069 26 4.5 G_front_inf-Opercular 552 296 1046 2.481 0.612 0.130 0.055 7 1.3 G_front_inf-Orbital 1734 974 2495 2.235 0.555 0.145 0.078 43 6.0 G_front_inf-Triangul 4390 2554 5771 2.021 0.502 0.141 0.051 67 9.6 G_front_middle 6702 4046 11666 2.494 0.720 0.139 0.055 101 15.9 G_front_sup 778 433 1301 3.253 0.721 0.121 0.046 8 1.4 G_Ins_lg&S_cent_ins 1074 587 1599 2.491 0.845 0.158 0.095 25 4.2 G_insular_short 2228 1248 3550 2.297 0.559 0.135 0.062 40 6.1 G_occipital_middle 1586 995 2483 2.235 0.626 0.144 0.050 21 3.1 G_occipital_sup 1713 1116 2903 2.265 0.669 0.164 0.067 35 5.3 G_oc-temp_lat-fusifor 3340 2158 4274 1.834 0.605 0.157 0.055 53 7.3 G_oc-temp_med-Lingual 1056 675 2963 3.220 0.925 0.122 0.049 17 1.7 G_oc-temp_med-Parahip 2386 1442 4487 2.464 0.864 0.153 0.076 51 8.0 G_orbital 1702 955 1696 1.662 0.398 0.143 0.051 32 3.7 G_pariet_inf-Angular 1988 1143 2704 2.157 0.612 0.127 0.050 29 3.8 G_pariet_inf-Supramar 2428 1399 2777 1.852 0.461 0.123 0.042 28 4.4 G_parietal_sup 2034 1119 2656 1.993 0.546 0.134 0.049 28 4.5 G_postcentral 2972 1790 4481 2.148 0.814 0.125 0.045 38 6.0 G_precentral 1923 1097 2490 1.835 0.564 0.129 0.051 35 4.1 G_precuneus 1066 678 1845 2.230 0.898 0.153 0.064 19 3.2 G_rectus 891 511 1357 2.754 1.034 0.093 0.047 9 1.2 G_subcallosal 560 269 883 2.467 0.428 0.108 0.036 6 0.7 G_temp_sup-G_T_transv 2014 1201 3847 2.434 0.620 0.147 0.066 47 5.0 G_temp_sup-Lateral 754 493 1494 2.718 0.883 0.085 0.022 3 0.7 G_temp_sup-Plan_polar 743 467 1092 1.963 0.425 0.107 0.042 8 1.1 G_temp_sup-Plan_tempo 2370 1553 5573 2.550 0.974 0.177 0.074 64 7.5 G_temporal_inf 1923 1118 3804 2.465 0.847 0.140 0.059 43 4.1 G_temporal_middle 327 216 442 2.305 0.335 0.101 0.025 2 0.3 Lat_Fis-ant-Horizont 272 203 394 2.382 0.480 0.143 0.043 2 0.5 Lat_Fis-ant-Vertical 942 629 1160 2.235 0.568 0.114 0.033 8 1.4 Lat_Fis-post 2257 1399 3059 2.049 0.645 0.157 0.055 38 4.9 Pole_occipital 1720 1224 5654 3.196 0.815 0.164 0.065 30 4.5 Pole_temporal 2534 1691 2684 1.835 0.560 0.125 0.034 25 3.6 S_calcarine 3154 2237 3437 1.752 0.540 0.119 0.029 19 4.4 S_central 811 586 1061 1.977 0.603 0.093 0.012 3 0.5 S_cingul-Marginalis 470 320 750 2.895 0.491 0.124 0.037 3 0.7 S_circular_insula_ant 1285 930 1823 2.444 0.723 0.096 0.019 6 1.1 S_circular_insula_inf 1702 1176 2410 2.569 0.517 0.114 0.028 9 2.2 S_circular_insula_sup 801 546 1254 2.460 0.592 0.136 0.043 10 1.5 S_collat_transv_ant 642 438 600 1.841 0.484 0.148 0.040 7 1.1 S_collat_transv_post 2421 1530 2687 1.893 0.475 0.126 0.032 23 3.3 S_front_inf 1202 749 1418 2.105 0.509 0.130 0.039 11 1.9 S_front_middle 3566 2327 3870 1.863 0.527 0.129 0.039 43 6.3 S_front_sup 200 108 231 2.277 0.533 0.152 0.066 4 0.5 S_interm_prim-Jensen 2235 1432 2215 1.612 0.378 0.138 0.040 30 3.8 S_intrapariet&P_trans 795 560 955 2.058 0.489 0.132 0.031 6 1.1 S_oc_middle&Lunatus 1122 733 1326 1.991 0.491 0.132 0.042 13 2.2 S_oc_sup&transversal 574 375 676 2.253 0.580 0.113 0.025 4 0.6 S_occipital_ant 675 457 863 2.075 0.526 0.122 0.046 8 1.4 S_oc-temp_lat 1734 1260 2662 2.356 0.630 0.153 0.044 25 3.1 S_oc-temp_med&Lingual 297 203 417 2.675 0.517 0.142 0.050 4 0.4 S_orbital_lateral 594 401 742 2.338 0.799 0.135 0.035 8 0.9 S_orbital_med-olfact 1531 1023 2721 2.697 0.631 0.149 0.049 22 3.4 S_orbital-H_Shaped 1823 1188 1945 1.764 0.514 0.126 0.034 19 2.4 S_parieto_occipital 1424 853 1372 2.454 1.298 0.122 0.032 25 1.6 S_pericallosal 2051 1354 2370 1.960 0.546 0.122 0.030 15 2.9 S_postcentral 1811 1203 2154 1.975 0.424 0.117 0.031 13 2.4 S_precentral-inf-part 1456 1019 1775 2.274 0.435 0.150 0.042 15 2.8 S_precentral-sup-part 664 443 1204 2.926 0.808 0.129 0.030 7 0.7 S_suborbital 627 390 703 1.853 0.420 0.145 0.038 11 1.0 S_subparietal 1051 704 1526 2.266 0.771 0.133 0.034 10 1.6 S_temporal_inf 3701 2488 4987 2.064 0.573 0.118 0.031 38 4.4 S_temporal_sup 369 253 400 2.111 0.420 0.136 0.032 3 0.6 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Jul 7 04:20:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 1151 721 1695 2.271 0.597 0.157 0.056 17 2.8 G&S_frontomargin 1136 708 2062 2.390 0.624 0.146 0.063 19 2.8 G&S_occipital_inf 1325 775 1751 2.085 0.682 0.127 0.043 16 2.2 G&S_paracentral 1421 885 2669 2.715 0.698 0.151 0.055 23 3.0 G&S_subcentral 1360 798 2247 2.343 0.598 0.147 0.063 23 3.7 G&S_transv_frontopol 2398 1568 4717 2.835 0.736 0.121 0.033 25 3.2 G&S_cingul-Ant 1372 908 2736 3.015 0.668 0.151 0.049 26 2.5 G&S_cingul-Mid-Ant 1494 916 2704 2.904 0.574 0.119 0.037 17 2.1 G&S_cingul-Mid-Post 331 218 726 2.669 0.786 0.169 0.078 7 0.9 G_cingul-Post-dorsal 327 203 579 2.314 0.606 0.153 0.074 7 1.1 G_cingul-Post-ventral 2097 1209 2596 2.057 0.686 0.147 0.058 40 5.3 G_cuneus 1624 951 2958 2.508 0.573 0.135 0.069 28 4.9 G_front_inf-Opercular 434 230 765 2.356 0.665 0.167 0.097 18 1.6 G_front_inf-Orbital 1048 617 1914 2.524 0.633 0.148 0.074 21 2.8 G_front_inf-Triangul 4288 2306 6407 2.236 0.573 0.141 0.068 81 13.1 G_front_middle 7485 4311 11787 2.467 0.675 0.148 0.060 133 19.7 G_front_sup 567 353 1411 3.673 0.913 0.119 0.054 9 1.1 G_Ins_lg&S_cent_ins 662 402 1750 3.368 1.006 0.160 0.089 20 2.7 G_insular_short 1608 1016 3309 2.614 0.645 0.153 0.063 30 3.9 G_occipital_middle 2028 1194 2938 2.180 0.550 0.144 0.059 30 4.7 G_occipital_sup 1887 1156 3310 2.412 0.695 0.159 0.072 44 5.5 G_oc-temp_lat-fusifor 2979 1905 4305 2.030 0.618 0.154 0.062 51 7.7 G_oc-temp_med-Lingual 1013 620 2869 3.191 0.931 0.121 0.061 16 1.9 G_oc-temp_med-Parahip 2818 1693 5273 2.426 0.964 0.156 0.074 60 8.6 G_orbital 2122 1237 3440 2.221 0.768 0.148 0.066 41 5.4 G_pariet_inf-Angular 2021 1160 3582 2.596 0.554 0.122 0.044 29 3.5 G_pariet_inf-Supramar 3094 1750 4415 2.150 0.575 0.141 0.054 47 6.9 G_parietal_sup 1787 996 2271 1.918 0.628 0.122 0.042 28 3.2 G_postcentral 2922 1660 4187 2.201 0.834 0.132 0.044 36 6.1 G_precentral 2628 1493 3464 1.945 0.574 0.129 0.050 46 5.5 G_precuneus 677 408 1099 2.052 0.663 0.139 0.054 14 1.4 G_rectus 501 335 1153 2.903 1.129 0.129 0.058 8 0.8 G_subcallosal 424 214 723 2.389 0.504 0.115 0.040 6 0.6 G_temp_sup-G_T_transv 1608 951 3090 2.486 0.545 0.149 0.062 32 4.0 G_temp_sup-Lateral 513 354 1293 2.964 0.962 0.084 0.021 3 0.3 G_temp_sup-Plan_polar 624 372 857 2.075 0.482 0.101 0.035 6 0.7 G_temp_sup-Plan_tempo 1828 1195 3721 2.541 1.083 0.156 0.055 37 4.1 G_temporal_inf 2254 1373 5056 2.518 0.764 0.149 0.068 51 6.7 G_temporal_middle 276 186 322 2.278 0.411 0.118 0.032 2 0.4 Lat_Fis-ant-Horizont 196 138 281 2.291 0.636 0.112 0.033 1 0.2 Lat_Fis-ant-Vertical 1370 920 1706 2.237 0.600 0.111 0.025 8 1.5 Lat_Fis-post 3379 2140 4933 2.212 0.747 0.148 0.056 48 7.4 Pole_occipital 1988 1308 6388 3.164 0.873 0.160 0.073 40 6.4 Pole_temporal 2089 1473 2338 1.847 0.531 0.136 0.037 20 3.5 S_calcarine 2719 1878 3062 1.886 0.762 0.109 0.025 16 3.1 S_central 1221 839 1651 2.208 0.599 0.116 0.029 11 1.5 S_cingul-Marginalis 413 297 780 3.157 0.476 0.131 0.043 3 0.8 S_circular_insula_ant 1149 793 1665 2.568 0.937 0.086 0.015 4 0.8 S_circular_insula_inf 1148 799 1922 2.929 0.499 0.113 0.024 6 1.3 S_circular_insula_sup 871 604 1347 2.242 0.655 0.133 0.038 11 1.3 S_collat_transv_ant 537 378 640 2.285 0.457 0.163 0.050 7 1.0 S_collat_transv_post 2059 1336 2799 2.226 0.526 0.124 0.037 18 3.1 S_front_inf 1836 1143 2311 2.305 0.575 0.121 0.034 14 2.6 S_front_middle 2671 1803 3314 2.115 0.544 0.132 0.040 26 4.4 S_front_sup 366 254 408 1.834 0.364 0.134 0.031 3 0.6 S_interm_prim-Jensen 2585 1649 3058 1.954 0.490 0.128 0.037 33 4.3 S_intrapariet&P_trans 576 384 773 2.494 0.495 0.125 0.032 4 0.8 S_oc_middle&Lunatus 1226 796 1682 2.237 0.600 0.132 0.033 14 1.6 S_oc_sup&transversal 541 369 649 2.258 0.512 0.142 0.045 5 0.9 S_occipital_ant 499 353 1120 3.039 0.684 0.140 0.035 5 0.8 S_oc-temp_lat 1658 1253 2681 2.391 0.678 0.113 0.021 11 1.4 S_oc-temp_med&Lingual 311 201 363 2.276 0.496 0.128 0.029 3 0.4 S_orbital_lateral 628 424 910 2.199 0.940 0.119 0.026 6 0.6 S_orbital_med-olfact 1729 1156 2910 2.568 0.734 0.150 0.049 23 3.8 S_orbital-H_Shaped 1324 879 1648 2.020 0.553 0.109 0.025 9 1.3 S_parieto_occipital 1052 707 1105 2.357 1.132 0.155 0.038 23 1.3 S_pericallosal 2282 1387 2829 2.107 0.469 0.121 0.036 24 3.4 S_postcentral 2157 1413 2817 2.290 0.548 0.123 0.038 19 3.3 S_precentral-inf-part 1577 1124 2017 2.273 0.455 0.140 0.041 14 2.9 S_precentral-sup-part 408 258 528 2.320 0.649 0.120 0.027 4 0.4 S_suborbital 888 588 1201 2.115 0.641 0.124 0.036 7 1.1 S_subparietal 886 626 1306 2.339 0.509 0.128 0.031 8 1.1 S_temporal_inf 3712 2554 5169 2.118 0.613 0.117 0.033 32 5.0 S_temporal_sup 258 195 341 2.093 0.453 0.133 0.022 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Jul 7 04:21:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 977 labels changed using aseg relabeling using gibbs priors... 000: 1774 changed, 123245 examined... 001: 418 changed, 8425 examined... 002: 124 changed, 2358 examined... 003: 66 changed, 747 examined... 004: 32 changed, 355 examined... 005: 23 changed, 174 examined... 006: 17 changed, 125 examined... 007: 15 changed, 90 examined... 008: 14 changed, 85 examined... 009: 10 changed, 77 examined... 010: 12 changed, 55 examined... 011: 10 changed, 62 examined... 012: 7 changed, 52 examined... 013: 11 changed, 51 examined... 014: 7 changed, 52 examined... 015: 6 changed, 36 examined... 016: 4 changed, 29 examined... 017: 4 changed, 27 examined... 018: 1 changed, 20 examined... 019: 3 changed, 8 examined... 020: 1 changed, 9 examined... 021: 0 changed, 9 examined... 289 labels changed using aseg 000: 52 total segments, 19 labels (387 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 976 vertices marked for relabeling... 976 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Jul 7 04:21:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 AD01 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 1.781 2016/06/13 21:20:50 fischl 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... 1226 labels changed using aseg relabeling using gibbs priors... 000: 1845 changed, 122501 examined... 001: 447 changed, 8486 examined... 002: 155 changed, 2482 examined... 003: 71 changed, 914 examined... 004: 41 changed, 375 examined... 005: 29 changed, 239 examined... 006: 15 changed, 166 examined... 007: 10 changed, 82 examined... 008: 10 changed, 61 examined... 009: 7 changed, 55 examined... 010: 6 changed, 41 examined... 011: 5 changed, 34 examined... 012: 5 changed, 30 examined... 013: 4 changed, 27 examined... 014: 2 changed, 26 examined... 015: 2 changed, 14 examined... 016: 3 changed, 15 examined... 017: 3 changed, 18 examined... 018: 2 changed, 18 examined... 019: 0 changed, 13 examined... 314 labels changed using aseg 000: 71 total segments, 38 labels (434 vertices) changed 001: 36 total segments, 3 labels (5 vertices) changed 002: 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... 561 vertices marked for relabeling... 561 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Jul 7 04:22:06 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 1397 913 2659 3.222 0.769 0.144 0.032 26 1.7 caudalanteriorcingulate 3442 2156 4006 1.943 0.481 0.130 0.040 37 6.2 caudalmiddlefrontal 2909 1796 4026 2.064 0.562 0.140 0.047 39 5.1 cuneus 484 315 1560 3.555 0.777 0.125 0.052 7 0.8 entorhinal 3568 2425 5677 2.258 0.663 0.155 0.059 63 9.2 fusiform 4456 2727 5079 1.763 0.441 0.143 0.046 76 8.5 inferiorparietal 4276 2836 9740 2.607 0.937 0.163 0.063 91 11.4 inferiortemporal 1645 956 1845 1.919 0.676 0.116 0.037 24 2.2 isthmuscingulate 8042 4960 11380 2.186 0.639 0.140 0.050 115 17.0 lateraloccipital 4453 2837 7597 2.587 0.794 0.149 0.062 79 11.7 lateralorbitofrontal 4940 3275 6291 1.898 0.611 0.152 0.049 71 9.9 lingual 2159 1374 3758 2.503 0.934 0.134 0.050 31 4.6 medialorbitofrontal 4375 2794 8099 2.414 0.808 0.132 0.047 70 7.8 middletemporal 761 502 1656 2.714 0.955 0.108 0.029 9 0.7 parahippocampal 2211 1367 3762 2.712 0.725 0.124 0.041 29 4.0 paracentral 2459 1455 3377 2.296 0.609 0.128 0.048 30 4.6 parsopercularis 1152 664 1884 2.377 0.636 0.125 0.053 16 2.8 parsorbitalis 2802 1720 3972 2.206 0.571 0.130 0.056 48 6.8 parstriangularis 1964 1300 1991 1.722 0.461 0.150 0.046 28 3.6 pericalcarine 6326 3853 8135 1.984 0.622 0.124 0.040 68 11.1 postcentral 1512 939 2252 2.463 0.683 0.132 0.046 22 2.8 posteriorcingulate 7512 4896 10590 2.144 0.687 0.131 0.043 84 15.0 precentral 4082 2520 4797 1.821 0.556 0.124 0.040 56 6.6 precuneus 1586 1017 3359 3.211 1.056 0.132 0.048 23 2.8 rostralanteriorcingulate 5653 3492 7704 2.130 0.559 0.143 0.047 77 11.5 rostralmiddlefrontal 11847 7385 17880 2.291 0.656 0.136 0.048 159 23.7 superiorfrontal 5280 3241 6030 1.834 0.466 0.130 0.041 61 9.3 superiorparietal 6564 4270 11369 2.381 0.725 0.122 0.042 86 10.9 superiortemporal 3548 2162 4580 2.104 0.614 0.122 0.041 40 5.7 supramarginal 686 367 1004 2.427 0.376 0.111 0.032 6 0.9 transversetemporal 3304 2054 5063 2.714 0.721 0.126 0.051 38 7.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Jul 7 04:22:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 943 647 1951 3.055 0.733 0.163 0.038 23 1.3 caudalanteriorcingulate 3659 2199 5072 2.272 0.559 0.129 0.050 43 8.4 caudalmiddlefrontal 2439 1442 3128 2.070 0.662 0.139 0.054 41 5.8 cuneus 418 268 1464 3.444 0.940 0.117 0.072 8 1.0 entorhinal 3570 2374 6215 2.464 0.717 0.149 0.054 63 8.1 fusiform 5035 3143 7316 2.109 0.605 0.139 0.051 74 9.8 inferiorparietal 3934 2636 8337 2.620 0.975 0.148 0.053 64 8.8 inferiortemporal 1224 777 1703 2.070 0.751 0.136 0.059 19 2.7 isthmuscingulate 7305 4675 11790 2.388 0.673 0.149 0.055 106 16.0 lateraloccipital 4476 2864 7606 2.438 0.926 0.155 0.059 72 11.5 lateralorbitofrontal 4347 2883 6105 2.020 0.599 0.143 0.052 61 9.5 lingual 1894 1248 3454 2.320 0.853 0.134 0.047 30 3.1 medialorbitofrontal 4316 2811 8451 2.386 0.744 0.136 0.054 72 9.9 middletemporal 866 591 1745 2.574 0.795 0.108 0.035 9 1.0 parahippocampal 2434 1383 3415 2.424 0.656 0.118 0.042 28 4.4 paracentral 2771 1699 4316 2.352 0.597 0.131 0.060 38 6.9 parsopercularis 919 561 1836 2.600 0.652 0.133 0.049 14 1.6 parsorbitalis 2005 1228 3153 2.396 0.593 0.142 0.062 40 4.8 parstriangularis 1813 1176 1769 1.733 0.473 0.142 0.045 23 3.2 pericalcarine 5802 3547 7370 1.970 0.700 0.121 0.037 68 9.1 postcentral 1468 1008 2773 2.759 0.789 0.162 0.050 31 2.9 posteriorcingulate 7260 4642 10616 2.321 0.742 0.128 0.038 72 12.3 precentral 5012 3096 6478 1.986 0.569 0.124 0.040 65 8.4 precuneus 935 565 2243 3.509 0.684 0.127 0.042 12 1.5 rostralanteriorcingulate 5866 3536 8194 2.226 0.550 0.141 0.058 91 14.2 rostralmiddlefrontal 14003 8520 21196 2.441 0.653 0.138 0.050 202 30.1 superiorfrontal 6727 3964 9414 2.166 0.561 0.134 0.049 96 13.7 superiorparietal 5574 3661 10828 2.507 0.824 0.124 0.042 72 9.1 superiortemporal 4145 2538 6259 2.371 0.608 0.125 0.040 49 6.7 supramarginal 473 248 744 2.277 0.429 0.109 0.039 6 0.6 transversetemporal 2808 1835 5863 3.238 0.897 0.119 0.044 35 5.2 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Jul 7 04:23:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts pctsurfcon --s AD01 --lh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts/pctsurfcon.log Thu Jul 7 04:23:15 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts /usr/local/freesurfer/stable6/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-92 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 FREESURFER_HOME /usr/local/freesurfer/stable6 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.wm.mgh --regheader AD01 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = 57093 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.wm.mgh Dim: 123245 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.gm.mgh --projfrac 0.3 --regheader AD01 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = 66983 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.gm.mgh Dim: 123245 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32133/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.w-g.pct.mgh --annot AD01 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/lh.w-g.pct.mgh --annot AD01 lh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/lh.w-g.pct.mgh Vertex Area is 0.630847 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 Thu Jul 7 04:23:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts pctsurfcon --s AD01 --rh-only Log file is /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts/pctsurfcon.log Thu Jul 7 04:23:21 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts /usr/local/freesurfer/stable6/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-0-92 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 FREESURFER_HOME /usr/local/freesurfer/stable6 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.wm.mgh --regheader AD01 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = 55391 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.wm.mgh Dim: 122501 1 1 mri_vol2surf --mov /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.gm.mgh --projfrac 0.3 --regheader AD01 --cortex srcvol = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 -0.00002; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label Reading surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = 66847 Masking with /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label Writing to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.gm.mgh Dim: 122501 1 1 mri_concat /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.wm.mgh /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/tmp.pctsurfcon.32187/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.w-g.pct.mgh --annot AD01 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.w-g.pct.mgh --annot AD01 rh aparc --sum /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.w-g.pct.mgh Vertex Area is 0.629302 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 Thu Jul 7 04:23:27 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 8960 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4786 voxels changed to hypointensity... 13475 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Jul 7 04:23:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/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/AD01/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 = 347138 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Jul 7 04:25:03 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask --aseg aseg.presurf.hypos --annot aparc.a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/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/AD01/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 = 347138 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Jul 7 04:26:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask --aseg aseg.presurf.hypos --annot aparc.DKTatlas SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/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/AD01/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 = 347138 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Jul 7 04:27:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Jul 7 04:27:31 EDT 2016 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc cd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri /usr/local/freesurfer/stable6/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160624 $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux compute-0-92 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 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 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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-0-92 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 Thu Jul 7 04:27:31 EDT 2016 Ended at Thu Jul 7 04:27:39 EDT 2016 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Jul 7 04:27:39 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 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 AD01 $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 AD01 sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Computing euler number orig.nofix lheno = -204, rheno = -138 orig.nofix lhholes = 103, rhholes = 70 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 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 Thu Jul 7 04:31:21 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --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 AD01 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/AD01/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7850 vertices from left hemi Ripped 8060 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/AD01/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 = 738282 Used brute-force search on 157 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1073.000000 5 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1248.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 5.000000 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 AD01 --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 AD01 --surf-wm-vol --ctab /usr/local/freesurfer/stable6/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-92 machine x86_64 user fdu0 UseRobust 0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 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/AD01/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Jul 7 04:41:33 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4294 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA2_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3a_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 293 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA3b_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6333 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4a_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 339 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6123 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA4p_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4348 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA6_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 1471 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15060 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA44_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 690 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4871 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA45_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 1106 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V1_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 1865 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6506 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.V2_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 3242 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11356 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.MT_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 380 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2398 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1405 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1051 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2197 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1589 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2083 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2453 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1630 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 641 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7676 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 360 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2272 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 505 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1656 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 1365 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4770 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 1427 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4761 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 621 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 521 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 AD01 --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 = AD01 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/AD01/surf/lh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 123245 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 520 mri_label2label: Done mris_label2annot --s AD01 --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/AD01/label cmdline mris_label2annot --s AD01 --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-0-92 machine x86_64 user fdu0 subject AD01 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/AD01/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 80300 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.BA_exvivo.annot mris_label2annot --s AD01 --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/AD01/label cmdline mris_label2annot --s AD01 --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-0-92 machine x86_64 user fdu0 subject AD01 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/AD01/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 97456 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 1035 655 1065 1.595 0.416 0.101 0.027 7 1.2 BA1_exvivo 3345 1963 4214 2.032 0.558 0.129 0.042 37 6.4 BA2_exvivo 1264 858 1639 2.076 0.706 0.155 0.058 24 3.5 BA3a_exvivo 2215 1449 2789 2.021 0.693 0.123 0.034 21 3.1 BA3b_exvivo 1518 876 2836 2.705 0.777 0.122 0.046 24 2.8 BA4a_exvivo 1388 904 1858 1.912 0.799 0.116 0.036 9 2.5 BA4p_exvivo 9787 6302 13698 2.246 0.666 0.137 0.044 110 19.8 BA6_exvivo 2722 1642 3461 2.108 0.533 0.123 0.042 29 4.5 BA44_exvivo 3538 2177 4948 2.134 0.549 0.141 0.056 63 8.5 BA45_exvivo 4053 2566 5159 1.884 0.620 0.153 0.053 62 8.5 V1_exvivo 8854 5696 11827 2.036 0.614 0.149 0.050 125 17.9 V2_exvivo 1894 1114 2618 2.286 0.565 0.119 0.042 26 3.1 MT_exvivo 565 395 1357 2.952 0.914 0.125 0.040 7 0.8 perirhinal_exvivo 767 520 1887 2.747 0.818 0.162 0.079 14 2.4 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 AD01 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 175170 Total vertex volume 171122 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 665 436 633 1.457 0.318 0.092 0.023 4 0.6 BA1_exvivo 1465 822 1933 1.970 0.595 0.134 0.046 19 3.1 BA2_exvivo 1017 736 1283 1.932 0.515 0.148 0.040 9 2.0 BA3a_exvivo 1316 936 1421 1.750 0.567 0.119 0.029 8 1.5 BA3b_exvivo 1495 894 2669 2.563 0.813 0.125 0.045 23 3.0 BA4a_exvivo 1153 766 1494 1.819 0.746 0.121 0.038 7 2.2 BA4p_exvivo 5327 3526 7729 2.270 0.663 0.141 0.045 51 11.1 BA6_exvivo 1849 1061 2357 2.137 0.566 0.124 0.048 24 3.6 BA44_exvivo 1558 966 2145 2.074 0.540 0.135 0.053 23 3.4 BA45_exvivo 4343 2749 5423 1.848 0.621 0.152 0.052 66 8.9 V1_exvivo 4400 2850 5587 2.033 0.617 0.156 0.051 65 9.0 V2_exvivo 537 327 678 2.204 0.544 0.101 0.027 4 0.6 MT_exvivo 283 189 685 2.948 0.870 0.138 0.055 5 0.6 perirhinal_exvivo 381 269 1098 2.899 0.925 0.154 0.076 6 1.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Jul 7 04:46:32 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA1_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 105 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA2_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6921 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3a_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA3b_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 136 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4658 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4a_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 335 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6082 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA4p_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4610 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA6_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 1371 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA44_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 1058 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7970 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.BA45_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 1057 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V1_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 826 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.V2_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 2174 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.MT_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 348 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2280 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 154 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1192 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 882 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 918 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2742 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1769 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2253 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1467 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1527 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 772 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7731 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1105 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 163 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1341 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 493 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3725 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 893 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4330 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 291 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 796 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 AD01 --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 = AD01 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/AD01/surf/rh.white Reading target registration /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 122501 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 366 mri_label2label: Done mris_label2annot --s AD01 --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/AD01/label cmdline mris_label2annot --s AD01 --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-0-92 machine x86_64 user fdu0 subject AD01 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/AD01/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 84853 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.BA_exvivo.annot mris_label2annot --s AD01 --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/AD01/label cmdline mris_label2annot --s AD01 --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-0-92 machine x86_64 user fdu0 subject AD01 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/AD01/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 102013 unhit vertices Writing annot to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 AD01 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 720 445 860 2.028 0.529 0.121 0.037 11 1.4 BA1_exvivo 2816 1650 3953 2.243 0.547 0.123 0.041 35 4.5 BA2_exvivo 1112 663 1383 1.802 0.773 0.113 0.033 12 1.6 BA3a_exvivo 1591 938 2127 2.063 0.668 0.113 0.034 17 2.0 BA3b_exvivo 1268 895 1613 1.909 0.558 0.147 0.041 12 2.4 BA4a_exvivo 1129 760 1110 1.563 0.465 0.121 0.030 9 1.5 BA4p_exvivo 8822 5424 12477 2.331 0.729 0.139 0.047 104 19.8 BA6_exvivo 3614 2196 5975 2.670 0.615 0.123 0.044 40 6.1 BA44_exvivo 3898 2406 6643 2.403 0.641 0.140 0.064 73 9.8 BA45_exvivo 2940 1945 3072 1.742 0.503 0.147 0.050 40 6.4 V1_exvivo 7078 4473 10084 2.128 0.637 0.145 0.054 102 16.0 V2_exvivo 1789 1170 3135 2.521 0.640 0.147 0.052 24 3.8 MT_exvivo 503 372 178 3.087 1.259 0.097 0.043 6 1.0 perirhinal_exvivo 368 197 420 2.868 1.121 0.146 0.082 8 1.3 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 AD01 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 184815 Total vertex volume 180803 (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) = 1321820 mm^3 (det: 1.473805 ) lhCtxGM: 169555.132 168574.000 diff= 981.1 pctdiff= 0.579 rhCtxGM: 180027.161 179435.000 diff= 592.2 pctdiff= 0.329 lhCtxWM: 199325.328 199743.000 diff= -417.7 pctdiff=-0.210 rhCtxWM: 191323.535 192535.000 diff=-1211.5 pctdiff=-0.633 SubCortGMVol 48560.000 SupraTentVol 826437.156 (824142.000) diff=2295.156 pctdiff=0.278 SupraTentVolNotVent 791145.156 (788850.000) diff=2295.156 pctdiff=0.290 BrainSegVol 948719.000 (945667.000) diff=3052.000 pctdiff=0.322 BrainSegVolNotVent 908570.000 (908327.156) diff=242.844 pctdiff=0.027 BrainSegVolNotVent 908570.000 CerebellumVol 119533.000 VentChorVol 35292.000 3rd4th5thCSF 4857.000 CSFVol 1805.000, OptChiasmVol 187.000 MaskVol 1406824.000 503 307 590 2.085 0.411 0.114 0.040 9 1.1 BA1_exvivo 1457 921 1861 2.126 0.443 0.122 0.034 14 2.0 BA2_exvivo 1010 592 1215 1.778 0.750 0.106 0.031 10 1.3 BA3a_exvivo 1323 755 1728 2.013 0.652 0.107 0.030 13 1.6 BA3b_exvivo 911 585 1355 1.937 0.673 0.131 0.047 9 2.2 BA4a_exvivo 914 637 907 1.585 0.489 0.118 0.027 7 1.1 BA4p_exvivo 5614 3523 7853 2.295 0.705 0.141 0.047 66 12.2 BA6_exvivo 779 459 1518 2.830 0.498 0.116 0.041 9 1.3 BA44_exvivo 909 570 1669 2.408 0.601 0.147 0.094 21 3.6 BA45_exvivo 2774 1837 2907 1.752 0.520 0.148 0.049 39 6.0 V1_exvivo 3533 2249 4856 1.988 0.563 0.141 0.050 49 7.3 V2_exvivo 216 149 595 3.284 0.682 0.158 0.071 3 0.6 MT_exvivo 286 213 37 3.180 1.227 0.075 0.013 1 0.2 perirhinal_exvivo 259 147 99 3.236 0.904 0.155 0.078 6 0.7 entorhinal_exvivo Started at Wed Jul 6 13:11:42 EDT 2016 Ended at Thu Jul 7 04:51:30 EDT 2016 #@#%# recon-all-run-time-hours 15.663 recon-all -s AD01 finished without error at Thu Jul 7 04:51:30 EDT 2016 New invocation of recon-all Mon Jul 11 15:21:33 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon2 -autorecon3 -no-isrunning -subjid AD01 subjid AD01 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-15 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 2731852 30145400 4 159240 787416 -/+ buffers/cache: 1785196 31092056 Swap: 67108860 90612 67018248 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/11-19:21:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-15 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Mon Jul 11 15:21:38 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (63, 57, 47) --> (197, 191, 199) using (108, 102, 123) as brain centroid... mean wm in atlas = 107, using box (92,86,104) --> (124, 118,141) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -7491.9 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-8.0, 5.7, -17.0): log p = -7285.200 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7199.4, old_max_log_p =-7285.2 (thresh=-7277.9) 1.075 0.000 0.000 -18.062; 0.000 0.931 0.497 -54.797; 0.000 -0.497 0.792 72.207; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7199.4, old_max_log_p =-7199.4 (thresh=-7192.2) 1.075 0.000 0.000 -18.062; 0.000 0.931 0.497 -54.797; 0.000 -0.497 0.792 72.207; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7169.8, old_max_log_p =-7199.4 (thresh=-7192.2) 1.065 -0.059 -0.123 7.446; 0.106 1.014 0.362 -59.427; 0.115 -0.361 0.905 22.841; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7148.6, old_max_log_p =-7169.8 (thresh=-7162.7) 1.055 0.050 -0.011 -17.858; -0.030 1.009 0.433 -49.455; 0.044 -0.438 0.918 37.840; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7148.6, old_max_log_p =-7148.6 (thresh=-7141.4) 1.055 0.050 -0.011 -17.858; -0.030 1.009 0.433 -49.455; 0.044 -0.438 0.918 37.840; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7140.6, old_max_log_p =-7148.6 (thresh=-7141.4) 1.052 0.006 -0.001 -13.595; 0.003 1.022 0.402 -52.108; 0.017 -0.406 0.933 36.746; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7140.2, old_max_log_p =-7140.6 (thresh=-7133.4) 1.052 0.010 -0.009 -12.572; 0.004 1.020 0.410 -52.865; 0.026 -0.414 0.930 36.532; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05185 0.00987 -0.00870 -12.57183; 0.00358 1.02004 0.41028 -52.86473; 0.02555 -0.41421 0.92998 36.53200; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.05185 0.00987 -0.00870 -12.57183; 0.00358 1.02004 0.41028 -52.86473; 0.02555 -0.41421 0.92998 36.53200; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7140.2 tol 0.000010 Resulting transform: 1.052 0.010 -0.009 -12.572; 0.004 1.020 0.410 -52.865; 0.026 -0.414 0.930 36.532; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7140.2 (old=-7491.9) transform before final EM align: 1.052 0.010 -0.009 -12.572; 0.004 1.020 0.410 -52.865; 0.026 -0.414 0.930 36.532; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05185 0.00987 -0.00870 -12.57183; 0.00358 1.02004 0.41028 -52.86473; 0.02555 -0.41421 0.92998 36.53200; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.05185 0.00987 -0.00870 -12.57183; 0.00358 1.02004 0.41028 -52.86473; 0.02555 -0.41421 0.92998 36.53200; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 842569.1 after pass:transform: ( 1.06, 0.02, -0.00, -12.57) ( 0.01, 1.03, 0.42, -52.86) ( 0.04, -0.40, 0.95, 36.53) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 842569.1 tol 0.000000 final transform: 1.059 0.016 -0.003 -12.572; 0.010 1.029 0.419 -52.865; 0.040 -0.401 0.947 36.532; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 22 minutes and 35 seconds. #-------------------------------------- #@# CA Normalize Mon Jul 11 15:44:13 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_ca_normalize -f /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/tmp/control.dat -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz reading manually defined control points from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/tmp/control.dat writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (63, 59, 47) --> (197, 191, 198) using (108, 103, 123) as brain centroid... mean wm in atlas = 107, using box (92,87,104) --> (124, 119,141) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.059 0.016 -0.003 -12.572; 0.010 1.029 0.419 -52.865; 0.040 -0.401 0.947 36.532; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 57, 46) --> (192, 171, 202) Left_Cerebral_White_Matter: limiting intensities to 102.0 --> 255.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 57, 47) --> (130, 163, 203) Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 255.0 0 of 9 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 142, 79) --> (176, 184, 129) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 255.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 142, 77) --> (129, 182, 132) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 255.0 0 of 16 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 108) --> (144, 191, 139) Reading 0 control points... Brain_Stem: limiting intensities to 92.0 --> 255.0 0 of 8 (0.0%) samples deleted using 54 total control points for intensity normalization... bias field = 0.879 +- 0.103 0 of 54 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 57, 46) --> (192, 171, 202) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 242.0 0 of 64 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 57, 47) --> (130, 163, 203) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 242.0 0 of 63 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 142, 79) --> (176, 184, 129) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 242.0 5 of 43 (11.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 142, 77) --> (129, 182, 132) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 242.0 0 of 44 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 108) --> (144, 191, 139) Reading 0 control points... Brain_Stem: limiting intensities to 76.0 --> 242.0 0 of 86 (0.0%) samples deleted using 300 total control points for intensity normalization... bias field = 0.963 +- 0.064 0 of 295 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 57, 46) --> (192, 171, 202) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 229.0 0 of 181 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 57, 47) --> (130, 163, 203) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 229.0 0 of 164 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 142, 79) --> (176, 184, 129) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 229.0 0 of 42 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 142, 77) --> (129, 182, 132) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 229.0 6 of 32 (18.8%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 108) --> (144, 191, 139) Reading 0 control points... Brain_Stem: limiting intensities to 72.0 --> 229.0 0 of 158 (0.0%) samples deleted using 577 total control points for intensity normalization... bias field = 1.014 +- 0.053 0 of 571 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 44 seconds. #-------------------------------------- #@# CA Reg Mon Jul 11 15:45:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.21 (predicted orig area = 6.6) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.994, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37657.086 ms 0001: dt=129.472000, rms=0.816 (17.928%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37155.027 ms 0002: dt=221.952000, rms=0.772 (5.437%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39517.664 ms 0003: dt=129.472000, rms=0.755 (2.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39677.336 ms 0004: dt=73.984000, rms=0.752 (0.470%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40049.664 ms 0005: dt=517.888000, rms=0.738 (1.877%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43491.641 ms 0006: dt=295.936000, rms=0.731 (0.853%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42924.781 ms 0007: dt=32.368000, rms=0.731 (0.114%), neg=0, invalid=766 0008: dt=32.368000, rms=0.730 (0.056%), neg=0, invalid=766 0009: dt=32.368000, rms=0.730 (0.034%), neg=0, invalid=766 0010: dt=32.368000, rms=0.730 (0.032%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43651.645 ms 0011: dt=369.920000, rms=0.725 (0.687%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41225.836 ms 0012: dt=32.368000, rms=0.723 (0.184%), neg=0, invalid=766 0013: dt=32.368000, rms=0.723 (0.066%), neg=0, invalid=766 0014: dt=32.368000, rms=0.723 (0.032%), neg=0, invalid=766 0015: dt=32.368000, rms=0.723 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43538.152 ms 0016: dt=369.920000, rms=0.718 (0.673%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43562.797 ms 0017: dt=295.936000, rms=0.715 (0.411%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41086.996 ms 0018: dt=129.472000, rms=0.713 (0.306%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43876.570 ms 0019: dt=443.904000, rms=0.711 (0.195%), neg=0, invalid=766 0020: dt=443.904000, rms=0.711 (-0.522%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.715, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41531.188 ms 0021: dt=124.416000, rms=0.693 (3.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39459.613 ms 0022: dt=31.104000, rms=0.686 (0.993%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39093.336 ms 0023: dt=145.152000, rms=0.672 (2.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39154.574 ms 0024: dt=24.900158, rms=0.664 (1.150%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38891.340 ms 0025: dt=20.736000, rms=0.663 (0.218%), neg=0, invalid=766 0026: dt=20.736000, rms=0.662 (0.168%), neg=0, invalid=766 0027: dt=20.736000, rms=0.660 (0.285%), neg=0, invalid=766 0028: dt=20.736000, rms=0.657 (0.398%), neg=0, invalid=766 0029: dt=20.736000, rms=0.654 (0.509%), neg=0, invalid=766 0030: dt=20.736000, rms=0.650 (0.633%), neg=0, invalid=766 0031: dt=20.736000, rms=0.645 (0.718%), neg=0, invalid=766 0032: dt=20.736000, rms=0.641 (0.718%), neg=0, invalid=766 0033: dt=20.736000, rms=0.636 (0.677%), neg=0, invalid=766 0034: dt=20.736000, rms=0.632 (0.587%), neg=0, invalid=766 0035: dt=20.736000, rms=0.629 (0.481%), neg=0, invalid=766 0036: dt=20.736000, rms=0.627 (0.408%), neg=0, invalid=766 0037: dt=20.736000, rms=0.625 (0.358%), neg=0, invalid=766 0038: dt=20.736000, rms=0.622 (0.343%), neg=0, invalid=766 0039: dt=20.736000, rms=0.620 (0.381%), neg=0, invalid=766 0040: dt=20.736000, rms=0.618 (0.366%), neg=0, invalid=766 0041: dt=20.736000, rms=0.616 (0.308%), neg=0, invalid=766 0042: dt=20.736000, rms=0.614 (0.236%), neg=0, invalid=766 0043: dt=20.736000, rms=0.613 (0.167%), neg=0, invalid=766 0044: dt=20.736000, rms=0.613 (0.112%), neg=0, invalid=766 0045: dt=20.736000, rms=0.612 (0.122%), neg=0, invalid=766 0046: dt=20.736000, rms=0.611 (0.127%), neg=0, invalid=766 0047: dt=20.736000, rms=0.611 (0.110%), neg=0, invalid=766 0048: dt=20.736000, rms=0.610 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43180.500 ms 0049: dt=20.736000, rms=0.610 (0.002%), neg=0, invalid=766 0050: dt=20.736000, rms=0.610 (0.028%), neg=0, invalid=766 0051: dt=20.736000, rms=0.610 (0.037%), neg=0, invalid=766 0052: dt=20.736000, rms=0.609 (0.056%), neg=0, invalid=766 0053: dt=20.736000, rms=0.609 (0.054%), neg=0, invalid=766 0054: dt=20.736000, rms=0.609 (0.064%), neg=0, invalid=766 0055: dt=20.736000, rms=0.608 (0.060%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.608, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45502.387 ms 0056: dt=82.944000, rms=0.606 (0.342%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41510.527 ms 0057: dt=7.776000, rms=0.606 (-0.000%), neg=0, invalid=766 0058: dt=7.776000, rms=0.606 (0.004%), neg=0, invalid=766 0059: dt=7.776000, rms=0.606 (-0.013%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44130.273 ms 0060: dt=2.800000, rms=0.639 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41418.270 ms 0061: dt=1.200000, rms=0.639 (0.005%), neg=0, invalid=766 0062: dt=1.200000, rms=0.639 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44079.633 ms 0063: dt=1.333333, rms=0.639 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44279.027 ms 0064: dt=0.700000, rms=0.639 (0.003%), neg=0, invalid=766 0065: dt=0.700000, rms=0.639 (0.001%), neg=0, invalid=766 0066: dt=0.700000, rms=0.639 (-0.005%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.728, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41594.023 ms 0067: dt=5.279133, rms=0.708 (2.711%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38998.617 ms 0068: dt=3.746032, rms=0.707 (0.239%), neg=0, invalid=766 0069: dt=3.746032, rms=0.707 (-0.047%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.707, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38915.977 ms 0070: dt=0.000000, rms=0.707 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.799, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38816.359 ms 0071: dt=0.909502, rms=0.796 (0.369%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38989.082 ms 0072: dt=2.172840, rms=0.790 (0.745%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38997.582 ms 0073: dt=1.280000, rms=0.789 (0.194%), neg=0, invalid=766 0074: dt=1.280000, rms=0.787 (0.225%), neg=0, invalid=766 0075: dt=1.280000, rms=0.786 (0.093%), neg=0, invalid=766 0076: dt=1.280000, rms=0.786 (-0.317%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38571.754 ms 0077: dt=0.192000, rms=0.786 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38577.676 ms 0078: dt=0.112000, rms=0.786 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.786, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39078.215 ms 0079: dt=0.859813, rms=0.786 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37552.031 ms 0080: dt=0.000000, rms=0.786 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40109.016 ms 0081: dt=0.384000, rms=0.698 (2.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34952.445 ms 0082: dt=0.000000, rms=0.697 (0.005%), neg=0, invalid=766 0083: dt=0.050000, rms=0.697 (-0.227%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34950.438 ms 0084: dt=0.000000, rms=0.697 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09738 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (2572 voxels, overlap=0.570) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (2572 voxels, peak = 20), gca=19.8 gca peak = 0.14022 (22) mri peak = 0.09564 (22) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2289 voxels, overlap=0.818) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2289 voxels, peak = 20), gca=20.4 gca peak = 0.24234 (100) mri peak = 0.06667 (97) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (423 voxels, overlap=0.993) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (423 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.06452 (98) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (368 voxels, overlap=0.775) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (368 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.03835 (98) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (698 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.55 x + 0.0 (698 voxels, peak = 98), gca=97.6 gca peak = 0.29892 (64) mri peak = 0.06969 (76) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (445 voxels, overlap=0.072) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (445 voxels, peak = 77), gca=76.8 gca peak = 0.12541 (104) mri peak = 0.06766 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (67829 voxels, overlap=0.930) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (67829 voxels, peak = 104), gca=104.0 gca peak = 0.13686 (104) mri peak = 0.06880 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (70247 voxels, overlap=0.904) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (70247 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03312 (90) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (24002 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (24002 voxels, peak = 83), gca=83.5 gca peak = 0.13270 (63) mri peak = 0.03756 (86) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (22382 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (22382 voxels, peak = 83), gca=83.5 gca peak = 0.15182 (70) mri peak = 0.09029 (86) Right_Caudate (50): linear fit = 1.15 x + 0.0 (495 voxels, overlap=0.203) Right_Caudate (50): linear fit = 1.15 x + 0.0 (495 voxels, peak = 80), gca=80.5 gca peak = 0.14251 (76) mri peak = 0.05666 (100) Left_Caudate (11): linear fit = 1.08 x + 0.0 (383 voxels, overlap=0.794) Left_Caudate (11): linear fit = 1.08 x + 0.0 (383 voxels, peak = 82), gca=81.7 gca peak = 0.12116 (60) mri peak = 0.04557 (81) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19005 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (19005 voxels, peak = 80), gca=79.5 gca peak = 0.12723 (61) mri peak = 0.05176 (79) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (21504 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (21504 voxels, peak = 81), gca=80.8 gca peak = 0.22684 (88) mri peak = 0.05445 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (9964 voxels, overlap=0.975) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (9964 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.04853 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8561 voxels, overlap=0.986) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8561 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.10256 (75) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (318 voxels, overlap=0.014) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (318 voxels, peak = 74), gca=74.4 gca peak = 0.39668 (62) mri peak = 0.07878 (71) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (371 voxels, overlap=0.209) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (371 voxels, peak = 70), gca=69.8 gca peak = 0.10129 (93) mri peak = 0.06431 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4182 voxels, overlap=0.953) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4182 voxels, peak = 93), gca=93.0 gca peak = 0.12071 (89) mri peak = 0.06512 (89) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, peak = 89), gca=89.0 gca peak = 0.13716 (82) mri peak = 0.07248 (91) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2652 voxels, overlap=0.455) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2652 voxels, peak = 90), gca=90.2 gca peak = 0.15214 (84) mri peak = 0.06820 (90) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2460 voxels, overlap=0.792) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2460 voxels, peak = 90), gca=90.3 gca peak = 0.08983 (85) mri peak = 0.07084 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11615 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11615 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.07355 (98) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1026 voxels, overlap=0.705) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1026 voxels, peak = 97), gca=96.6 gca peak = 0.12914 (94) mri peak = 0.07038 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1134 voxels, overlap=0.603) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1134 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) mri peak = 0.12360 (24) Third_Ventricle (14): linear fit = 0.73 x + 0.0 (89 voxels, overlap=0.159) Third_Ventricle (14): linear fit = 0.73 x + 0.0 (89 voxels, peak = 26), gca=26.1 gca peak = 0.13542 (27) mri peak = 0.08184 (25) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (267 voxels, overlap=0.454) Fourth_Ventricle (15): linear fit = 0.85 x + 0.0 (267 voxels, peak = 23), gca=23.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Hippocampus = 0.24007 (63) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.20 x + 0: 77 estimating mean gm scale to be 1.23 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.83 x + 0.0 Left_Pallidum too bright - rescaling by 0.980 (from 1.075) to 102.1 (was 104.3) Right_Pallidum too bright - rescaling by 0.996 (from 1.025) to 102.1 (was 102.5) saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.762, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34275.449 ms 0085: dt=32.368000, rms=0.741 (2.677%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34575.809 ms 0086: dt=32.368000, rms=0.731 (1.393%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34572.871 ms 0087: dt=27.744000, rms=0.726 (0.706%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29307.072 ms 0088: dt=2.023000, rms=0.726 (0.039%), neg=0, invalid=766 0089: dt=2.023000, rms=0.725 (0.039%), neg=0, invalid=766 0090: dt=0.505750, rms=0.725 (0.009%), neg=0, invalid=766 0091: dt=0.252875, rms=0.725 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26148.262 ms 0092: dt=0.126438, rms=0.725 (0.002%), neg=0, invalid=766 0093: dt=0.063219, rms=0.725 (0.001%), neg=0, invalid=766 0094: dt=0.015805, rms=0.725 (0.000%), neg=0, invalid=766 0095: dt=0.000988, rms=0.725 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18715.490 ms 0096: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18148.020 ms 0097: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18166.928 ms 0098: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18196.471 ms 0099: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18166.006 ms 0100: dt=0.000000, rms=0.725 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37178.598 ms 0101: dt=1.008000, rms=0.713 (1.755%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36958.051 ms 0102: dt=0.720000, rms=0.705 (1.165%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31953.600 ms 0103: dt=0.063000, rms=0.704 (0.097%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29320.979 ms 0104: dt=0.015750, rms=0.704 (0.024%), neg=0, invalid=766 0105: dt=0.015750, rms=0.704 (0.024%), neg=0, invalid=766 0106: dt=0.000492, rms=0.704 (0.001%), neg=0, invalid=766 0107: dt=0.000123, rms=0.704 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18769.176 ms 0108: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18761.793 ms 0109: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.704, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35890.969 ms 0110: dt=0.448000, rms=0.696 (1.257%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38977.242 ms 0111: dt=1.280000, rms=0.674 (3.170%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36750.535 ms 0112: dt=0.448000, rms=0.668 (0.760%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38110.180 ms 0113: dt=1.792000, rms=0.650 (2.693%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38490.859 ms 0114: dt=1.536000, rms=0.642 (1.364%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36226.047 ms 0115: dt=0.448000, rms=0.640 (0.280%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39323.367 ms 0116: dt=1.792000, rms=0.633 (1.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39589.195 ms 0117: dt=1.792000, rms=0.629 (0.727%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39844.977 ms 0118: dt=1.792000, rms=0.625 (0.549%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39921.168 ms 0119: dt=1.792000, rms=0.622 (0.436%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39847.918 ms 0120: dt=1.792000, rms=0.620 (0.356%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39867.559 ms 0121: dt=1.792000, rms=0.618 (0.301%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39470.367 ms 0122: dt=1.536000, rms=0.617 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38641.156 ms 0123: dt=1.792000, rms=0.616 (0.230%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39577.434 ms 0124: dt=1.536000, rms=0.614 (0.171%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38631.570 ms 0125: dt=1.536000, rms=0.614 (0.156%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38121.180 ms 0126: dt=1.536000, rms=0.613 (0.137%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38144.379 ms 0127: dt=1.792000, rms=0.612 (0.153%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36085.523 ms 0128: dt=0.541667, rms=0.611 (0.042%), neg=0, invalid=766 0129: dt=0.541667, rms=0.611 (0.040%), neg=0, invalid=766 0130: dt=0.541667, rms=0.611 (0.075%), neg=0, invalid=766 0131: dt=0.541667, rms=0.610 (0.103%), neg=0, invalid=766 0132: dt=0.541667, rms=0.610 (0.035%), neg=0, invalid=766 0133: dt=0.541667, rms=0.610 (0.065%), neg=0, invalid=766 0134: dt=0.541667, rms=0.609 (0.089%), neg=0, invalid=766 0135: dt=0.541667, rms=0.608 (0.110%), neg=0, invalid=766 0136: dt=0.541667, rms=0.608 (0.126%), neg=0, invalid=766 0137: dt=0.541667, rms=0.607 (0.137%), neg=0, invalid=766 0138: dt=0.541667, rms=0.606 (0.141%), neg=0, invalid=766 0139: dt=0.541667, rms=0.605 (0.142%), neg=0, invalid=766 0140: dt=0.541667, rms=0.604 (0.142%), neg=0, invalid=766 0141: dt=0.541667, rms=0.603 (0.135%), neg=0, invalid=766 0142: dt=0.541667, rms=0.603 (0.129%), neg=0, invalid=766 0143: dt=0.541667, rms=0.602 (0.118%), neg=0, invalid=766 0144: dt=0.541667, rms=0.601 (0.107%), neg=0, invalid=766 0145: dt=0.541667, rms=0.601 (0.097%), neg=0, invalid=766 0146: dt=0.541667, rms=0.600 (0.088%), neg=0, invalid=766 0147: dt=0.541667, rms=0.600 (0.073%), neg=0, invalid=766 0148: dt=0.541667, rms=0.600 (-0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48015.059 ms 0149: dt=0.000018, rms=0.600 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36526.957 ms 0150: dt=0.750000, rms=0.599 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38623.531 ms 0151: dt=1.792000, rms=0.597 (0.230%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39768.617 ms 0152: dt=1.792000, rms=0.597 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38126.938 ms 0153: dt=1.536000, rms=0.596 (0.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38086.387 ms 0154: dt=1.792000, rms=0.596 (0.045%), neg=0, invalid=766 0155: dt=1.792000, rms=0.596 (0.031%), neg=0, invalid=766 0156: dt=0.896000, rms=0.596 (0.011%), neg=0, invalid=766 0157: dt=0.896000, rms=0.596 (0.017%), neg=0, invalid=766 0158: dt=0.896000, rms=0.596 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38395.773 ms 0159: dt=1.792000, rms=0.596 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40109.102 ms 0160: dt=1.792000, rms=0.596 (0.009%), neg=0, invalid=766 0161: dt=1.792000, rms=0.596 (0.013%), neg=0, invalid=766 0162: dt=1.792000, rms=0.596 (0.014%), neg=0, invalid=766 0163: dt=1.792000, rms=0.595 (0.006%), neg=0, invalid=766 0164: dt=1.792000, rms=0.595 (0.006%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.585, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33311.336 ms 0165: dt=0.028000, rms=0.583 (0.235%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35677.809 ms 0166: dt=0.168233, rms=0.576 (1.320%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33418.172 ms 0167: dt=0.028000, rms=0.575 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35854.719 ms 0168: dt=0.112000, rms=0.571 (0.611%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35556.273 ms 0169: dt=0.131202, rms=0.568 (0.595%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33190.719 ms 0170: dt=0.028000, rms=0.567 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33199.488 ms 0171: dt=0.028000, rms=0.567 (0.100%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35944.430 ms 0172: dt=0.118702, rms=0.564 (0.406%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35676.180 ms 0173: dt=0.096000, rms=0.563 (0.280%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35634.570 ms 0174: dt=0.112000, rms=0.561 (0.287%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35676.293 ms 0175: dt=0.112000, rms=0.560 (0.251%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35745.789 ms 0176: dt=0.112000, rms=0.559 (0.221%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35638.266 ms 0177: dt=0.112000, rms=0.558 (0.197%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35488.422 ms 0178: dt=0.112000, rms=0.557 (0.174%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35555.922 ms 0179: dt=0.112000, rms=0.556 (0.157%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36099.746 ms 0180: dt=0.080000, rms=0.555 (0.102%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33258.438 ms 0181: dt=0.020000, rms=0.555 (0.024%), neg=0, invalid=766 0182: dt=0.020000, rms=0.555 (0.024%), neg=0, invalid=766 0183: dt=0.020000, rms=0.555 (0.044%), neg=0, invalid=766 0184: dt=0.020000, rms=0.554 (0.062%), neg=0, invalid=766 0185: dt=0.020000, rms=0.554 (0.078%), neg=0, invalid=766 0186: dt=0.020000, rms=0.553 (0.090%), neg=0, invalid=766 0187: dt=0.020000, rms=0.553 (0.101%), neg=0, invalid=766 0188: dt=0.020000, rms=0.552 (0.107%), neg=0, invalid=766 0189: dt=0.020000, rms=0.552 (0.111%), neg=0, invalid=766 0190: dt=0.020000, rms=0.551 (0.115%), neg=0, invalid=766 0191: dt=0.020000, rms=0.550 (0.116%), neg=0, invalid=766 0192: dt=0.020000, rms=0.550 (0.117%), neg=0, invalid=766 0193: dt=0.020000, rms=0.549 (0.114%), neg=0, invalid=766 0194: dt=0.020000, rms=0.548 (0.111%), neg=0, invalid=766 0195: dt=0.020000, rms=0.548 (0.105%), neg=0, invalid=766 0196: dt=0.020000, rms=0.547 (0.101%), neg=0, invalid=766 0197: dt=0.020000, rms=0.547 (0.097%), neg=0, invalid=766 0198: dt=0.020000, rms=0.546 (0.090%), neg=0, invalid=766 0199: dt=0.020000, rms=0.546 (0.087%), neg=0, invalid=766 0200: dt=0.020000, rms=0.545 (0.080%), neg=0, invalid=766 0201: dt=0.020000, rms=0.545 (0.074%), neg=0, invalid=766 0202: dt=0.020000, rms=0.545 (0.004%), neg=0, invalid=766 0203: dt=0.020000, rms=0.545 (0.006%), neg=0, invalid=766 0204: dt=0.020000, rms=0.545 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35865.516 ms 0205: dt=0.112000, rms=0.545 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33603.633 ms 0206: dt=0.028000, rms=0.545 (0.004%), neg=0, invalid=766 0207: dt=0.028000, rms=0.545 (0.005%), neg=0, invalid=766 0208: dt=0.028000, rms=0.545 (0.010%), neg=0, invalid=766 0209: dt=0.028000, rms=0.545 (0.012%), neg=0, invalid=766 0210: dt=0.028000, rms=0.545 (0.014%), neg=0, invalid=766 0211: dt=0.028000, rms=0.544 (0.017%), neg=0, invalid=766 0212: dt=0.028000, rms=0.544 (0.006%), neg=0, invalid=766 0213: dt=0.028000, rms=0.544 (0.010%), neg=0, invalid=766 0214: dt=0.028000, rms=0.544 (0.014%), neg=0, invalid=766 0215: dt=0.028000, rms=0.544 (0.018%), neg=0, invalid=766 0216: dt=0.028000, rms=0.544 (0.017%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35477.770 ms 0217: dt=0.096000, rms=0.543 (0.274%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33196.484 ms 0218: dt=0.028000, rms=0.542 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38122.512 ms 0219: dt=0.320000, rms=0.539 (0.649%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33364.379 ms 0220: dt=0.028000, rms=0.539 (0.017%), neg=0, invalid=766 0221: dt=0.028000, rms=0.539 (0.018%), neg=0, invalid=766 0222: dt=0.028000, rms=0.538 (0.030%), neg=0, invalid=766 0223: dt=0.028000, rms=0.538 (0.015%), neg=0, invalid=766 0224: dt=0.028000, rms=0.538 (0.025%), neg=0, invalid=766 0225: dt=0.028000, rms=0.538 (0.034%), neg=0, invalid=766 0226: dt=0.028000, rms=0.538 (0.040%), neg=0, invalid=766 0227: dt=0.028000, rms=0.538 (0.043%), neg=0, invalid=766 0228: dt=0.028000, rms=0.537 (0.043%), neg=0, invalid=766 0229: dt=0.028000, rms=0.537 (0.041%), neg=0, invalid=766 0230: dt=0.028000, rms=0.537 (0.038%), neg=0, invalid=766 0231: dt=0.028000, rms=0.537 (0.032%), neg=0, invalid=766 0232: dt=0.028000, rms=0.537 (-0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33166.676 ms 0233: dt=0.000000, rms=0.537 (0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43133.625 ms iter 0, gcam->neg = 38 after 52 iterations, nbhd size=3, neg = 0 0234: dt=44.800000, rms=0.512 (4.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43213.324 ms iter 0, gcam->neg = 45 after 29 iterations, nbhd size=3, neg = 0 0235: dt=38.400000, rms=0.505 (1.419%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45829.109 ms iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0236: dt=11.200000, rms=0.502 (0.526%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45900.469 ms 0237: dt=11.200000, rms=0.501 (0.233%), neg=0, invalid=766 0238: dt=11.200000, rms=0.500 (0.266%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 29 iterations, nbhd size=4, neg = 0 0239: dt=11.200000, rms=0.498 (0.335%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 55 iterations, nbhd size=4, neg = 0 0240: dt=11.200000, rms=0.496 (0.404%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 18 iterations, nbhd size=2, neg = 0 0241: dt=11.200000, rms=0.494 (0.373%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0242: dt=11.200000, rms=0.492 (0.478%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 6 iterations, nbhd size=1, neg = 0 0243: dt=11.200000, rms=0.490 (0.364%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0244: dt=11.200000, rms=0.489 (0.311%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0245: dt=11.200000, rms=0.487 (0.263%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0246: dt=11.200000, rms=0.486 (0.305%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0247: dt=11.200000, rms=0.485 (0.177%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0248: dt=11.200000, rms=0.484 (0.213%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 24 iterations, nbhd size=3, neg = 0 0249: dt=11.200000, rms=0.483 (0.156%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24821.369 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.005 (9.796%) 0250: dt=11.200000, rms=0.483 (0.119%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0251: dt=11.200000, rms=0.482 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43270.594 ms iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24864.086 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.005 (8.900%) 0252: dt=19.200000, rms=0.482 (0.042%), neg=0, invalid=766 0253: dt=19.200000, rms=0.482 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0254: dt=19.200000, rms=0.481 (0.079%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0255: dt=19.200000, rms=0.481 (0.042%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.481, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43547.223 ms 0256: dt=32.000000, rms=0.479 (0.417%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47085.336 ms 0257: dt=7.506173, rms=0.478 (0.190%), neg=0, invalid=766 0258: dt=7.506173, rms=0.478 (0.113%), neg=0, invalid=766 0259: dt=7.506173, rms=0.477 (0.108%), neg=0, invalid=766 0260: dt=7.506173, rms=0.476 (0.119%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0261: dt=7.506173, rms=0.476 (0.110%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43374.930 ms 0262: dt=11.200000, rms=0.476 (0.037%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46780.145 ms iter 0, gcam->neg = 16 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25151.936 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.002 (27.965%) 0263: dt=4.032000, rms=0.489 (0.094%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46375.992 ms iter 0, gcam->neg = 8 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25176.367 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.002 (25.011%) 0264: dt=2.880000, rms=0.489 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25185.139 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.002 (26.008%) 0265: dt=2.880000, rms=0.489 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24924.045 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.001 (22.352%) 0266: dt=2.880000, rms=0.489 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45902.004 ms iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24932.949 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.001 (31.840%) 0267: dt=6.400000, rms=0.488 (0.230%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46011.555 ms iter 0, gcam->neg = 25 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25037.162 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.001 (30.127%) 0268: dt=6.000000, rms=0.487 (0.125%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23742.367 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.001 (19.136%) 0269: dt=6.000000, rms=0.487 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24095.193 ms iter 1, dt=0.003500: new neg 0, old_neg 1, delta 1, rms=0.001 (31.640%) 0270: dt=6.000000, rms=0.486 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 33 iterations, nbhd size=4, neg = 0 0271: dt=6.000000, rms=0.486 (0.097%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43644.910 ms 0272: dt=0.000000, rms=0.497 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43375.203 ms 0273: dt=0.000000, rms=0.497 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45813.129 ms iter 0, gcam->neg = 835 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.008, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31136.811 ms iter 1, dt=0.000120: new neg 0, old_neg 1, delta 1, rms=0.005 (40.286%) 0274: dt=1.792000, rms=0.441 (7.718%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43632.734 ms 0275: dt=0.000000, rms=0.441 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 73 after 7 iterations, nbhd size=1, neg = 0 0276: dt=0.050000, rms=0.441 (-0.331%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45874.941 ms 0277: dt=0.000438, rms=0.441 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43294.383 ms 0278: dt=0.000000, rms=0.441 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45970.660 ms iter 0, gcam->neg = 330 after 29 iterations, nbhd size=3, neg = 0 0279: dt=0.510169, rms=0.418 (2.162%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47227.773 ms 0280: dt=0.001000, rms=0.418 (0.005%), neg=0, invalid=766 0281: dt=0.001000, rms=0.418 (0.000%), neg=0, invalid=766 0282: dt=0.001000, rms=0.418 (0.000%), neg=0, invalid=766 0283: dt=0.001000, rms=0.418 (0.001%), neg=0, invalid=766 0284: dt=0.001000, rms=0.418 (0.001%), neg=0, invalid=766 0285: dt=0.001000, rms=0.418 (0.001%), neg=0, invalid=766 0286: dt=0.001000, rms=0.418 (0.002%), neg=0, invalid=766 0287: dt=0.001000, rms=0.418 (0.002%), neg=0, invalid=766 0288: dt=0.001000, rms=0.418 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45567.758 ms iter 0, gcam->neg = 10 after 18 iterations, nbhd size=2, neg = 0 0289: dt=0.080000, rms=0.418 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45696.645 ms 0290: dt=0.001500, rms=0.418 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45384.309 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0291: dt=0.003000, rms=0.418 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45494.062 ms iter 0, gcam->neg = 143 after 26 iterations, nbhd size=3, neg = 0 0292: dt=0.320000, rms=0.415 (0.753%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45747.648 ms 0293: dt=0.001750, rms=0.415 (-0.002%), neg=0, invalid=766 0294: dt=0.001750, rms=0.415 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0295: dt=0.001750, rms=0.415 (0.002%), neg=0, invalid=766 0296: dt=0.001750, rms=0.415 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0297: dt=0.001750, rms=0.415 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0298: dt=0.001750, rms=0.415 (0.007%), neg=0, invalid=766 0299: dt=0.001750, rms=0.415 (0.011%), neg=0, invalid=766 0300: dt=0.001750, rms=0.415 (0.010%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45754.801 ms iter 0, gcam->neg = 62 after 9 iterations, nbhd size=1, neg = 0 0301: dt=0.112000, rms=0.412 (0.504%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45648.254 ms iter 0, gcam->neg = 11 after 6 iterations, nbhd size=1, neg = 0 0302: dt=0.016000, rms=0.411 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0303: dt=0.016000, rms=0.411 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0304: dt=0.016000, rms=0.411 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 6 iterations, nbhd size=1, neg = 0 0305: dt=0.016000, rms=0.410 (0.136%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 7 iterations, nbhd size=1, neg = 0 0306: dt=0.016000, rms=0.410 (0.163%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 16 iterations, nbhd size=2, neg = 0 0307: dt=0.016000, rms=0.409 (0.176%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 8 iterations, nbhd size=1, neg = 0 0308: dt=0.016000, rms=0.408 (0.193%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 9 iterations, nbhd size=1, neg = 0 0309: dt=0.016000, rms=0.407 (0.196%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 9 iterations, nbhd size=1, neg = 0 0310: dt=0.016000, rms=0.407 (0.190%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 8 iterations, nbhd size=1, neg = 0 0311: dt=0.016000, rms=0.406 (0.187%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 16 iterations, nbhd size=2, neg = 0 0312: dt=0.016000, rms=0.405 (0.173%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 16 iterations, nbhd size=2, neg = 0 0313: dt=0.016000, rms=0.405 (0.138%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 9 iterations, nbhd size=1, neg = 0 0314: dt=0.016000, rms=0.404 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 7 iterations, nbhd size=1, neg = 0 0315: dt=0.016000, rms=0.403 (0.119%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 23 iterations, nbhd size=2, neg = 0 0316: dt=0.016000, rms=0.403 (0.081%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45666.992 ms 0317: dt=0.000109, rms=0.403 (0.001%), neg=0, invalid=766 0318: dt=0.000109, rms=0.403 (0.000%), neg=0, invalid=766 0319: dt=0.000109, rms=0.403 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45757.352 ms iter 0, gcam->neg = 16 after 15 iterations, nbhd size=2, neg = 0 0320: dt=0.048000, rms=0.403 (0.084%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45712.754 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0321: dt=0.007000, rms=0.403 (0.014%), neg=0, invalid=766 0322: dt=0.007000, rms=0.403 (0.013%), neg=0, invalid=766 0323: dt=0.007000, rms=0.403 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0324: dt=0.007000, rms=0.402 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0325: dt=0.007000, rms=0.402 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0326: dt=0.007000, rms=0.402 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0327: dt=0.007000, rms=0.402 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0328: dt=0.007000, rms=0.402 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 17 iterations, nbhd size=2, neg = 0 0329: dt=0.007000, rms=0.402 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=1, neg = 0 0330: dt=0.007000, rms=0.401 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=2, neg = 0 0331: dt=0.007000, rms=0.401 (0.045%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42609.711 ms iter 0, gcam->neg = 72 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23665.611 ms iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.003 (26.976%) gcamFindOptimalTimeStep: Complete in 24994.092 ms iter 2, dt=0.000148: new neg 0, old_neg 1, delta 1, rms=0.001 (58.896%) 0332: dt=11.200000, rms=0.401 (-0.040%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42560.504 ms iter 0, gcam->neg = 136 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.004, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23537.281 ms iter 1, dt=0.000031: new neg 0, old_neg 3, delta 3, rms=0.002 (62.766%) 0333: dt=25.600000, rms=0.399 (0.283%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42845.980 ms iter 0, gcam->neg = 82 after 200 iterations, nbhd size=3, neg = 4 starting rms=0.006, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23697.480 ms iter 1, dt=0.000023: new neg 1, old_neg 4, delta 3, rms=0.003 (47.527%) gcamFindOptimalTimeStep: Complete in 24907.029 ms iter 2, dt=0.000123: new neg 0, old_neg 1, delta 1, rms=0.001 (59.433%) 0334: dt=25.600000, rms=0.399 (0.154%), neg=0, invalid=766 iter 0, gcam->neg = 61 after 200 iterations, nbhd size=3, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23604.215 ms iter 1, dt=0.000023: new neg 2, old_neg 7, delta 5, rms=0.003 (51.337%) gcamFindOptimalTimeStep: Complete in 23679.787 ms iter 2, dt=0.000031: new neg 0, old_neg 2, delta 2, rms=0.001 (54.564%) 0335: dt=25.600000, rms=0.398 (0.127%), neg=0, invalid=766 iter 0, gcam->neg = 94 after 200 iterations, nbhd size=3, neg = 11 starting rms=0.008, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24661.363 ms iter 1, dt=0.000023: new neg 2, old_neg 11, delta 9, rms=0.003 (69.725%) gcamFindOptimalTimeStep: Complete in 23529.703 ms iter 2, dt=0.000009: new neg 0, old_neg 2, delta 2, rms=0.002 (17.505%) 0336: dt=25.600000, rms=0.398 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 82 after 200 iterations, nbhd size=2, neg = 18 starting rms=0.011, neg=18, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23617.674 ms iter 1, dt=0.000023: new neg 2, old_neg 18, delta 16, rms=0.004 (59.174%) gcamFindOptimalTimeStep: Complete in 23700.330 ms iter 2, dt=0.000015: new neg 1, old_neg 2, delta 1, rms=0.002 (50.147%) gcamFindOptimalTimeStep: Complete in 23618.035 ms iter 3, dt=0.000009: new neg 0, old_neg 1, delta 1, rms=0.002 (8.034%) 0337: dt=25.600000, rms=0.398 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 60 after 200 iterations, nbhd size=4, neg = 14 starting rms=0.008, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23697.273 ms iter 1, dt=0.000023: new neg 3, old_neg 14, delta 11, rms=0.005 (42.473%) gcamFindOptimalTimeStep: Complete in 23947.557 ms iter 2, dt=0.000020: new neg 0, old_neg 3, delta 3, rms=0.002 (51.638%) 0338: dt=25.600000, rms=0.398 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42654.438 ms iter 0, gcam->neg = 36 after 200 iterations, nbhd size=1, neg = 13 starting rms=0.010, neg=13, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23562.979 ms iter 1, dt=0.000023: new neg 3, old_neg 13, delta 10, rms=0.003 (68.456%) gcamFindOptimalTimeStep: Complete in 23640.516 ms iter 2, dt=0.000020: new neg 0, old_neg 3, delta 3, rms=0.002 (40.304%) 0339: dt=11.200000, rms=0.398 (0.044%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42784.758 ms iter 0, gcam->neg = 20 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.007, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25039.969 ms iter 1, dt=0.000156: new neg 4, old_neg 5, delta 1, rms=0.004 (48.424%) gcamFindOptimalTimeStep: Complete in 23636.025 ms iter 2, dt=0.000009: new neg 2, old_neg 4, delta 2, rms=0.003 (32.104%) gcamFindOptimalTimeStep: Complete in 23675.057 ms iter 3, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.033%) gcamFindOptimalTimeStep: Complete in 23505.385 ms iter 4, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.033%) gcamFindOptimalTimeStep: Complete in 23695.316 ms iter 5, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.008%) ---------- unfolding failed - restoring original position -------------------- 0340: dt=11.200000, rms=0.398 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.398, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45208.848 ms iter 0, gcam->neg = 53 after 200 iterations, nbhd size=2, neg = 17 starting rms=0.010, neg=17, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23776.369 ms iter 1, dt=0.000023: new neg 3, old_neg 17, delta 14, rms=0.005 (56.146%) gcamFindOptimalTimeStep: Complete in 23894.799 ms iter 2, dt=0.000015: new neg 0, old_neg 3, delta 3, rms=0.002 (63.110%) 0341: dt=1.450000, rms=0.398 (0.100%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45392.316 ms iter 0, gcam->neg = 38 after 200 iterations, nbhd size=3, neg = 14 starting rms=0.009, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24198.586 ms iter 1, dt=0.000023: new neg 3, old_neg 14, delta 11, rms=0.004 (49.474%) gcamFindOptimalTimeStep: Complete in 23749.701 ms iter 2, dt=0.000015: new neg 0, old_neg 3, delta 3, rms=0.002 (64.906%) 0342: dt=1.181818, rms=0.398 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 37 after 200 iterations, nbhd size=2, neg = 14 starting rms=0.009, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24042.590 ms iter 1, dt=0.000023: new neg 3, old_neg 14, delta 11, rms=0.004 (49.636%) gcamFindOptimalTimeStep: Complete in 24123.590 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.002 (61.579%) gcamFindOptimalTimeStep: Complete in 24092.344 ms iter 3, dt=0.000004: new neg 0, old_neg 1, delta 1, rms=0.002 (9.304%) 0343: dt=1.181818, rms=0.397 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 39 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.007, neg=10, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23970.471 ms iter 1, dt=0.000023: new neg 3, old_neg 10, delta 7, rms=0.004 (31.435%) gcamFindOptimalTimeStep: Complete in 25684.424 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.002 (59.082%) gcamFindOptimalTimeStep: Complete in 25875.869 ms iter 3, dt=0.000004: new neg 0, old_neg 1, delta 1, rms=0.002 (8.198%) 0344: dt=1.181818, rms=0.397 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.007, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24217.018 ms iter 1, dt=0.000023: new neg 3, old_neg 11, delta 8, rms=0.004 (35.709%) gcamFindOptimalTimeStep: Complete in 23939.543 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.002 (59.136%) gcamFindOptimalTimeStep: Complete in 23961.836 ms iter 3, dt=0.000004: new neg 0, old_neg 1, delta 1, rms=0.002 (8.105%) 0345: dt=1.181818, rms=0.397 (0.031%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45835.074 ms iter 0, gcam->neg = 61 after 200 iterations, nbhd size=1, neg = 11 starting rms=0.006, neg=11, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23780.359 ms iter 1, dt=0.000023: new neg 3, old_neg 11, delta 8, rms=0.004 (30.002%) gcamFindOptimalTimeStep: Complete in 23802.393 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.002 (64.302%) gcamFindOptimalTimeStep: Complete in 23857.598 ms iter 3, dt=0.000005: new neg 0, old_neg 1, delta 1, rms=0.001 (8.817%) 0346: dt=2.094118, rms=0.397 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45660.484 ms iter 0, gcam->neg = 58 after 200 iterations, nbhd size=3, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23929.186 ms iter 1, dt=0.000023: new neg 3, old_neg 12, delta 9, rms=0.004 (43.753%) gcamFindOptimalTimeStep: Complete in 23843.172 ms iter 2, dt=0.000015: new neg 0, old_neg 3, delta 3, rms=0.001 (65.285%) 0347: dt=2.543478, rms=0.396 (0.130%), neg=0, invalid=766 iter 0, gcam->neg = 81 after 200 iterations, nbhd size=3, neg = 13 starting rms=0.007, neg=13, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24434.916 ms iter 1, dt=0.000023: new neg 3, old_neg 13, delta 10, rms=0.004 (39.628%) gcamFindOptimalTimeStep: Complete in 23849.857 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.002 (63.792%) gcamFindOptimalTimeStep: Complete in 23607.605 ms iter 3, dt=0.000004: new neg 0, old_neg 1, delta 1, rms=0.001 (12.653%) 0348: dt=2.543478, rms=0.396 (0.126%), neg=0, invalid=766 iter 0, gcam->neg = 81 after 200 iterations, nbhd size=1, neg = 14 starting rms=0.009, neg=14, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23656.291 ms iter 1, dt=0.000023: new neg 2, old_neg 14, delta 12, rms=0.004 (52.426%) gcamFindOptimalTimeStep: Complete in 23646.539 ms iter 2, dt=0.000015: new neg 1, old_neg 2, delta 1, rms=0.002 (60.140%) gcamFindOptimalTimeStep: Complete in 23638.865 ms iter 3, dt=0.000002: new neg 0, old_neg 1, delta 1, rms=0.001 (14.712%) 0349: dt=2.543478, rms=0.395 (0.117%), neg=0, invalid=766 iter 0, gcam->neg = 80 after 200 iterations, nbhd size=2, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23962.314 ms iter 1, dt=0.000023: new neg 1, old_neg 12, delta 11, rms=0.004 (53.690%) gcamFindOptimalTimeStep: Complete in 23865.844 ms iter 2, dt=0.000015: new neg 1, old_neg 1, delta 0, rms=0.002 (57.914%) gcamFindOptimalTimeStep: Complete in 23733.885 ms iter 3, dt=0.000002: new neg 0, old_neg 1, delta 1, rms=0.001 (16.920%) 0350: dt=2.543478, rms=0.395 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45505.617 ms iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 12 starting rms=0.008, neg=12, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23664.080 ms iter 1, dt=0.000023: new neg 3, old_neg 12, delta 9, rms=0.004 (45.448%) gcamFindOptimalTimeStep: Complete in 24039.471 ms iter 2, dt=0.000015: new neg 1, old_neg 3, delta 2, rms=0.001 (63.992%) gcamFindOptimalTimeStep: Complete in 23706.549 ms iter 3, dt=0.000002: new neg 0, old_neg 1, delta 1, rms=0.001 (21.131%) 0351: dt=1.008000, rms=0.395 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30084.646 ms iter 1, dt=0.000047: new neg 0, old_neg 6, delta 6, rms=0.001 (83.011%) 0352: dt=1.008000, rms=0.394 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=3, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25954.045 ms iter 1, dt=0.000023: new neg 0, old_neg 4, delta 4, rms=0.001 (77.521%) 0353: dt=1.008000, rms=0.394 (0.045%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23639.383 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0354: dt=1.008000, rms=0.394 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45144.168 ms iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 31958.611 ms iter 1, dt=0.000025: new neg 0, old_neg 4, delta 4, rms=0.001 (83.043%) 0355: dt=0.096000, rms=0.396 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48200.266 ms iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 25002.693 ms iter 1, dt=0.000023: new neg 1, old_neg 5, delta 4, rms=0.001 (66.585%) gcamFindOptimalTimeStep: Complete in 26315.625 ms iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.001 (47.627%) 0356: dt=0.112000, rms=0.396 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0357: dt=0.112000, rms=0.396 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 37 iterations, nbhd size=4, neg = 0 0358: dt=0.112000, rms=0.396 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 200 iterations, nbhd size=3, neg = 7 starting rms=0.004, neg=7, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 28005.996 ms iter 1, dt=0.000000: new neg 7, old_neg 7, delta 0, rms=0.004 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0359: dt=0.112000, rms=0.396 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50858.008 ms iter 0, gcam->neg = 31 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.004, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23752.854 ms iter 1, dt=0.000023: new neg 0, old_neg 6, delta 6, rms=0.001 (74.531%) 0360: dt=0.448000, rms=0.395 (0.087%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45382.570 ms iter 0, gcam->neg = 14 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23836.758 ms iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.001 (47.593%) gcamFindOptimalTimeStep: Complete in 23780.338 ms iter 2, dt=0.000026: new neg 0, old_neg 1, delta 1, rms=0.001 (51.339%) 0361: dt=0.256000, rms=0.395 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23823.713 ms iter 1, dt=0.000023: new neg 0, old_neg 5, delta 5, rms=0.001 (79.982%) 0362: dt=0.256000, rms=0.395 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23901.807 ms iter 1, dt=0.000023: new neg 1, old_neg 5, delta 4, rms=0.002 (70.069%) gcamFindOptimalTimeStep: Complete in 23628.777 ms iter 2, dt=0.000009: new neg 0, old_neg 1, delta 1, rms=0.001 (49.874%) 0363: dt=0.256000, rms=0.395 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23563.443 ms iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.001 (45.872%) gcamFindOptimalTimeStep: Complete in 23743.771 ms iter 2, dt=0.000026: new neg 0, old_neg 1, delta 1, rms=0.001 (43.190%) 0364: dt=0.256000, rms=0.394 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23958.744 ms iter 1, dt=0.000023: new neg 1, old_neg 6, delta 5, rms=0.001 (75.045%) gcamFindOptimalTimeStep: Complete in 24058.264 ms iter 2, dt=0.000009: new neg 0, old_neg 1, delta 1, rms=0.001 (36.320%) 0365: dt=0.256000, rms=0.394 (0.032%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45208.332 ms iter 0, gcam->neg = 39 after 10 iterations, nbhd size=1, neg = 0 0366: dt=0.064000, rms=0.391 (0.262%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45212.383 ms iter 0, gcam->neg = 18 after 6 iterations, nbhd size=1, neg = 0 0367: dt=0.028000, rms=0.391 (0.094%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0368: dt=0.028000, rms=0.390 (0.091%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 15 iterations, nbhd size=2, neg = 0 0369: dt=0.028000, rms=0.390 (0.161%), neg=0, invalid=766 iter 0, gcam->neg = 55 after 17 iterations, nbhd size=2, neg = 0 0370: dt=0.028000, rms=0.389 (0.207%), neg=0, invalid=766 iter 0, gcam->neg = 85 after 9 iterations, nbhd size=1, neg = 0 0371: dt=0.028000, rms=0.388 (0.234%), neg=0, invalid=766 iter 0, gcam->neg = 97 after 17 iterations, nbhd size=2, neg = 0 0372: dt=0.028000, rms=0.387 (0.238%), neg=0, invalid=766 iter 0, gcam->neg = 111 after 19 iterations, nbhd size=2, neg = 0 0373: dt=0.028000, rms=0.386 (0.219%), neg=0, invalid=766 iter 0, gcam->neg = 123 after 27 iterations, nbhd size=3, neg = 0 0374: dt=0.028000, rms=0.385 (0.205%), neg=0, invalid=766 iter 0, gcam->neg = 139 after 20 iterations, nbhd size=2, neg = 0 0375: dt=0.028000, rms=0.385 (0.171%), neg=0, invalid=766 iter 0, gcam->neg = 164 after 29 iterations, nbhd size=3, neg = 0 0376: dt=0.028000, rms=0.384 (0.140%), neg=0, invalid=766 iter 0, gcam->neg = 176 after 30 iterations, nbhd size=3, neg = 0 0377: dt=0.028000, rms=0.384 (0.095%), neg=0, invalid=766 iter 0, gcam->neg = 209 after 25 iterations, nbhd size=3, neg = 0 0378: dt=0.028000, rms=0.384 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45298.293 ms 0379: dt=0.000438, rms=0.384 (0.001%), neg=0, invalid=766 0380: dt=0.000438, rms=0.384 (0.000%), neg=0, invalid=766 0381: dt=0.000438, rms=0.384 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45121.953 ms iter 0, gcam->neg = 10 after 17 iterations, nbhd size=2, neg = 0 0382: dt=0.020150, rms=0.384 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45020.734 ms 0383: dt=0.000438, rms=0.384 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0384: dt=0.000438, rms=0.384 (0.001%), neg=0, invalid=766 0385: dt=0.000438, rms=0.384 (0.002%), neg=0, invalid=766 0386: dt=0.000438, rms=0.384 (0.002%), neg=0, invalid=766 0387: dt=0.000438, rms=0.384 (0.003%), neg=0, invalid=766 0388: dt=0.000438, rms=0.384 (0.003%), neg=0, invalid=766 0389: dt=0.000438, rms=0.384 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0390: dt=0.000438, rms=0.383 (0.004%), neg=0, invalid=766 0391: dt=0.000438, rms=0.383 (0.005%), neg=0, invalid=766 0392: dt=0.000438, rms=0.383 (0.005%), neg=0, invalid=766 0393: dt=0.000438, rms=0.383 (0.005%), neg=0, invalid=766 0394: dt=0.000438, rms=0.383 (0.005%), neg=0, invalid=766 0395: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0396: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0397: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0398: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0399: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0400: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0401: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0402: dt=0.000438, rms=0.383 (0.006%), neg=0, invalid=766 0403: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0404: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0405: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0406: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0407: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0408: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 0409: dt=0.000438, rms=0.383 (0.007%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.382, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47248.395 ms iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0410: dt=0.028000, rms=0.381 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46193.391 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0411: dt=0.007000, rms=0.381 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0412: dt=0.007000, rms=0.381 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0413: dt=0.007000, rms=0.381 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 14 iterations, nbhd size=2, neg = 0 0414: dt=0.007000, rms=0.381 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 13 iterations, nbhd size=2, neg = 0 0415: dt=0.007000, rms=0.381 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 8 iterations, nbhd size=1, neg = 0 0416: dt=0.007000, rms=0.380 (0.089%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0417: dt=0.007000, rms=0.380 (0.099%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 17 iterations, nbhd size=2, neg = 0 0418: dt=0.007000, rms=0.379 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 19 iterations, nbhd size=2, neg = 0 0419: dt=0.007000, rms=0.379 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 16 iterations, nbhd size=2, neg = 0 0420: dt=0.007000, rms=0.379 (0.109%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 19 iterations, nbhd size=2, neg = 0 0421: dt=0.007000, rms=0.378 (0.109%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 18 iterations, nbhd size=2, neg = 0 0422: dt=0.007000, rms=0.378 (0.106%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.378, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53092.852 ms iter 0, gcam->neg = 16 after 16 iterations, nbhd size=2, neg = 0 0423: dt=0.020000, rms=0.378 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51733.184 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0424: dt=0.004000, rms=0.378 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0425: dt=0.004000, rms=0.378 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0426: dt=0.004000, rms=0.377 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0427: dt=0.004000, rms=0.377 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 18 iterations, nbhd size=2, neg = 0 0428: dt=0.004000, rms=0.377 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 16 iterations, nbhd size=2, neg = 0 0429: dt=0.004000, rms=0.377 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 16 iterations, nbhd size=2, neg = 0 0430: dt=0.004000, rms=0.377 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0431: dt=0.004000, rms=0.377 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0432: dt=0.004000, rms=0.376 (0.064%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=2, neg = 0 0433: dt=0.004000, rms=0.376 (0.066%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0434: dt=0.004000, rms=0.376 (0.066%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 11 iterations, nbhd size=1, neg = 0 0435: dt=0.004000, rms=0.376 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 18 iterations, nbhd size=2, neg = 0 0436: dt=0.004000, rms=0.375 (0.061%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45300.383 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0437: dt=0.005000, rms=0.375 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45239.848 ms 0438: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0439: dt=0.000438, rms=0.375 (0.002%), neg=0, invalid=766 0440: dt=0.000438, rms=0.375 (0.003%), neg=0, invalid=766 0441: dt=0.000438, rms=0.375 (0.004%), neg=0, invalid=766 0442: dt=0.000438, rms=0.375 (0.005%), neg=0, invalid=766 0443: dt=0.000438, rms=0.375 (0.006%), neg=0, invalid=766 0444: dt=0.000438, rms=0.375 (0.007%), neg=0, invalid=766 0445: dt=0.000438, rms=0.375 (0.008%), neg=0, invalid=766 0446: dt=0.000438, rms=0.375 (0.009%), neg=0, invalid=766 0447: dt=0.000438, rms=0.375 (0.009%), neg=0, invalid=766 0448: dt=0.000438, rms=0.375 (0.010%), neg=0, invalid=766 0449: dt=0.000438, rms=0.375 (0.010%), neg=0, invalid=766 0450: dt=0.000438, rms=0.375 (0.011%), neg=0, invalid=766 0451: dt=0.000438, rms=0.375 (0.011%), neg=0, invalid=766 0452: dt=0.000438, rms=0.375 (0.012%), neg=0, invalid=766 0453: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0454: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0455: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 0456: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0457: dt=0.000438, rms=0.374 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0458: dt=0.000438, rms=0.374 (0.013%), neg=0, invalid=766 0459: dt=0.000438, rms=0.374 (0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45330.117 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0460: dt=0.001250, rms=0.374 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45348.516 ms iter 0, gcam->neg = 6 after 19 iterations, nbhd size=2, neg = 0 0461: dt=0.007000, rms=0.374 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45250.039 ms iter 0, gcam->neg = 10 after 22 iterations, nbhd size=3, neg = 0 0462: dt=0.012000, rms=0.374 (0.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45313.547 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0463: dt=0.006000, rms=0.374 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0464: dt=0.006000, rms=0.374 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 17 iterations, nbhd size=2, neg = 0 0465: dt=0.006000, rms=0.373 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 15 iterations, nbhd size=2, neg = 0 0466: dt=0.006000, rms=0.373 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=1, neg = 0 0467: dt=0.006000, rms=0.373 (0.089%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 0468: dt=0.006000, rms=0.372 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 19 iterations, nbhd size=2, neg = 0 0469: dt=0.006000, rms=0.372 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 38 iterations, nbhd size=4, neg = 0 0470: dt=0.006000, rms=0.372 (0.116%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 17 iterations, nbhd size=2, neg = 0 0471: dt=0.006000, rms=0.371 (0.127%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 19 iterations, nbhd size=2, neg = 0 0472: dt=0.006000, rms=0.371 (0.128%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 22 iterations, nbhd size=2, neg = 0 0473: dt=0.006000, rms=0.370 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 26 iterations, nbhd size=3, neg = 0 0474: dt=0.006000, rms=0.370 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 19 iterations, nbhd size=2, neg = 0 0475: dt=0.006000, rms=0.369 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 29 iterations, nbhd size=2, neg = 0 0476: dt=0.006000, rms=0.369 (0.113%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 22 iterations, nbhd size=2, neg = 0 0477: dt=0.006000, rms=0.368 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44905.242 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0478: dt=0.004000, rms=0.368 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0479: dt=0.004000, rms=0.368 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0480: dt=0.004000, rms=0.368 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 15 iterations, nbhd size=2, neg = 0 0481: dt=0.004000, rms=0.368 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 17 iterations, nbhd size=2, neg = 0 0482: dt=0.004000, rms=0.368 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0483: dt=0.004000, rms=0.368 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 15 iterations, nbhd size=2, neg = 0 0484: dt=0.004000, rms=0.368 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 14 iterations, nbhd size=2, neg = 0 0485: dt=0.004000, rms=0.368 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 24 iterations, nbhd size=2, neg = 0 0486: dt=0.004000, rms=0.368 (0.015%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 7 hours, 7 minutes and 38 seconds. #-------------------------------------- #@# CA Reg Inv Mon Jul 11 22:53:36 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Jul 11 22:54:47 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11747674 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 20 seconds. #-------------------------------------- #@# SkullLTA Mon Jul 11 22:56:07 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/autofs/space/plato_002/users/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=5.0 skull bounding box = (44, 41, 33) --> (215, 220, 225) using (101, 101, 129) as brain centroid... mean wm in atlas = 126, using box (80,79,105) --> (122, 123,152) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10330.6, old_max_log_p =-10379.1 (thresh=-10368.7) 1.123 0.122 -0.133 -18.107; 0.022 0.947 0.691 -76.785; 0.179 -0.743 0.919 62.774; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10330.6, old_max_log_p =-10330.6 (thresh=-10320.2) 1.123 0.122 -0.133 -18.107; 0.022 0.947 0.691 -76.785; 0.179 -0.743 0.919 62.774; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10321.9, old_max_log_p =-10330.6 (thresh=-10320.2) 1.154 0.020 -0.070 -19.066; 0.064 0.960 0.744 -91.915; 0.061 -0.741 0.852 85.770; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10320.0, old_max_log_p =-10321.9 (thresh=-10311.6) 1.151 0.020 -0.070 -18.726; 0.064 0.960 0.744 -91.915; 0.061 -0.741 0.852 85.770; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15088 0.01958 -0.07017 -18.72645; 0.06428 0.95954 0.74368 -91.91453; 0.06052 -0.74070 0.85247 85.77016; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.15088 0.01958 -0.07017 -18.72645; 0.06428 0.95954 0.74368 -91.91453; 0.06052 -0.74070 0.85247 85.77016; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10320.0 tol 0.000010 Resulting transform: 1.151 0.020 -0.070 -18.726; 0.064 0.960 0.744 -91.915; 0.061 -0.741 0.852 85.770; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10320.0 (old=-10379.1) transform before final EM align: 1.151 0.020 -0.070 -18.726; 0.064 0.960 0.744 -91.915; 0.061 -0.741 0.852 85.770; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15088 0.01958 -0.07017 -18.72645; 0.06428 0.95954 0.74368 -91.91453; 0.06052 -0.74070 0.85247 85.77016; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.15088 0.01958 -0.07017 -18.72645; 0.06428 0.95954 0.74368 -91.91453; 0.06052 -0.74070 0.85247 85.77016; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 1145717.2 tol 0.000000 final transform: 1.151 0.020 -0.070 -18.726; 0.064 0.960 0.744 -91.915; 0.061 -0.741 0.852 85.770; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 43 seconds. #-------------------------------------- #@# SubCort Seg Mon Jul 11 23:13:50 EDT 2016 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute-0-15 machine x86_64 user fdu0 Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations A difference found, saving. mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /autofs/space/plato_002/users/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.08684 (23) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (7040 voxels, overlap=0.850) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (7040 voxels, peak = 24), gca=24.3 gca peak = 0.14982 (20) mri peak = 0.09086 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (5053 voxels, overlap=0.849) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (5053 voxels, peak = 20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.09199 (97) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (335 voxels, peak = 95), gca=94.6 gca peak = 0.18160 (96) mri peak = 0.07675 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (441 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (441 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.08737 (77) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (833 voxels, overlap=0.064) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (833 voxels, peak = 71), gca=71.3 gca peak = 0.32745 (63) mri peak = 0.08576 (78) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (865 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (865 voxels, peak = 76), gca=75.6 gca peak = 0.08597 (105) mri peak = 0.08014 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31169 voxels, overlap=0.846) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31169 voxels, peak = 105), gca=105.0 gca peak = 0.09209 (106) mri peak = 0.08185 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (27151 voxels, overlap=0.779) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (27151 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04272 (83) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (27011 voxels, overlap=0.038) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (27011 voxels, peak = 80), gca=80.3 gca peak = 0.08598 (64) mri peak = 0.04334 (86) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (29270 voxels, overlap=0.046) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (29270 voxels, peak = 83), gca=83.2 gca peak = 0.24164 (71) mri peak = 0.11850 (85) Right_Caudate (50): linear fit = 1.15 x + 0.0 (827 voxels, overlap=0.001) Right_Caudate (50): linear fit = 1.15 x + 0.0 (827 voxels, peak = 82), gca=81.7 gca peak = 0.18227 (75) mri peak = 0.09902 (82) Left_Caudate (11): linear fit = 1.02 x + 0.0 (744 voxels, overlap=0.870) Left_Caudate (11): linear fit = 1.02 x + 0.0 (744 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.06625 (80) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (23054 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (23054 voxels, peak = 82), gca=82.2 gca peak = 0.11668 (59) mri peak = 0.07111 (79) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23730 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23730 voxels, peak = 78), gca=78.2 gca peak = 0.17849 (88) mri peak = 0.09498 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5156 voxels, overlap=0.423) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5156 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.09283 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (4363 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (4363 voxels, peak = 95), gca=94.6 gca peak = 0.41688 (64) mri peak = 0.14169 (75) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (365 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (365 voxels, peak = 77), gca=76.8 gca peak = 0.42394 (62) mri peak = 0.09204 (77) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (279 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (279 voxels, peak = 74), gca=74.4 gca peak = 0.10041 (96) mri peak = 0.07299 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3430 voxels, overlap=0.992) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3430 voxels, peak = 96), gca=96.0 gca peak = 0.13978 (88) mri peak = 0.07446 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3585 voxels, overlap=0.984) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3585 voxels, peak = 88), gca=88.0 gca peak = 0.08514 (81) mri peak = 0.09367 (91) Left_Putamen (12): linear fit = 1.08 x + 0.0 (1728 voxels, overlap=0.469) Left_Putamen (12): linear fit = 1.08 x + 0.0 (1728 voxels, peak = 87), gca=87.1 gca peak = 0.09624 (82) mri peak = 0.09211 (90) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1545 voxels, overlap=0.585) Right_Putamen (51): linear fit = 1.08 x + 0.0 (1545 voxels, peak = 88), gca=88.2 gca peak = 0.07543 (88) mri peak = 0.06875 (91) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12450 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12450 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.07029 (97) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (972 voxels, overlap=0.767) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (972 voxels, peak = 100), gca=99.7 gca peak = 0.17004 (92) mri peak = 0.07066 (101) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1152 voxels, overlap=0.815) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1152 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.11382 (24) Third_Ventricle (14): linear fit = 0.68 x + 0.0 (243 voxels, overlap=0.115) Third_Ventricle (14): linear fit = 0.68 x + 0.0 (243 voxels, peak = 24), gca=24.3 gca peak = 0.26069 (23) mri peak = 0.08388 (24) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (145 voxels, overlap=0.713) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (145 voxels, peak = 20), gca=20.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.22 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.87 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14647 (25) mri peak = 0.08684 (23) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (7040 voxels, overlap=0.940) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (7040 voxels, peak = 24), gca=23.8 gca peak = 0.19381 (21) mri peak = 0.09086 (22) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (5053 voxels, overlap=0.831) Right_Lateral_Ventricle (43): linear fit = 0.95 x + 0.0 (5053 voxels, peak = 20), gca=19.9 gca peak = 0.33371 (95) mri peak = 0.09199 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (335 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (335 voxels, peak = 95), gca=95.0 gca peak = 0.18507 (101) mri peak = 0.07675 (102) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (441 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (441 voxels, peak = 104), gca=103.5 gca peak = 0.24969 (71) mri peak = 0.08737 (77) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (833 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (833 voxels, peak = 71), gca=71.0 gca peak = 0.26453 (76) mri peak = 0.08576 (78) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (865 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (865 voxels, peak = 76), gca=76.0 gca peak = 0.08618 (105) mri peak = 0.08014 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31169 voxels, overlap=0.846) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31169 voxels, peak = 105), gca=105.0 gca peak = 0.08536 (108) mri peak = 0.08185 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27151 voxels, overlap=0.797) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27151 voxels, peak = 108), gca=108.0 gca peak = 0.06272 (80) mri peak = 0.04272 (83) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27011 voxels, overlap=0.912) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27011 voxels, peak = 80), gca=80.0 gca peak = 0.06786 (82) mri peak = 0.04334 (86) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (29270 voxels, overlap=0.886) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (29270 voxels, peak = 80), gca=80.0 gca peak = 0.22553 (81) mri peak = 0.11850 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (827 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (827 voxels, peak = 81), gca=81.0 gca peak = 0.18162 (77) mri peak = 0.09902 (82) Left_Caudate (11): linear fit = 1.00 x + 0.0 (744 voxels, overlap=0.998) Left_Caudate (11): linear fit = 1.00 x + 0.0 (744 voxels, peak = 77), gca=77.0 gca peak = 0.08220 (82) mri peak = 0.06625 (80) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (23054 voxels, overlap=0.922) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (23054 voxels, peak = 80), gca=80.0 gca peak = 0.09537 (79) mri peak = 0.07111 (79) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (23730 voxels, overlap=0.909) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (23730 voxels, peak = 77), gca=77.0 gca peak = 0.17133 (94) mri peak = 0.09498 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5156 voxels, overlap=0.945) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5156 voxels, peak = 96), gca=96.3 gca peak = 0.15537 (95) mri peak = 0.09283 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4363 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4363 voxels, peak = 95), gca=95.0 gca peak = 0.31570 (76) mri peak = 0.14169 (75) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (365 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (365 voxels, peak = 74), gca=74.1 gca peak = 0.32960 (75) mri peak = 0.09204 (77) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (279 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (279 voxels, peak = 75), gca=75.0 gca peak = 0.10555 (96) mri peak = 0.07299 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3430 voxels, overlap=0.988) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3430 voxels, peak = 96), gca=96.0 gca peak = 0.13882 (88) mri peak = 0.07446 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3585 voxels, overlap=0.982) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3585 voxels, peak = 88), gca=88.0 gca peak = 0.08262 (87) mri peak = 0.09367 (91) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1728 voxels, overlap=0.828) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1728 voxels, peak = 89), gca=89.2 gca peak = 0.10371 (82) mri peak = 0.09211 (90) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1545 voxels, overlap=0.895) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1545 voxels, peak = 82), gca=82.0 gca peak = 0.07219 (90) mri peak = 0.06875 (91) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12450 voxels, overlap=0.855) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12450 voxels, peak = 90), gca=90.0 gca peak = 0.10335 (99) mri peak = 0.07029 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (972 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (972 voxels, peak = 99), gca=99.0 gca peak = 0.15044 (99) mri peak = 0.07066 (101) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1152 voxels, overlap=0.930) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1152 voxels, peak = 101), gca=101.5 gca peak = 0.25067 (24) mri peak = 0.11382 (24) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (243 voxels, overlap=1.000) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (243 voxels, peak = 25), gca=24.6 gca peak = 0.24174 (20) mri peak = 0.08388 (24) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (145 voxels, overlap=0.875) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (145 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26961 (42) gca peak CSF = 0.17894 (40) gca peak Left_Accumbens_area = 0.49875 (72) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.30136 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (37) gca peak WM_hypointensities = 0.14439 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34497 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 Left_Pallidum too bright - rescaling by 0.998 (from 1.025) to 103.3 (was 103.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 40467 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 329 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 77731 changed. image ll: -2.146, PF=1.000 pass 2: 12910 changed. image ll: -2.144, PF=1.000 pass 3: 4174 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 21 minutes and 39 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/transforms/cc_up.lta AD01 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/AD01/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/norm.mgz 17989 voxels in left wm, 39252 in right wm, xrange [125, 135] searching rotation angles z=[-9 5], y=[-10 4] searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 global minimum found at slice 130.6, rotations (-2.98, -1.59) final transformation (x=130.6, yr=-2.983, zr=-1.591): 0.998 0.028 -0.052 0.455; -0.028 1.000 0.001 28.503; 0.052 -0.000 0.999 11.350; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 150 120 eigenvectors: -0.002 0.007 1.000; -0.323 -0.946 0.006; 0.946 -0.323 0.004; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Mon Jul 11 23:36:26 EDT 2016 mri_seg_diff --seg aseg.auto.mgz --diff-in aseg.manedit.mgz --merged aseg.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri cmdline mri_seg_diff --seg aseg.auto.mgz --diff-in aseg.manedit.mgz --merged aseg.mgz sysname Linux hostname compute-0-15 machine x86_64 user fdu0 Seg1 aseg.auto.mgz Seg2 (null) Diff (null) InDiff aseg.manedit.mgz Merged aseg.mgz ForceDiff 0 Merging difference segmentation #-------------------------------------------- #@# Intensity Normalization2 Mon Jul 11 23:36:34 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_normalize -f /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 0 control points... MRI3dGentleNormalize: mean = 0.0, nctrl = 0, norm failed using MR volume brainmask.mgz to mask input volume... removing outliers in the aseg WM... 4233 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 43 seconds. white matter peak found at 111 white matter peak found at 108 gm peak at 86 (86), valley at 59 (59) csf peak at 41, setting threshold to 71 white matter peak found at 111 white matter peak found at 92 gm peak at 55 (55), valley at 44 (44) csf peak at 28, setting threshold to 46 #-------------------------------------------- #@# Mask BFS Mon Jul 11 23:41:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1358277 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jul 11 23:41:24 EDT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-15 machine x86_64 user fdu0 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-15 machine x86_64 user fdu0 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 5.7 [80.0 --> 125.0] GM (73.0) : 70.7 +- 13.2 [30.0 --> 96.0] setting bottom of white matter range to 83.9 setting top of gray matter range to 97.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 6392 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2942 filled 781 bright non-wm voxels segmented. 5810 diagonally connected voxels added... white matter segmentation took 2.2 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.65 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2965 additional wm voxels added 0 additional wm voxels added SEG EDIT: 58207 voxels turned on, 66858 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 107 new 107 115,126,128 old 107 new 107 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 245 found - 245 modified | TOTAL: 245 pass 2 (xy+): 0 found - 245 modified | TOTAL: 245 pass 1 (xy-): 207 found - 207 modified | TOTAL: 452 pass 2 (xy-): 0 found - 207 modified | TOTAL: 452 pass 1 (yz+): 186 found - 186 modified | TOTAL: 638 pass 2 (yz+): 0 found - 186 modified | TOTAL: 638 pass 1 (yz-): 180 found - 180 modified | TOTAL: 818 pass 2 (yz-): 0 found - 180 modified | TOTAL: 818 pass 1 (xz+): 173 found - 173 modified | TOTAL: 991 pass 2 (xz+): 0 found - 173 modified | TOTAL: 991 pass 1 (xz-): 145 found - 145 modified | TOTAL: 1136 pass 2 (xz-): 0 found - 145 modified | TOTAL: 1136 Iteration Number : 1 pass 1 (+++): 48 found - 48 modified | TOTAL: 48 pass 2 (+++): 0 found - 48 modified | TOTAL: 48 pass 1 (+++): 39 found - 39 modified | TOTAL: 87 pass 2 (+++): 0 found - 39 modified | TOTAL: 87 pass 1 (+++): 34 found - 34 modified | TOTAL: 121 pass 2 (+++): 0 found - 34 modified | TOTAL: 121 pass 1 (+++): 36 found - 36 modified | TOTAL: 157 pass 2 (+++): 0 found - 36 modified | TOTAL: 157 Iteration Number : 1 pass 1 (++): 134 found - 134 modified | TOTAL: 134 pass 2 (++): 0 found - 134 modified | TOTAL: 134 pass 1 (+-): 130 found - 130 modified | TOTAL: 264 pass 2 (+-): 1 found - 131 modified | TOTAL: 265 pass 3 (+-): 0 found - 131 modified | TOTAL: 265 pass 1 (--): 127 found - 127 modified | TOTAL: 392 pass 2 (--): 0 found - 127 modified | TOTAL: 392 pass 1 (-+): 133 found - 133 modified | TOTAL: 525 pass 2 (-+): 0 found - 133 modified | TOTAL: 525 Iteration Number : 2 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 4 found - 4 modified | TOTAL: 15 pass 2 (xy-): 0 found - 4 modified | TOTAL: 15 pass 1 (yz+): 12 found - 12 modified | TOTAL: 27 pass 2 (yz+): 0 found - 12 modified | TOTAL: 27 pass 1 (yz-): 20 found - 20 modified | TOTAL: 47 pass 2 (yz-): 0 found - 20 modified | TOTAL: 47 pass 1 (xz+): 12 found - 12 modified | TOTAL: 59 pass 2 (xz+): 0 found - 12 modified | TOTAL: 59 pass 1 (xz-): 7 found - 7 modified | TOTAL: 66 pass 2 (xz-): 0 found - 7 modified | TOTAL: 66 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 5 found - 5 modified | TOTAL: 11 pass 2 (+++): 0 found - 5 modified | TOTAL: 11 Iteration Number : 2 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 1 found - 1 modified | TOTAL: 9 pass 2 (+-): 0 found - 1 modified | TOTAL: 9 pass 1 (--): 13 found - 13 modified | TOTAL: 22 pass 2 (--): 1 found - 14 modified | TOTAL: 23 pass 3 (--): 0 found - 14 modified | TOTAL: 23 pass 1 (-+): 4 found - 4 modified | TOTAL: 27 pass 2 (-+): 0 found - 4 modified | TOTAL: 27 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 1931 (out of 480796: 0.401626) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Mon Jul 11 23:44:37 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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 1.059 0.016 -0.003 -12.572; 0.010 1.029 0.419 -52.865; 0.040 -0.401 0.947 36.532; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.059 0.016 -0.003 -12.572; 0.010 1.029 0.419 -52.865; 0.040 -0.401 0.947 36.532; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1107 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (130, 116, 149), TAL = (-2.0, 21.0, 12.0) talairach voxel to voxel transform 0.944 -0.011 0.008 10.981; 0.005 0.829 -0.367 57.292; -0.037 0.351 0.901 -14.808; 0.000 0.000 0.000 1.000; segmentation indicates cc at (130, 116, 149) --> (-2.0, 21.0, 12.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (-2.00, 21.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(16.00, 21.00, 12.00) SRC: (116.63, 99.43, 155.99) search lh wm seed point around talairach space (-20.00, 21.00, 12.00), SRC: (150.63, 99.63, 154.66) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Mon Jul 11 23:45:30 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 = 8 (out of 245881: 0.003254) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 3437 vertices, 3692 faces slice 70: 12709 vertices, 13119 faces slice 80: 24312 vertices, 24786 faces slice 90: 36036 vertices, 36480 faces slice 100: 47616 vertices, 48041 faces slice 110: 58963 vertices, 59397 faces slice 120: 69287 vertices, 69747 faces slice 130: 80273 vertices, 80774 faces slice 140: 90108 vertices, 90532 faces slice 150: 99217 vertices, 99638 faces slice 160: 107574 vertices, 108001 faces slice 170: 114860 vertices, 115211 faces slice 180: 119729 vertices, 120036 faces slice 190: 122930 vertices, 123148 faces slice 200: 123350 vertices, 123510 faces slice 210: 123350 vertices, 123510 faces slice 220: 123350 vertices, 123510 faces slice 230: 123350 vertices, 123510 faces slice 240: 123350 vertices, 123510 faces slice 250: 123350 vertices, 123510 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 123350 voxel in cpt #1: X=-160 [v=123350,e=370530,f=247020] located at (-30.449671, -14.018459, 14.627264) For the whole surface: X=-160 [v=123350,e=370530,f=247020] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jul 11 23:45:40 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Jul 11 23:45:45 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts avg radius = 44.7 mm, total surface area = 62500 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.069 (target=0.015) step 015: RMS=0.062 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.043 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.041 (target=0.015) step 060: RMS=0.041 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Jul 11 23:46:33 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.04 +- 0.61 (0.00-->7.03) (max @ vno 93606 --> 93607) face area 0.03 +- 0.04 (-0.15-->0.70) scaling brain by 0.368... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.482, avgs=0 005/300: dt: 0.9000, rms radial error=174.225, avgs=0 010/300: dt: 0.9000, rms radial error=173.673, avgs=0 015/300: dt: 0.9000, rms radial error=172.947, avgs=0 020/300: dt: 0.9000, rms radial error=172.121, avgs=0 025/300: dt: 0.9000, rms radial error=171.237, avgs=0 030/300: dt: 0.9000, rms radial error=170.321, avgs=0 035/300: dt: 0.9000, rms radial error=169.387, avgs=0 040/300: dt: 0.9000, rms radial error=168.445, avgs=0 045/300: dt: 0.9000, rms radial error=167.504, avgs=0 050/300: dt: 0.9000, rms radial error=166.564, avgs=0 055/300: dt: 0.9000, rms radial error=165.626, avgs=0 060/300: dt: 0.9000, rms radial error=164.693, avgs=0 065/300: dt: 0.9000, rms radial error=163.766, avgs=0 070/300: dt: 0.9000, rms radial error=162.850, avgs=0 075/300: dt: 0.9000, rms radial error=161.938, avgs=0 080/300: dt: 0.9000, rms radial error=161.031, avgs=0 085/300: dt: 0.9000, rms radial error=160.127, avgs=0 090/300: dt: 0.9000, rms radial error=159.228, avgs=0 095/300: dt: 0.9000, rms radial error=158.334, avgs=0 100/300: dt: 0.9000, rms radial error=157.445, avgs=0 105/300: dt: 0.9000, rms radial error=156.561, avgs=0 110/300: dt: 0.9000, rms radial error=155.680, avgs=0 115/300: dt: 0.9000, rms radial error=154.803, avgs=0 120/300: dt: 0.9000, rms radial error=153.932, avgs=0 125/300: dt: 0.9000, rms radial error=153.066, avgs=0 130/300: dt: 0.9000, rms radial error=152.204, avgs=0 135/300: dt: 0.9000, rms radial error=151.348, avgs=0 140/300: dt: 0.9000, rms radial error=150.495, avgs=0 145/300: dt: 0.9000, rms radial error=149.647, avgs=0 150/300: dt: 0.9000, rms radial error=148.804, avgs=0 155/300: dt: 0.9000, rms radial error=147.965, avgs=0 160/300: dt: 0.9000, rms radial error=147.131, avgs=0 165/300: dt: 0.9000, rms radial error=146.301, avgs=0 170/300: dt: 0.9000, rms radial error=145.477, avgs=0 175/300: dt: 0.9000, rms radial error=144.656, avgs=0 180/300: dt: 0.9000, rms radial error=143.840, avgs=0 185/300: dt: 0.9000, rms radial error=143.029, avgs=0 190/300: dt: 0.9000, rms radial error=142.222, avgs=0 195/300: dt: 0.9000, rms radial error=141.419, avgs=0 200/300: dt: 0.9000, rms radial error=140.621, avgs=0 205/300: dt: 0.9000, rms radial error=139.827, avgs=0 210/300: dt: 0.9000, rms radial error=139.037, avgs=0 215/300: dt: 0.9000, rms radial error=138.252, avgs=0 220/300: dt: 0.9000, rms radial error=137.471, avgs=0 225/300: dt: 0.9000, rms radial error=136.695, avgs=0 230/300: dt: 0.9000, rms radial error=135.922, avgs=0 235/300: dt: 0.9000, rms radial error=135.154, avgs=0 240/300: dt: 0.9000, rms radial error=134.390, avgs=0 245/300: dt: 0.9000, rms radial error=133.631, avgs=0 250/300: dt: 0.9000, rms radial error=132.876, avgs=0 255/300: dt: 0.9000, rms radial error=132.125, avgs=0 260/300: dt: 0.9000, rms radial error=131.379, avgs=0 265/300: dt: 0.9000, rms radial error=130.637, avgs=0 270/300: dt: 0.9000, rms radial error=129.900, avgs=0 275/300: dt: 0.9000, rms radial error=129.166, avgs=0 280/300: dt: 0.9000, rms radial error=128.437, avgs=0 285/300: dt: 0.9000, rms radial error=127.711, avgs=0 290/300: dt: 0.9000, rms radial error=126.990, avgs=0 295/300: dt: 0.9000, rms radial error=126.273, avgs=0 300/300: dt: 0.9000, rms radial error=125.559, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13711.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2135.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00022 epoch 3 (K=160.0), pass 1, starting sse = 215.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00300 epoch 4 (K=640.0), pass 1, starting sse = 21.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00554 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Jul 11 23:52:06 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 AD01 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-160 (nv=123350, nf=247020, ne=370530, g=81) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 9047 ambiguous faces found in tessellation segmenting defects... 83 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 39 into 34 -merging segment 58 into 57 -merging segment 72 into 65 80 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0305 (-4.5152) -vertex loglikelihood: -6.1530 (-3.0765) -normal dot loglikelihood: -3.5317 (-3.5317) -quad curv loglikelihood: -6.4985 (-3.2493) Total Loglikelihood : -25.2137 CORRECTING DEFECT 0 (vertices=24, convex hull=50) After retessellation of defect 0, euler #=-76 (117775,350827,232976) : difference with theory (-77) = -1 CORRECTING DEFECT 1 (vertices=24, convex hull=56) After retessellation of defect 1, euler #=-75 (117787,350886,233024) : difference with theory (-76) = -1 CORRECTING DEFECT 2 (vertices=34, convex hull=89) After retessellation of defect 2, euler #=-74 (117802,350964,233088) : difference with theory (-75) = -1 CORRECTING DEFECT 3 (vertices=81, convex hull=99) After retessellation of defect 3, euler #=-73 (117835,351113,233205) : difference with theory (-74) = -1 CORRECTING DEFECT 4 (vertices=39, convex hull=80) After retessellation of defect 4, euler #=-72 (117855,351211,233284) : difference with theory (-73) = -1 CORRECTING DEFECT 5 (vertices=60, convex hull=84) After retessellation of defect 5, euler #=-71 (117868,351286,233347) : difference with theory (-72) = -1 CORRECTING DEFECT 6 (vertices=37, convex hull=69) After retessellation of defect 6, euler #=-70 (117877,351342,233395) : difference with theory (-71) = -1 CORRECTING DEFECT 7 (vertices=32, convex hull=76) After retessellation of defect 7, euler #=-69 (117893,351423,233461) : difference with theory (-70) = -1 CORRECTING DEFECT 8 (vertices=34, convex hull=67) After retessellation of defect 8, euler #=-68 (117905,351488,233515) : difference with theory (-69) = -1 CORRECTING DEFECT 9 (vertices=82, convex hull=98) After retessellation of defect 9, euler #=-67 (117939,351633,233627) : difference with theory (-68) = -1 CORRECTING DEFECT 10 (vertices=45, convex hull=88) After retessellation of defect 10, euler #=-66 (117968,351755,233721) : difference with theory (-67) = -1 CORRECTING DEFECT 11 (vertices=26, convex hull=43) After retessellation of defect 11, euler #=-65 (117979,351804,233760) : difference with theory (-66) = -1 CORRECTING DEFECT 12 (vertices=48, convex hull=62) After retessellation of defect 12, euler #=-64 (117984,351849,233801) : difference with theory (-65) = -1 CORRECTING DEFECT 13 (vertices=71, convex hull=126) After retessellation of defect 13, euler #=-63 (118029,352044,233952) : difference with theory (-64) = -1 CORRECTING DEFECT 14 (vertices=31, convex hull=26) After retessellation of defect 14, euler #=-62 (118032,352060,233966) : difference with theory (-63) = -1 CORRECTING DEFECT 15 (vertices=37, convex hull=63) After retessellation of defect 15, euler #=-61 (118041,352111,234009) : difference with theory (-62) = -1 CORRECTING DEFECT 16 (vertices=10, convex hull=14) After retessellation of defect 16, euler #=-60 (118041,352115,234014) : difference with theory (-61) = -1 CORRECTING DEFECT 17 (vertices=64, convex hull=42) After retessellation of defect 17, euler #=-59 (118050,352156,234047) : difference with theory (-60) = -1 CORRECTING DEFECT 18 (vertices=23, convex hull=48) After retessellation of defect 18, euler #=-58 (118066,352219,234095) : difference with theory (-59) = -1 CORRECTING DEFECT 19 (vertices=31, convex hull=55) After retessellation of defect 19, euler #=-57 (118077,352277,234143) : difference with theory (-58) = -1 CORRECTING DEFECT 20 (vertices=29, convex hull=25) After retessellation of defect 20, euler #=-56 (118081,352296,234159) : difference with theory (-57) = -1 CORRECTING DEFECT 21 (vertices=42, convex hull=55) After retessellation of defect 21, euler #=-56 (118091,352352,234205) : difference with theory (-56) = 0 CORRECTING DEFECT 22 (vertices=32, convex hull=69) After retessellation of defect 22, euler #=-55 (118105,352419,234259) : difference with theory (-55) = 0 CORRECTING DEFECT 23 (vertices=46, convex hull=67) After retessellation of defect 23, euler #=-54 (118124,352504,234326) : difference with theory (-54) = 0 CORRECTING DEFECT 24 (vertices=25, convex hull=52) After retessellation of defect 24, euler #=-53 (118136,352560,234371) : difference with theory (-53) = 0 CORRECTING DEFECT 25 (vertices=228, convex hull=130) After retessellation of defect 25, euler #=-52 (118200,352810,234558) : difference with theory (-52) = 0 CORRECTING DEFECT 26 (vertices=57, convex hull=70) After retessellation of defect 26, euler #=-51 (118209,352868,234608) : difference with theory (-51) = 0 CORRECTING DEFECT 27 (vertices=51, convex hull=77) After retessellation of defect 27, euler #=-50 (118234,352974,234690) : difference with theory (-50) = 0 CORRECTING DEFECT 28 (vertices=22, convex hull=29) Warning - incorrect dp selected!!!!(-71.364476 >= -71.364483 ) After retessellation of defect 28, euler #=-49 (118236,352988,234703) : difference with theory (-49) = 0 CORRECTING DEFECT 29 (vertices=20, convex hull=49) After retessellation of defect 29, euler #=-48 (118248,353040,234744) : difference with theory (-48) = 0 CORRECTING DEFECT 30 (vertices=22, convex hull=46) After retessellation of defect 30, euler #=-47 (118257,353084,234780) : difference with theory (-47) = 0 CORRECTING DEFECT 31 (vertices=44, convex hull=48) After retessellation of defect 31, euler #=-46 (118272,353150,234832) : difference with theory (-46) = 0 CORRECTING DEFECT 32 (vertices=29, convex hull=43) After retessellation of defect 32, euler #=-45 (118284,353201,234872) : difference with theory (-45) = 0 CORRECTING DEFECT 33 (vertices=25, convex hull=59) After retessellation of defect 33, euler #=-44 (118296,353258,234918) : difference with theory (-44) = 0 CORRECTING DEFECT 34 (vertices=127, convex hull=195) After retessellation of defect 34, euler #=-42 (118321,353428,235065) : difference with theory (-43) = -1 CORRECTING DEFECT 35 (vertices=28, convex hull=57) After retessellation of defect 35, euler #=-41 (118339,353502,235122) : difference with theory (-42) = -1 CORRECTING DEFECT 36 (vertices=13, convex hull=29) After retessellation of defect 36, euler #=-40 (118342,353520,235138) : difference with theory (-41) = -1 CORRECTING DEFECT 37 (vertices=31, convex hull=59) After retessellation of defect 37, euler #=-39 (118357,353588,235192) : difference with theory (-40) = -1 CORRECTING DEFECT 38 (vertices=28, convex hull=70) After retessellation of defect 38, euler #=-38 (118373,353665,235254) : difference with theory (-39) = -1 CORRECTING DEFECT 39 (vertices=30, convex hull=55) After retessellation of defect 39, euler #=-37 (118387,353729,235305) : difference with theory (-38) = -1 CORRECTING DEFECT 40 (vertices=141, convex hull=33) After retessellation of defect 40, euler #=-36 (118396,353770,235338) : difference with theory (-37) = -1 CORRECTING DEFECT 41 (vertices=19, convex hull=51) After retessellation of defect 41, euler #=-35 (118406,353815,235374) : difference with theory (-36) = -1 CORRECTING DEFECT 42 (vertices=64, convex hull=86) After retessellation of defect 42, euler #=-35 (118421,353903,235447) : difference with theory (-35) = 0 CORRECTING DEFECT 43 (vertices=41, convex hull=62) After retessellation of defect 43, euler #=-34 (118443,353996,235519) : difference with theory (-34) = 0 CORRECTING DEFECT 44 (vertices=22, convex hull=41) After retessellation of defect 44, euler #=-33 (118451,354036,235552) : difference with theory (-33) = 0 CORRECTING DEFECT 45 (vertices=181, convex hull=84) After retessellation of defect 45, euler #=-32 (118481,354163,235650) : difference with theory (-32) = 0 CORRECTING DEFECT 46 (vertices=51, convex hull=57) After retessellation of defect 46, euler #=-31 (118508,354267,235728) : difference with theory (-31) = 0 CORRECTING DEFECT 47 (vertices=125, convex hull=126) After retessellation of defect 47, euler #=-30 (118520,354356,235806) : difference with theory (-30) = 0 CORRECTING DEFECT 48 (vertices=60, convex hull=69) After retessellation of defect 48, euler #=-29 (118534,354426,235863) : difference with theory (-29) = 0 CORRECTING DEFECT 49 (vertices=140, convex hull=135) After retessellation of defect 49, euler #=-28 (118583,354636,236025) : difference with theory (-28) = 0 CORRECTING DEFECT 50 (vertices=20, convex hull=18) After retessellation of defect 50, euler #=-27 (118586,354649,236036) : difference with theory (-27) = 0 CORRECTING DEFECT 51 (vertices=29, convex hull=76) After retessellation of defect 51, euler #=-26 (118601,354723,236096) : difference with theory (-26) = 0 CORRECTING DEFECT 52 (vertices=79, convex hull=87) After retessellation of defect 52, euler #=-25 (118637,354867,236205) : difference with theory (-25) = 0 CORRECTING DEFECT 53 (vertices=38, convex hull=70) After retessellation of defect 53, euler #=-24 (118657,354952,236271) : difference with theory (-24) = 0 CORRECTING DEFECT 54 (vertices=956, convex hull=379) After retessellation of defect 54, euler #=-23 (118762,355456,236671) : difference with theory (-23) = 0 CORRECTING DEFECT 55 (vertices=16, convex hull=22) Warning - incorrect dp selected!!!!(-72.850186 >= -72.850187 ) After retessellation of defect 55, euler #=-22 (118764,355471,236685) : difference with theory (-22) = 0 CORRECTING DEFECT 56 (vertices=83, convex hull=113) After retessellation of defect 56, euler #=-20 (118789,355598,236789) : difference with theory (-21) = -1 CORRECTING DEFECT 57 (vertices=39, convex hull=32) After retessellation of defect 57, euler #=-19 (118796,355628,236813) : difference with theory (-20) = -1 CORRECTING DEFECT 58 (vertices=7, convex hull=32) After retessellation of defect 58, euler #=-18 (118800,355649,236831) : difference with theory (-19) = -1 CORRECTING DEFECT 59 (vertices=53, convex hull=71) After retessellation of defect 59, euler #=-17 (118818,355730,236895) : difference with theory (-18) = -1 CORRECTING DEFECT 60 (vertices=34, convex hull=80) After retessellation of defect 60, euler #=-16 (118831,355802,236955) : difference with theory (-17) = -1 CORRECTING DEFECT 61 (vertices=92, convex hull=29) After retessellation of defect 61, euler #=-15 (118835,355825,236975) : difference with theory (-16) = -1 CORRECTING DEFECT 62 (vertices=34, convex hull=71) After retessellation of defect 62, euler #=-14 (118856,355918,237048) : difference with theory (-15) = -1 CORRECTING DEFECT 63 (vertices=502, convex hull=261) After retessellation of defect 63, euler #=-12 (118975,356419,237432) : difference with theory (-14) = -2 CORRECTING DEFECT 64 (vertices=21, convex hull=20) Warning - incorrect dp selected!!!!(-66.135962 >= -66.135971 ) After retessellation of defect 64, euler #=-11 (118978,356434,237445) : difference with theory (-13) = -2 CORRECTING DEFECT 65 (vertices=21, convex hull=34) After retessellation of defect 65, euler #=-10 (118987,356473,237476) : difference with theory (-12) = -2 CORRECTING DEFECT 66 (vertices=63, convex hull=74) After retessellation of defect 66, euler #=-10 (119004,356560,237546) : difference with theory (-11) = -1 CORRECTING DEFECT 67 (vertices=72, convex hull=99) After retessellation of defect 67, euler #=-9 (119033,356694,237652) : difference with theory (-10) = -1 CORRECTING DEFECT 68 (vertices=126, convex hull=112) After retessellation of defect 68, euler #=-8 (119077,356877,237792) : difference with theory (-9) = -1 CORRECTING DEFECT 69 (vertices=102, convex hull=80) After retessellation of defect 69, euler #=-7 (119100,356982,237875) : difference with theory (-8) = -1 CORRECTING DEFECT 70 (vertices=24, convex hull=18) After retessellation of defect 70, euler #=-6 (119104,356997,237887) : difference with theory (-7) = -1 CORRECTING DEFECT 71 (vertices=109, convex hull=37) After retessellation of defect 71, euler #=-5 (119109,357027,237913) : difference with theory (-6) = -1 CORRECTING DEFECT 72 (vertices=22, convex hull=22) After retessellation of defect 72, euler #=-4 (119112,357043,237927) : difference with theory (-5) = -1 CORRECTING DEFECT 73 (vertices=73, convex hull=68) After retessellation of defect 73, euler #=-3 (119130,357126,237993) : difference with theory (-4) = -1 CORRECTING DEFECT 74 (vertices=41, convex hull=86) After retessellation of defect 74, euler #=-2 (119157,357243,238084) : difference with theory (-3) = -1 CORRECTING DEFECT 75 (vertices=46, convex hull=91) After retessellation of defect 75, euler #=-1 (119178,357340,238161) : difference with theory (-2) = -1 CORRECTING DEFECT 76 (vertices=113, convex hull=152) After retessellation of defect 76, euler #=-1 (119244,357625,238380) : difference with theory (-1) = 0 CORRECTING DEFECT 77 (vertices=80, convex hull=79) After retessellation of defect 77, euler #=0 (119267,357730,238463) : difference with theory (0) = 0 CORRECTING DEFECT 78 (vertices=27, convex hull=63) After retessellation of defect 78, euler #=1 (119283,357805,238523) : difference with theory (1) = 0 CORRECTING DEFECT 79 (vertices=53, convex hull=92) After retessellation of defect 79, euler #=2 (119299,357891,238594) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.02-->11.01) (max @ vno 73753 --> 83746) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.02-->11.01) (max @ vno 73753 --> 83746) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 262 mutations (31.6%), 568 crossovers (68.4%), 391 vertices were eliminated building final representation... 4051 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119299, nf=238594, ne=357891, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 53.9 minutes 0 defective edges removing intersecting faces 000: 583 intersecting 001: 14 intersecting 002: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 119299 - 357891 + 238594 = 2 --> 0 holes F =2V-4: 238594 = 238598-4 (0) 2E=3F: 715782 = 715782 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 96 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Jul 12 00:46:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD01 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 11342 bright wm thresholded. 1184 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 82.8 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.5 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.3 (was 40) setting MAX_GRAY to 91.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 71.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->4.76) (max @ vno 118894 --> 118895) face area 0.27 +- 0.13 (0.00-->6.34) mean absolute distance = 0.82 +- 1.06 4077 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=98, GM=78 using class modes intead of means.... mean inside = 93.9, mean outside = 80.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.5, 501 (501) missing vertices, mean dist 0.1 [0.9 (%38.5)->0.8 (%61.5))] %34 local maxima, %60 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.28 (0.04-->5.19) (max @ vno 103994 --> 118918) face area 0.27 +- 0.15 (0.00-->5.02) mean absolute distance = 0.60 +- 0.92 6625 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3784977.0, rms=8.17 001: dt: 0.5000, sse=4933401.0, rms=6.07 002: dt: 0.5000, sse=5185543.0, rms=4.84 003: dt: 0.5000, sse=5560656.0, rms=4.16 004: dt: 0.5000, sse=5649744.5, rms=3.74 005: dt: 0.5000, sse=5816620.0, rms=3.44 006: dt: 0.5000, sse=5818760.0, rms=3.22 007: dt: 0.5000, sse=5927742.0, rms=3.09 008: dt: 0.5000, sse=5886087.5, rms=2.98 009: dt: 0.5000, sse=5955134.5, rms=2.89 010: dt: 0.5000, sse=5896885.0, rms=2.84 rms = 2.80, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=5967922.5, rms=2.80 012: dt: 0.2500, sse=4020146.5, rms=2.27 013: dt: 0.2500, sse=3816162.8, rms=2.19 rms = 2.18, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3733308.8, rms=2.18 rms = 2.13, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3680923.8, rms=2.13 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.6, 287 (154) missing vertices, mean dist -0.4 [0.8 (%61.3)->0.3 (%38.7))] %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 0.87 +- 0.27 (0.05-->5.10) (max @ vno 103994 --> 118918) face area 0.33 +- 0.18 (0.00-->5.97) mean absolute distance = 0.49 +- 0.61 4478 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3992667.2, rms=3.88 016: dt: 0.5000, sse=4282777.5, rms=2.90 017: dt: 0.5000, sse=4974056.0, rms=2.58 rms = 2.57, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=5078716.0, rms=2.57 019: dt: 0.2500, sse=4290594.5, rms=2.19 020: dt: 0.2500, sse=4146599.0, rms=2.10 rms = 2.06, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4104058.0, rms=2.06 022: dt: 0.1250, sse=4048532.0, rms=2.00 rms = 1.96, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4028161.5, rms=1.96 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.4, 284 (99) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %61 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 0.86 +- 0.27 (0.07-->4.96) (max @ vno 118638 --> 86186) face area 0.32 +- 0.17 (0.00-->5.54) mean absolute distance = 0.39 +- 0.47 3817 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4175495.8, rms=3.34 024: dt: 0.5000, sse=4489078.0, rms=2.35 025: dt: 0.5000, sse=5146707.0, rms=2.17 rms = 2.23, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4609878.0, rms=1.92 027: dt: 0.2500, sse=4357121.5, rms=1.82 rms = 1.81, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4297145.0, rms=1.81 029: dt: 0.1250, sse=4254548.0, rms=1.75 rms = 1.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4223522.0, rms=1.73 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=91.3, 289 (74) missing vertices, mean dist -0.1 [0.5 (%57.2)->0.3 (%42.8))] %71 local maxima, %23 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/AD01/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4258337.0, rms=2.21 031: dt: 0.5000, sse=5407695.5, rms=1.74 rms = 1.94, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4946918.0, rms=1.54 rms = 1.56, time step reduction 2 of 3 to 0.125... rms = 1.50, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4895837.5, rms=1.50 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 21 non-cortical segments detected only using segment with 2056 vertices erasing segment 1 (vno[0] = 58283) erasing segment 2 (vno[0] = 60273) erasing segment 3 (vno[0] = 78516) erasing segment 4 (vno[0] = 79474) erasing segment 5 (vno[0] = 83345) erasing segment 6 (vno[0] = 86229) erasing segment 7 (vno[0] = 87953) erasing segment 8 (vno[0] = 88046) erasing segment 9 (vno[0] = 88870) erasing segment 10 (vno[0] = 90550) erasing segment 11 (vno[0] = 91451) erasing segment 12 (vno[0] = 91477) erasing segment 13 (vno[0] = 92369) erasing segment 14 (vno[0] = 93134) erasing segment 15 (vno[0] = 94001) erasing segment 16 (vno[0] = 94146) erasing segment 17 (vno[0] = 94166) erasing segment 18 (vno[0] = 96510) erasing segment 19 (vno[0] = 118609) erasing segment 20 (vno[0] = 118636) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.cortex.label writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.area vertex spacing 0.87 +- 0.28 (0.03-->4.99) (max @ vno 86186 --> 118638) face area 0.31 +- 0.17 (0.00-->5.28) refinement took 5.3 minutes #-------------------------------------------- #@# Smooth2 lh Tue Jul 12 00:51:21 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Jul 12 00:51:25 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 44.7 mm, total surface area = 67257 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.123 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.067 (target=0.015) step 015: RMS=0.055 (target=0.015) step 020: RMS=0.046 (target=0.015) step 025: RMS=0.041 (target=0.015) step 030: RMS=0.034 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 260 vertices thresholded to be in k1 ~ [-0.37 0.59], k2 ~ [-0.15 0.07] total integrated curvature = 0.387*4pi (4.869) --> 1 handles ICI = 1.3, FI = 8.1, variation=141.100 161 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 124 vertices thresholded to be in [-0.20 0.26] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.018, std = 0.023 done. #-------------------------------------------- #@# Sphere lh Tue Jul 12 00:53:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 0.99 hours scaling brain by 0.349... pass 1: epoch 1 of 3 starting distance error %20.39 pass 1: epoch 2 of 3 starting distance error %20.37 unfolding complete - removing small folds... starting distance error %20.30 removing remaining folds... final distance error %20.32 #-------------------------------------------- #@# Surf Reg lh Tue Jul 12 01:52:55 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.575 curvature mean = 0.033, std = 0.933 curvature mean = 0.027, std = 0.875 curvature mean = -0.011, std = 0.964 curvature mean = 0.009, std = 0.948 curvature mean = -0.013, std = 0.978 curvature mean = 0.004, std = 0.977 curvature mean = -0.013, std = 0.982 curvature mean = 0.001, std = 0.990 curvature mean = -0.040, std = 0.440 curvature mean = 0.003, std = 0.067 curvature mean = 0.055, std = 0.242 curvature mean = 0.002, std = 0.079 curvature mean = 0.032, std = 0.367 curvature mean = 0.002, std = 0.086 curvature mean = 0.021, std = 0.467 curvature mean = 0.002, std = 0.088 curvature mean = 0.007, std = 0.563 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Jul 12 02:28:02 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Jul 12 02:28:04 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jul 12 02:28:06 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1081 labels changed using aseg relabeling using gibbs priors... 000: 2726 changed, 119299 examined... 001: 631 changed, 11799 examined... 002: 158 changed, 3436 examined... 003: 52 changed, 934 examined... 004: 9 changed, 312 examined... 005: 4 changed, 61 examined... 006: 3 changed, 23 examined... 007: 2 changed, 19 examined... 008: 0 changed, 6 examined... 186 labels changed using aseg 000: 130 total segments, 79 labels (254 vertices) changed 001: 55 total segments, 13 labels (26 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1769 vertices marked for relabeling... 1769 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 45 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jul 12 02:28:51 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD01 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 11342 bright wm thresholded. 1184 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 82.8 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.5 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.3 (was 40) setting MAX_GRAY to 91.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 71.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=98, GM=78 using class modes intead of means.... mean inside = 93.9, mean outside = 80.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->4.76) (max @ vno 118894 --> 118895) face area 0.27 +- 0.13 (0.00-->6.34) mean absolute distance = 0.83 +- 1.07 3997 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 540 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 20 points - only 5.00% unknown deleting segment 8 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown mean border=86.5, 503 (501) missing vertices, mean dist 0.1 [0.9 (%38.5)->0.8 (%61.5))] %34 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.28 (0.04-->5.19) (max @ vno 103994 --> 118918) face area 0.27 +- 0.14 (0.00-->5.02) mean absolute distance = 0.60 +- 0.93 5887 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3798159.0, rms=8.16 001: dt: 0.5000, sse=4955813.5, rms=6.06 002: dt: 0.5000, sse=5203011.5, rms=4.83 003: dt: 0.5000, sse=5576064.0, rms=4.15 004: dt: 0.5000, sse=5669829.5, rms=3.73 005: dt: 0.5000, sse=5836718.0, rms=3.44 006: dt: 0.5000, sse=5846223.5, rms=3.22 007: dt: 0.5000, sse=5953561.0, rms=3.09 008: dt: 0.5000, sse=5916808.5, rms=2.98 009: dt: 0.5000, sse=5984281.0, rms=2.89 010: dt: 0.5000, sse=5930242.0, rms=2.83 rms = 2.80, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=6000951.0, rms=2.80 012: dt: 0.2500, sse=4047062.0, rms=2.27 013: dt: 0.2500, sse=3841012.0, rms=2.19 rms = 2.18, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3761698.8, rms=2.18 rms = 2.13, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3706842.2, rms=2.13 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 4.35% unknown deleting segment 4 with 316 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 86 points - only 53.49% unknown deleting segment 9 with 53 points - only 49.06% unknown removing 3 vertex label from ripped group deleting segment 11 with 27 points - only 0.00% unknown mean border=88.6, 308 (165) missing vertices, mean dist -0.4 [0.8 (%61.2)->0.3 (%38.8))] %47 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 0.87 +- 0.27 (0.05-->5.10) (max @ vno 103994 --> 118918) face area 0.33 +- 0.17 (0.00-->5.97) mean absolute distance = 0.49 +- 0.61 4560 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4034540.5, rms=3.88 016: dt: 0.5000, sse=4333050.0, rms=2.90 017: dt: 0.5000, sse=5026546.5, rms=2.58 rms = 2.57, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=5128315.5, rms=2.57 019: dt: 0.2500, sse=4332240.5, rms=2.19 020: dt: 0.2500, sse=4188347.0, rms=2.11 rms = 2.06, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4146061.5, rms=2.06 022: dt: 0.1250, sse=4091290.2, rms=2.01 rms = 1.96, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4071290.8, rms=1.96 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 4.35% unknown deleting segment 1 with 324 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 13 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 111 points - only 41.44% unknown deleting segment 8 with 75 points - only 34.67% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 25 points - only 0.00% unknown mean border=90.4, 320 (112) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %62 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 0.86 +- 0.27 (0.07-->4.96) (max @ vno 103994 --> 118918) face area 0.32 +- 0.17 (0.00-->5.54) mean absolute distance = 0.39 +- 0.47 3882 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4218662.5, rms=3.34 024: dt: 0.5000, sse=4533102.0, rms=2.35 025: dt: 0.5000, sse=5195987.5, rms=2.17 rms = 2.23, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4657222.0, rms=1.92 027: dt: 0.2500, sse=4402116.0, rms=1.82 rms = 1.81, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4341471.0, rms=1.81 029: dt: 0.1250, sse=4296945.0, rms=1.75 rms = 1.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4266340.5, rms=1.73 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 2 with 486 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 105 points - only 43.81% unknown deleting segment 6 with 21 points - only 4.76% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=91.3, 329 (88) missing vertices, mean dist -0.1 [0.5 (%57.3)->0.3 (%42.7))] %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4300530.5, rms=2.21 031: dt: 0.5000, sse=5462467.0, rms=1.74 rms = 1.94, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5000690.0, rms=1.54 rms = 1.56, time step reduction 2 of 3 to 0.125... rms = 1.50, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4949529.0, rms=1.50 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 3 with 6 points - only 16.67% unknown smoothing surface for 5 iterations... mean border=66.2, 404 (404) missing vertices, mean dist 2.0 [0.1 (%0.0)->2.4 (%100.0))] %38 local maxima, %41 large gradients and %16 min vals, 684 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=17153128.0, rms=25.66 001: dt: 0.5000, sse=14299946.0, rms=23.05 002: dt: 0.5000, sse=11890635.0, rms=20.62 003: dt: 0.5000, sse=10105376.0, rms=18.42 004: dt: 0.5000, sse=8883289.0, rms=16.40 005: dt: 0.5000, sse=7961107.0, rms=14.51 006: dt: 0.5000, sse=7312941.0, rms=12.78 007: dt: 0.5000, sse=6809855.5, rms=11.17 008: dt: 0.5000, sse=6538200.5, rms=9.71 009: dt: 0.5000, sse=6294898.0, rms=8.39 010: dt: 0.5000, sse=6165020.5, rms=7.26 011: dt: 0.5000, sse=6091233.0, rms=6.43 012: dt: 0.5000, sse=6148091.5, rms=5.85 013: dt: 0.5000, sse=6168502.0, rms=5.48 014: dt: 0.5000, sse=6224654.5, rms=5.21 015: dt: 0.5000, sse=6226509.5, rms=5.01 016: dt: 0.5000, sse=6244095.5, rms=4.86 017: dt: 0.5000, sse=6235825.5, rms=4.76 018: dt: 0.5000, sse=6259684.5, rms=4.66 019: dt: 0.5000, sse=6259045.5, rms=4.60 020: dt: 0.5000, sse=6240822.5, rms=4.53 rms = 4.50, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6256413.5, rms=4.50 022: dt: 0.2500, sse=3984543.2, rms=3.49 023: dt: 0.2500, sse=3717991.0, rms=3.20 024: dt: 0.2500, sse=3544957.8, rms=3.12 rms = 3.09, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3487125.2, rms=3.09 026: dt: 0.1250, sse=3315250.5, rms=2.96 rms = 2.94, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3281904.2, rms=2.94 positioning took 2.6 minutes mean border=63.9, 647 (62) missing vertices, mean dist 0.2 [0.2 (%41.5)->0.5 (%58.5))] %61 local maxima, %25 large gradients and % 9 min vals, 246 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=3818396.2, rms=5.04 028: dt: 0.5000, sse=4305168.5, rms=4.47 rms = 4.47, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=5356072.0, rms=4.47 030: dt: 0.2500, sse=3951207.2, rms=3.42 031: dt: 0.2500, sse=3961248.5, rms=3.15 032: dt: 0.2500, sse=3844638.0, rms=3.10 033: dt: 0.2500, sse=3851122.2, rms=3.04 rms = 3.02, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=3803146.2, rms=3.02 035: dt: 0.1250, sse=3665328.0, rms=2.88 rms = 2.86, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=3646802.5, rms=2.86 positioning took 0.8 minutes mean border=62.6, 884 (44) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.4 (%56.1))] %70 local maxima, %16 large gradients and % 9 min vals, 243 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=3774872.2, rms=3.66 rms = 4.10, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=3660802.2, rms=3.14 038: dt: 0.2500, sse=3710392.2, rms=2.93 rms = 2.89, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3805691.8, rms=2.89 040: dt: 0.1250, sse=3687806.5, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3694458.5, rms=2.74 positioning took 0.5 minutes mean border=61.8, 1576 (42) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.3 (%51.7))] %72 local maxima, %13 large gradients and % 9 min vals, 246 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/AD01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3731838.5, rms=3.05 rms = 3.65, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=3673808.8, rms=2.79 043: dt: 0.2500, sse=3807186.2, rms=2.72 rms = 2.71, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=3856092.8, rms=2.71 045: dt: 0.1250, sse=3785131.8, rms=2.60 rms = 2.57, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=3786205.2, rms=2.57 positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.area.pial vertex spacing 0.93 +- 0.40 (0.03-->6.26) (max @ vno 103607 --> 102862) face area 0.36 +- 0.28 (0.00-->6.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119299 vertices processed 25000 of 119299 vertices processed 50000 of 119299 vertices processed 75000 of 119299 vertices processed 100000 of 119299 vertices processed 0 of 119299 vertices processed 25000 of 119299 vertices processed 50000 of 119299 vertices processed 75000 of 119299 vertices processed 100000 of 119299 vertices processed thickness calculation complete, 1085:1127 truncations. 54979 vertices at 0 distance 73194 vertices at 1 distance 55217 vertices at 2 distance 26143 vertices at 3 distance 10850 vertices at 4 distance 4107 vertices at 5 distance 1564 vertices at 6 distance 679 vertices at 7 distance 326 vertices at 8 distance 207 vertices at 9 distance 132 vertices at 10 distance 70 vertices at 11 distance 54 vertices at 12 distance 42 vertices at 13 distance 35 vertices at 14 distance 23 vertices at 15 distance 23 vertices at 16 distance 14 vertices at 17 distance 10 vertices at 18 distance 9 vertices at 19 distance 16 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.thickness positioning took 10.4 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jul 12 02:39:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Jul 12 02:39:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab AD01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 974 681 1262 1.950 0.497 0.113 0.031 6 1.4 bankssts 902 599 1920 3.653 0.698 0.164 0.060 21 2.2 caudalanteriorcingulate 3428 2062 3993 1.973 0.557 0.170 0.167 311 24.5 caudalmiddlefrontal 1982 1226 2554 1.940 0.531 0.181 0.108 66 9.4 cuneus 552 360 1977 3.825 0.586 0.158 0.077 10 1.6 entorhinal 3319 2260 6955 2.652 0.742 0.190 0.105 103 14.5 fusiform 4827 2915 5634 1.780 0.536 0.172 0.109 141 23.5 inferiorparietal 3560 2342 7398 2.460 0.946 0.214 0.163 204 21.4 inferiortemporal 1585 932 1714 1.839 0.604 0.156 0.131 109 9.4 isthmuscingulate 7424 4564 10778 2.212 0.656 0.180 0.149 293 38.4 lateraloccipital 3465 2284 6497 2.601 0.855 0.173 0.139 91 14.4 lateralorbitofrontal 4950 3194 6087 1.841 0.613 0.174 0.106 129 24.3 lingual 2550 1658 4578 2.590 1.061 0.187 0.167 211 20.1 medialorbitofrontal 3067 1884 5887 2.394 0.913 0.193 0.367 802 27.6 middletemporal 696 473 1552 2.666 0.901 0.150 0.058 15 1.5 parahippocampal 2041 1182 3395 2.754 0.686 0.166 0.172 135 19.3 paracentral 2701 1646 3972 2.235 0.688 0.162 0.112 69 13.2 parsopercularis 790 479 1583 2.469 0.745 0.169 0.123 21 4.5 parsorbitalis 1883 1231 3217 2.367 0.556 0.165 0.098 41 8.1 parstriangularis 1846 1212 1738 1.539 0.439 0.180 0.092 41 6.9 pericalcarine 4962 3006 6497 1.978 0.656 0.158 0.096 122 21.2 postcentral 1397 869 2333 2.674 0.788 0.157 0.087 29 4.9 posteriorcingulate 7874 4834 10754 2.242 0.673 0.180 0.164 513 58.4 precentral 4361 2633 4958 1.780 0.582 0.156 0.165 118 20.3 precuneus 1114 719 2636 3.439 0.956 0.173 0.106 25 5.0 rostralanteriorcingulate 7869 4847 10670 2.031 0.591 0.179 0.989 1793 43.8 rostralmiddlefrontal 10399 6378 15088 2.264 0.670 0.175 0.145 596 62.1 superiorfrontal 7465 4562 8756 1.803 0.546 0.163 0.092 164 29.7 superiorparietal 4697 3069 8125 2.353 0.714 0.162 0.108 192 22.8 superiortemporal 4015 2437 5459 2.093 0.644 0.174 0.195 248 31.5 supramarginal 428 243 702 2.235 0.634 0.218 0.178 15 2.9 frontalpole 538 414 1963 3.225 0.841 0.212 0.100 15 2.6 temporalpole 648 347 1006 2.488 0.441 0.153 0.090 14 2.3 transversetemporal 3139 1981 6102 3.067 0.942 0.161 0.161 153 21.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jul 12 02:39:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 21 labels changed using aseg relabeling using gibbs priors... 000: 8405 changed, 119299 examined... 001: 2019 changed, 32375 examined... 002: 616 changed, 10440 examined... 003: 272 changed, 3400 examined... 004: 131 changed, 1481 examined... 005: 76 changed, 710 examined... 006: 44 changed, 431 examined... 007: 30 changed, 248 examined... 008: 17 changed, 167 examined... 009: 8 changed, 92 examined... 010: 5 changed, 57 examined... 011: 3 changed, 32 examined... 012: 0 changed, 10 examined... 6 labels changed using aseg 000: 245 total segments, 160 labels (1444 vertices) changed 001: 90 total segments, 5 labels (14 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 96 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 980 vertices marked for relabeling... 980 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 52 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jul 12 02:40:20 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab AD01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1092 705 1572 2.087 0.626 0.191 0.134 35 7.0 G_and_S_frontomargin 2068 1259 2995 2.116 0.670 0.182 0.122 64 10.9 G_and_S_occipital_inf 1448 798 2176 2.386 0.778 0.172 0.162 78 11.6 G_and_S_paracentral 1297 799 2248 2.398 0.677 0.186 0.162 144 9.8 G_and_S_subcentral 818 467 1341 2.268 0.552 0.189 0.127 29 4.2 G_and_S_transv_frontopol 1687 1153 3452 2.907 0.924 0.167 0.090 30 6.5 G_and_S_cingul-Ant 1414 946 2666 2.967 0.633 0.162 0.116 49 3.7 G_and_S_cingul-Mid-Ant 1044 701 1925 2.804 0.597 0.161 0.072 19 3.3 G_and_S_cingul-Mid-Post 433 215 573 2.147 0.576 0.160 0.204 15 4.7 G_cingul-Post-dorsal 386 232 415 1.647 0.554 0.161 0.096 13 1.7 G_cingul-Post-ventral 1912 1147 2650 2.035 0.520 0.178 0.106 47 8.4 G_cuneus 1468 818 2424 2.331 0.677 0.166 0.147 49 9.1 G_front_inf-Opercular 292 160 724 2.909 0.586 0.189 0.178 11 2.7 G_front_inf-Orbital 1448 912 2708 2.368 0.612 0.186 0.130 45 8.5 G_front_inf-Triangul 4194 2401 5682 1.975 0.553 0.198 1.667 1888 35.9 G_front_middle 7274 4226 11331 2.378 0.721 0.187 0.175 561 58.4 G_front_sup 411 253 990 3.617 0.568 0.197 0.185 27 2.4 G_Ins_lg_and_S_cent_ins 716 393 1960 3.771 1.028 0.201 0.292 59 9.9 G_insular_short 1547 878 2620 2.326 0.643 0.195 0.248 127 12.0 G_occipital_middle 1879 1158 2832 2.157 0.652 0.168 0.103 41 7.8 G_occipital_sup 1323 868 2832 2.678 0.660 0.199 0.124 50 6.9 G_oc-temp_lat-fusifor 3639 2289 4628 1.822 0.605 0.187 0.122 113 20.9 G_oc-temp_med-Lingual 943 614 2995 3.444 0.882 0.159 0.070 22 2.7 G_oc-temp_med-Parahip 2339 1426 4780 2.561 0.931 0.181 0.199 93 13.6 G_orbital 2127 1165 2402 1.801 0.565 0.188 0.146 95 13.3 G_pariet_inf-Angular 2135 1234 2988 2.142 0.660 0.186 0.269 201 23.7 G_pariet_inf-Supramar 2912 1696 3364 1.782 0.494 0.162 0.102 75 12.8 G_parietal_sup 1949 1043 2675 2.110 0.589 0.172 0.142 71 12.3 G_postcentral 2896 1623 4206 2.231 0.766 0.196 0.242 227 31.3 G_precentral 2050 1142 2550 1.860 0.581 0.172 0.120 66 10.9 G_precuneus 817 542 1383 2.061 0.896 0.189 0.122 29 3.8 G_rectus 434 278 886 2.864 1.087 0.269 0.391 106 8.3 G_subcallosal 457 223 751 2.551 0.423 0.145 0.078 10 1.4 G_temp_sup-G_T_transv 1928 1210 3985 2.521 0.717 0.191 0.140 76 11.2 G_temp_sup-Lateral 663 444 1388 2.633 0.796 0.194 0.209 96 7.4 G_temp_sup-Plan_polar 776 511 1269 2.126 0.483 0.142 0.065 12 1.9 G_temp_sup-Plan_tempo 2050 1344 4726 2.599 1.001 0.236 0.203 155 14.3 G_temporal_inf 2117 1235 3937 2.350 0.871 0.194 0.214 148 22.5 G_temporal_middle 266 173 335 2.283 0.381 0.118 0.040 2 0.4 Lat_Fis-ant-Horizont 247 174 359 2.373 0.539 0.166 0.079 3 0.9 Lat_Fis-ant-Vertical 1102 746 1378 2.169 0.556 0.136 0.059 13 2.7 Lat_Fis-post 2159 1345 3197 2.216 0.657 0.195 0.118 63 11.3 Pole_occipital 1458 1069 5253 3.212 0.856 0.221 0.526 676 9.5 Pole_temporal 2752 1816 2791 1.692 0.590 0.159 0.179 53 9.2 S_calcarine 3243 2198 3593 1.877 0.667 0.166 0.094 131 13.6 S_central 974 668 1270 1.995 0.632 0.111 0.032 7 1.5 S_cingul-Marginalis 405 292 776 3.084 0.613 0.151 0.090 5 1.1 S_circular_insula_ant 1366 932 2053 2.522 0.845 0.121 0.080 35 4.6 S_circular_insula_inf 1512 1056 2290 2.628 0.612 0.126 0.051 17 3.5 S_circular_insula_sup 672 453 1176 2.517 0.819 0.163 0.065 18 2.0 S_collat_transv_ant 527 363 590 2.095 0.532 0.155 0.070 6 1.4 S_collat_transv_post 2785 1795 3316 1.959 0.561 0.155 0.072 46 9.1 S_front_inf 1255 801 1491 1.948 0.475 0.157 0.561 50 4.1 S_front_middle 2826 1823 3077 1.810 0.542 0.160 0.133 87 15.6 S_front_sup 39 25 31 1.385 0.228 0.149 0.048 0 0.1 S_interm_prim-Jensen 2470 1566 2532 1.653 0.467 0.160 0.081 45 8.6 S_intrapariet_and_P_trans 897 590 1084 1.922 0.485 0.147 0.061 11 2.3 S_oc_middle_and_Lunatus 1076 657 1260 1.924 0.594 0.162 0.094 24 4.5 S_oc_sup_and_transversal 719 449 888 2.373 0.580 0.167 0.254 41 3.5 S_occipital_ant 450 316 558 1.927 0.498 0.165 0.101 7 1.6 S_oc-temp_lat 1361 989 2041 2.313 0.623 0.169 0.072 25 4.1 S_oc-temp_med_and_Lingual 278 188 387 2.474 0.620 0.155 0.084 4 0.7 S_orbital_lateral 905 580 1416 2.574 1.155 0.154 0.091 22 3.0 S_orbital_med-olfact 1275 876 2199 2.577 0.690 0.169 0.078 21 4.1 S_orbital-H_Shaped 1842 1225 1922 1.657 0.517 0.155 0.098 61 8.8 S_parieto_occipital 1277 754 1626 2.892 1.302 0.152 0.104 89 4.9 S_pericallosal 1516 988 1770 1.901 0.566 0.143 0.060 19 3.7 S_postcentral 1722 1106 1986 1.965 0.439 0.149 0.102 52 6.9 S_precentral-inf-part 1654 1070 1996 2.411 0.461 0.161 0.089 33 6.6 S_precentral-sup-part 552 355 996 2.917 0.981 0.164 0.146 53 4.8 S_suborbital 561 334 576 1.643 0.530 0.165 0.078 20 2.0 S_subparietal 1015 669 1554 2.105 0.887 0.190 0.110 34 4.5 S_temporal_inf 3510 2317 4480 1.992 0.649 0.144 0.069 57 10.6 S_temporal_sup 397 257 465 2.149 0.528 0.146 0.063 5 1.2 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Tue Jul 12 02:40:35 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 221227: 0.002712) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 1525 vertices, 1733 faces slice 70: 9223 vertices, 9562 faces slice 80: 20109 vertices, 20550 faces slice 90: 31202 vertices, 31579 faces slice 100: 41548 vertices, 41985 faces slice 110: 51537 vertices, 51987 faces slice 120: 61966 vertices, 62459 faces slice 130: 72826 vertices, 73296 faces slice 140: 82755 vertices, 83236 faces slice 150: 92655 vertices, 93133 faces slice 160: 101586 vertices, 102044 faces slice 170: 109425 vertices, 109852 faces slice 180: 115423 vertices, 115780 faces slice 190: 119598 vertices, 119889 faces slice 200: 120308 vertices, 120494 faces slice 210: 120308 vertices, 120494 faces slice 220: 120308 vertices, 120494 faces slice 230: 120308 vertices, 120494 faces slice 240: 120308 vertices, 120494 faces slice 250: 120308 vertices, 120494 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 120308 voxel in cpt #1: X=-186 [v=120308,e=361482,f=240988] located at (24.651112, -9.768079, 18.202705) For the whole surface: X=-186 [v=120308,e=361482,f=240988] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Jul 12 02:40:43 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue Jul 12 02:40:47 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts avg radius = 44.0 mm, total surface area = 60945 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.092 (target=0.015) step 010: RMS=0.074 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.046 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Jul 12 02:41:29 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.04 +- 0.63 (0.00-->7.86) (max @ vno 88554 --> 88555) face area 0.04 +- 0.04 (-0.29-->0.88) scaling brain by 0.373... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.228, avgs=0 005/300: dt: 0.9000, rms radial error=173.974, avgs=0 010/300: dt: 0.9000, rms radial error=173.430, avgs=0 015/300: dt: 0.9000, rms radial error=172.713, avgs=0 020/300: dt: 0.9000, rms radial error=171.897, avgs=0 025/300: dt: 0.9000, rms radial error=171.023, avgs=0 030/300: dt: 0.9000, rms radial error=170.118, avgs=0 035/300: dt: 0.9000, rms radial error=169.195, avgs=0 040/300: dt: 0.9000, rms radial error=168.264, avgs=0 045/300: dt: 0.9000, rms radial error=167.330, avgs=0 050/300: dt: 0.9000, rms radial error=166.397, avgs=0 055/300: dt: 0.9000, rms radial error=165.465, avgs=0 060/300: dt: 0.9000, rms radial error=164.536, avgs=0 065/300: dt: 0.9000, rms radial error=163.610, avgs=0 070/300: dt: 0.9000, rms radial error=162.689, avgs=0 075/300: dt: 0.9000, rms radial error=161.772, avgs=0 080/300: dt: 0.9000, rms radial error=160.859, avgs=0 085/300: dt: 0.9000, rms radial error=159.951, avgs=0 090/300: dt: 0.9000, rms radial error=159.051, avgs=0 095/300: dt: 0.9000, rms radial error=158.156, avgs=0 100/300: dt: 0.9000, rms radial error=157.266, avgs=0 105/300: dt: 0.9000, rms radial error=156.381, avgs=0 110/300: dt: 0.9000, rms radial error=155.502, avgs=0 115/300: dt: 0.9000, rms radial error=154.627, avgs=0 120/300: dt: 0.9000, rms radial error=153.757, avgs=0 125/300: dt: 0.9000, rms radial error=152.892, avgs=0 130/300: dt: 0.9000, rms radial error=152.031, avgs=0 135/300: dt: 0.9000, rms radial error=151.175, avgs=0 140/300: dt: 0.9000, rms radial error=150.323, avgs=0 145/300: dt: 0.9000, rms radial error=149.476, avgs=0 150/300: dt: 0.9000, rms radial error=148.633, avgs=0 155/300: dt: 0.9000, rms radial error=147.796, avgs=0 160/300: dt: 0.9000, rms radial error=146.963, avgs=0 165/300: dt: 0.9000, rms radial error=146.135, avgs=0 170/300: dt: 0.9000, rms radial error=145.311, avgs=0 175/300: dt: 0.9000, rms radial error=144.492, avgs=0 180/300: dt: 0.9000, rms radial error=143.677, avgs=0 185/300: dt: 0.9000, rms radial error=142.867, avgs=0 190/300: dt: 0.9000, rms radial error=142.061, avgs=0 195/300: dt: 0.9000, rms radial error=141.259, avgs=0 200/300: dt: 0.9000, rms radial error=140.462, avgs=0 205/300: dt: 0.9000, rms radial error=139.670, avgs=0 210/300: dt: 0.9000, rms radial error=138.881, avgs=0 215/300: dt: 0.9000, rms radial error=138.097, avgs=0 220/300: dt: 0.9000, rms radial error=137.318, avgs=0 225/300: dt: 0.9000, rms radial error=136.543, avgs=0 230/300: dt: 0.9000, rms radial error=135.772, avgs=0 235/300: dt: 0.9000, rms radial error=135.005, avgs=0 240/300: dt: 0.9000, rms radial error=134.243, avgs=0 245/300: dt: 0.9000, rms radial error=133.485, avgs=0 250/300: dt: 0.9000, rms radial error=132.731, avgs=0 255/300: dt: 0.9000, rms radial error=131.982, avgs=0 260/300: dt: 0.9000, rms radial error=131.236, avgs=0 265/300: dt: 0.9000, rms radial error=130.495, avgs=0 270/300: dt: 0.9000, rms radial error=129.758, avgs=0 275/300: dt: 0.9000, rms radial error=129.025, avgs=0 280/300: dt: 0.9000, rms radial error=128.296, avgs=0 285/300: dt: 0.9000, rms radial error=127.570, avgs=0 290/300: dt: 0.9000, rms radial error=126.849, avgs=0 295/300: dt: 0.9000, rms radial error=126.132, avgs=0 300/300: dt: 0.9000, rms radial error=125.419, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13303.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 2073.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 219.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00300 epoch 4 (K=640.0), pass 1, starting sse = 23.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00571 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.08 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Jul 12 02:46:20 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 AD01 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-186 (nv=120308, nf=240988, ne=361482, g=94) 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... 8709 ambiguous faces found in tessellation segmenting defects... 98 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 33 into 26 -merging segment 35 into 26 -merging segment 57 into 55 -merging segment 67 into 65 -merging segment 76 into 70 93 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7780 (-4.3890) -vertex loglikelihood: -6.1508 (-3.0754) -normal dot loglikelihood: -3.5704 (-3.5704) -quad curv loglikelihood: -6.5883 (-3.2942) Total Loglikelihood : -25.0876 CORRECTING DEFECT 0 (vertices=429, convex hull=226) After retessellation of defect 0, euler #=-94 (114765,341431,226572) : difference with theory (-90) = 4 CORRECTING DEFECT 1 (vertices=20, convex hull=46) After retessellation of defect 1, euler #=-93 (114772,341465,226600) : difference with theory (-89) = 4 CORRECTING DEFECT 2 (vertices=313, convex hull=240) After retessellation of defect 2, euler #=-92 (114838,341785,226855) : difference with theory (-88) = 4 CORRECTING DEFECT 3 (vertices=104, convex hull=50) After retessellation of defect 3, euler #=-91 (114847,341830,226892) : difference with theory (-87) = 4 CORRECTING DEFECT 4 (vertices=15, convex hull=22) After retessellation of defect 4, euler #=-90 (114847,341837,226900) : difference with theory (-86) = 4 CORRECTING DEFECT 5 (vertices=53, convex hull=81) After retessellation of defect 5, euler #=-89 (114867,341932,226976) : difference with theory (-85) = 4 CORRECTING DEFECT 6 (vertices=24, convex hull=58) After retessellation of defect 6, euler #=-88 (114876,341983,227019) : difference with theory (-84) = 4 CORRECTING DEFECT 7 (vertices=34, convex hull=85) After retessellation of defect 7, euler #=-87 (114896,342080,227097) : difference with theory (-83) = 4 CORRECTING DEFECT 8 (vertices=32, convex hull=75) After retessellation of defect 8, euler #=-86 (114914,342161,227161) : difference with theory (-82) = 4 CORRECTING DEFECT 9 (vertices=23, convex hull=57) After retessellation of defect 9, euler #=-85 (114929,342232,227218) : difference with theory (-81) = 4 CORRECTING DEFECT 10 (vertices=6, convex hull=14) After retessellation of defect 10, euler #=-84 (114929,342234,227221) : difference with theory (-80) = 4 CORRECTING DEFECT 11 (vertices=40, convex hull=84) After retessellation of defect 11, euler #=-83 (114952,342340,227305) : difference with theory (-79) = 4 CORRECTING DEFECT 12 (vertices=21, convex hull=62) After retessellation of defect 12, euler #=-82 (114961,342389,227346) : difference with theory (-78) = 4 CORRECTING DEFECT 13 (vertices=34, convex hull=71) After retessellation of defect 13, euler #=-81 (114972,342448,227395) : difference with theory (-77) = 4 CORRECTING DEFECT 14 (vertices=17, convex hull=58) After retessellation of defect 14, euler #=-80 (114979,342491,227432) : difference with theory (-76) = 4 CORRECTING DEFECT 15 (vertices=49, convex hull=89) After retessellation of defect 15, euler #=-79 (115010,342616,227527) : difference with theory (-75) = 4 CORRECTING DEFECT 16 (vertices=37, convex hull=67) After retessellation of defect 16, euler #=-78 (115020,342670,227572) : difference with theory (-74) = 4 CORRECTING DEFECT 17 (vertices=47, convex hull=90) After retessellation of defect 17, euler #=-77 (115037,342751,227637) : difference with theory (-73) = 4 CORRECTING DEFECT 18 (vertices=6, convex hull=27) After retessellation of defect 18, euler #=-76 (115038,342760,227646) : difference with theory (-72) = 4 CORRECTING DEFECT 19 (vertices=18, convex hull=31) After retessellation of defect 19, euler #=-75 (115047,342801,227679) : difference with theory (-71) = 4 CORRECTING DEFECT 20 (vertices=25, convex hull=76) After retessellation of defect 20, euler #=-74 (115060,342870,227736) : difference with theory (-70) = 4 CORRECTING DEFECT 21 (vertices=114, convex hull=112) After retessellation of defect 21, euler #=-73 (115104,343058,227881) : difference with theory (-69) = 4 CORRECTING DEFECT 22 (vertices=29, convex hull=70) After retessellation of defect 22, euler #=-72 (115119,343132,227941) : difference with theory (-68) = 4 CORRECTING DEFECT 23 (vertices=7, convex hull=17) After retessellation of defect 23, euler #=-71 (115121,343142,227950) : difference with theory (-67) = 4 CORRECTING DEFECT 24 (vertices=35, convex hull=53) After retessellation of defect 24, euler #=-70 (115140,343216,228006) : difference with theory (-66) = 4 CORRECTING DEFECT 25 (vertices=106, convex hull=104) After retessellation of defect 25, euler #=-69 (115164,343335,228102) : difference with theory (-65) = 4 CORRECTING DEFECT 26 (vertices=98, convex hull=128) After retessellation of defect 26, euler #=-66 (115200,343501,228235) : difference with theory (-64) = 2 CORRECTING DEFECT 27 (vertices=60, convex hull=87) After retessellation of defect 27, euler #=-65 (115237,343650,228348) : difference with theory (-63) = 2 CORRECTING DEFECT 28 (vertices=32, convex hull=62) After retessellation of defect 28, euler #=-64 (115259,343745,228422) : difference with theory (-62) = 2 CORRECTING DEFECT 29 (vertices=74, convex hull=91) After retessellation of defect 29, euler #=-63 (115296,343901,228542) : difference with theory (-61) = 2 CORRECTING DEFECT 30 (vertices=34, convex hull=61) After retessellation of defect 30, euler #=-62 (115310,343971,228599) : difference with theory (-60) = 2 CORRECTING DEFECT 31 (vertices=32, convex hull=21) After retessellation of defect 31, euler #=-61 (115312,343982,228609) : difference with theory (-59) = 2 CORRECTING DEFECT 32 (vertices=34, convex hull=81) After retessellation of defect 32, euler #=-60 (115333,344074,228681) : difference with theory (-58) = 2 CORRECTING DEFECT 33 (vertices=68, convex hull=91) After retessellation of defect 33, euler #=-59 (115369,344225,228797) : difference with theory (-57) = 2 CORRECTING DEFECT 34 (vertices=59, convex hull=87) After retessellation of defect 34, euler #=-58 (115387,344316,228871) : difference with theory (-56) = 2 CORRECTING DEFECT 35 (vertices=34, convex hull=67) After retessellation of defect 35, euler #=-57 (115399,344382,228926) : difference with theory (-55) = 2 CORRECTING DEFECT 36 (vertices=40, convex hull=57) After retessellation of defect 36, euler #=-56 (115408,344436,228972) : difference with theory (-54) = 2 CORRECTING DEFECT 37 (vertices=58, convex hull=70) After retessellation of defect 37, euler #=-55 (115443,344569,229071) : difference with theory (-53) = 2 CORRECTING DEFECT 38 (vertices=31, convex hull=49) After retessellation of defect 38, euler #=-54 (115457,344630,229119) : difference with theory (-52) = 2 CORRECTING DEFECT 39 (vertices=32, convex hull=72) After retessellation of defect 39, euler #=-53 (115479,344728,229196) : difference with theory (-51) = 2 CORRECTING DEFECT 40 (vertices=7, convex hull=31) After retessellation of defect 40, euler #=-52 (115482,344745,229211) : difference with theory (-50) = 2 CORRECTING DEFECT 41 (vertices=34, convex hull=68) After retessellation of defect 41, euler #=-51 (115494,344808,229263) : difference with theory (-49) = 2 CORRECTING DEFECT 42 (vertices=23, convex hull=47) After retessellation of defect 42, euler #=-50 (115503,344852,229299) : difference with theory (-48) = 2 CORRECTING DEFECT 43 (vertices=72, convex hull=117) After retessellation of defect 43, euler #=-49 (115541,345015,229425) : difference with theory (-47) = 2 CORRECTING DEFECT 44 (vertices=62, convex hull=92) After retessellation of defect 44, euler #=-48 (115564,345127,229515) : difference with theory (-46) = 2 CORRECTING DEFECT 45 (vertices=30, convex hull=54) After retessellation of defect 45, euler #=-47 (115577,345186,229562) : difference with theory (-45) = 2 CORRECTING DEFECT 46 (vertices=12, convex hull=18) After retessellation of defect 46, euler #=-46 (115578,345193,229569) : difference with theory (-44) = 2 CORRECTING DEFECT 47 (vertices=213, convex hull=245) After retessellation of defect 47, euler #=-46 (115676,345615,229893) : difference with theory (-43) = 3 CORRECTING DEFECT 48 (vertices=102, convex hull=47) After retessellation of defect 48, euler #=-45 (115691,345681,229945) : difference with theory (-42) = 3 CORRECTING DEFECT 49 (vertices=44, convex hull=83) After retessellation of defect 49, euler #=-44 (115717,345794,230033) : difference with theory (-41) = 3 CORRECTING DEFECT 50 (vertices=24, convex hull=30) After retessellation of defect 50, euler #=-43 (115719,345808,230046) : difference with theory (-40) = 3 CORRECTING DEFECT 51 (vertices=53, convex hull=52) After retessellation of defect 51, euler #=-42 (115729,345855,230084) : difference with theory (-39) = 3 CORRECTING DEFECT 52 (vertices=92, convex hull=110) After retessellation of defect 52, euler #=-41 (115771,346026,230214) : difference with theory (-38) = 3 CORRECTING DEFECT 53 (vertices=131, convex hull=92) After retessellation of defect 53, euler #=-39 (115783,346105,230283) : difference with theory (-37) = 2 CORRECTING DEFECT 54 (vertices=13, convex hull=21) After retessellation of defect 54, euler #=-38 (115786,346122,230298) : difference with theory (-36) = 2 CORRECTING DEFECT 55 (vertices=22, convex hull=54) After retessellation of defect 55, euler #=-37 (115796,346168,230335) : difference with theory (-35) = 2 CORRECTING DEFECT 56 (vertices=33, convex hull=54) After retessellation of defect 56, euler #=-36 (115811,346237,230390) : difference with theory (-34) = 2 CORRECTING DEFECT 57 (vertices=87, convex hull=110) After retessellation of defect 57, euler #=-35 (115868,346461,230558) : difference with theory (-33) = 2 CORRECTING DEFECT 58 (vertices=52, convex hull=61) After retessellation of defect 58, euler #=-34 (115877,346511,230600) : difference with theory (-32) = 2 CORRECTING DEFECT 59 (vertices=45, convex hull=74) After retessellation of defect 59, euler #=-33 (115907,346635,230695) : difference with theory (-31) = 2 CORRECTING DEFECT 60 (vertices=9, convex hull=19) After retessellation of defect 60, euler #=-32 (115910,346650,230708) : difference with theory (-30) = 2 CORRECTING DEFECT 61 (vertices=22, convex hull=29) After retessellation of defect 61, euler #=-31 (115911,346663,230721) : difference with theory (-29) = 2 CORRECTING DEFECT 62 (vertices=281, convex hull=258) After retessellation of defect 62, euler #=-29 (116053,347232,231150) : difference with theory (-28) = 1 CORRECTING DEFECT 63 (vertices=8, convex hull=19) After retessellation of defect 63, euler #=-28 (116053,347236,231155) : difference with theory (-27) = 1 CORRECTING DEFECT 64 (vertices=84, convex hull=78) After retessellation of defect 64, euler #=-27 (116076,347339,231236) : difference with theory (-26) = 1 CORRECTING DEFECT 65 (vertices=84, convex hull=41) After retessellation of defect 65, euler #=-26 (116080,347373,231267) : difference with theory (-25) = 1 CORRECTING DEFECT 66 (vertices=144, convex hull=126) After retessellation of defect 66, euler #=-24 (116132,347587,231431) : difference with theory (-24) = 0 CORRECTING DEFECT 67 (vertices=71, convex hull=87) After retessellation of defect 67, euler #=-23 (116175,347756,231558) : difference with theory (-23) = 0 CORRECTING DEFECT 68 (vertices=102, convex hull=73) After retessellation of defect 68, euler #=-22 (116242,347996,231732) : difference with theory (-22) = 0 CORRECTING DEFECT 69 (vertices=89, convex hull=104) After retessellation of defect 69, euler #=-21 (116287,348179,231871) : difference with theory (-21) = 0 CORRECTING DEFECT 70 (vertices=19, convex hull=48) After retessellation of defect 70, euler #=-20 (116299,348233,231914) : difference with theory (-20) = 0 CORRECTING DEFECT 71 (vertices=20, convex hull=40) After retessellation of defect 71, euler #=-19 (116309,348278,231950) : difference with theory (-19) = 0 CORRECTING DEFECT 72 (vertices=31, convex hull=68) After retessellation of defect 72, euler #=-18 (116326,348355,232011) : difference with theory (-18) = 0 CORRECTING DEFECT 73 (vertices=38, convex hull=60) After retessellation of defect 73, euler #=-17 (116339,348415,232059) : difference with theory (-17) = 0 CORRECTING DEFECT 74 (vertices=24, convex hull=49) After retessellation of defect 74, euler #=-16 (116353,348475,232106) : difference with theory (-16) = 0 CORRECTING DEFECT 75 (vertices=22, convex hull=51) After retessellation of defect 75, euler #=-15 (116365,348532,232152) : difference with theory (-15) = 0 CORRECTING DEFECT 76 (vertices=27, convex hull=28) After retessellation of defect 76, euler #=-14 (116369,348553,232170) : difference with theory (-14) = 0 CORRECTING DEFECT 77 (vertices=17, convex hull=28) After retessellation of defect 77, euler #=-13 (116371,348568,232184) : difference with theory (-13) = 0 CORRECTING DEFECT 78 (vertices=36, convex hull=65) After retessellation of defect 78, euler #=-12 (116390,348651,232249) : difference with theory (-12) = 0 CORRECTING DEFECT 79 (vertices=380, convex hull=202) After retessellation of defect 79, euler #=-11 (116504,349104,232589) : difference with theory (-11) = 0 CORRECTING DEFECT 80 (vertices=6, convex hull=20) After retessellation of defect 80, euler #=-10 (116505,349114,232599) : difference with theory (-10) = 0 CORRECTING DEFECT 81 (vertices=6, convex hull=27) After retessellation of defect 81, euler #=-9 (116506,349123,232608) : difference with theory (-9) = 0 CORRECTING DEFECT 82 (vertices=38, convex hull=75) After retessellation of defect 82, euler #=-8 (116518,349191,232665) : difference with theory (-8) = 0 CORRECTING DEFECT 83 (vertices=79, convex hull=66) After retessellation of defect 83, euler #=-7 (116528,349251,232716) : difference with theory (-7) = 0 CORRECTING DEFECT 84 (vertices=48, convex hull=85) After retessellation of defect 84, euler #=-6 (116551,349359,232802) : difference with theory (-6) = 0 CORRECTING DEFECT 85 (vertices=17, convex hull=23) After retessellation of defect 85, euler #=-5 (116554,349376,232817) : difference with theory (-5) = 0 CORRECTING DEFECT 86 (vertices=26, convex hull=67) After retessellation of defect 86, euler #=-4 (116565,349434,232865) : difference with theory (-4) = 0 CORRECTING DEFECT 87 (vertices=66, convex hull=117) After retessellation of defect 87, euler #=-3 (116605,349608,233000) : difference with theory (-3) = 0 CORRECTING DEFECT 88 (vertices=90, convex hull=136) After retessellation of defect 88, euler #=-2 (116642,349772,233128) : difference with theory (-2) = 0 CORRECTING DEFECT 89 (vertices=90, convex hull=143) After retessellation of defect 89, euler #=-1 (116694,349995,233300) : difference with theory (-1) = 0 CORRECTING DEFECT 90 (vertices=37, convex hull=76) After retessellation of defect 90, euler #=0 (116715,350086,233371) : difference with theory (0) = 0 CORRECTING DEFECT 91 (vertices=83, convex hull=89) After retessellation of defect 91, euler #=1 (116745,350210,233466) : difference with theory (1) = 0 CORRECTING DEFECT 92 (vertices=34, convex hull=52) After retessellation of defect 92, euler #=2 (116754,350256,233504) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.03-->16.45) (max @ vno 299 --> 2907) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.03-->16.45) (max @ vno 299 --> 2907) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 263 mutations (34.7%), 495 crossovers (65.3%), 269 vertices were eliminated building final representation... 3554 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=116754, nf=233504, ne=350256, g=0) writing corrected surface to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 58.9 minutes 0 defective edges removing intersecting faces 000: 557 intersecting 001: 20 intersecting 002: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 116754 - 350256 + 233504 = 2 --> 0 holes F =2V-4: 233504 = 233508-4 (0) 2E=3F: 700512 = 700512 (0) total defect index = 0 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 70 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Jul 12 03:45:22 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs AD01 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 10970 bright wm thresholded. 1109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.3 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 61.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 76.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->7.83) (max @ vno 299 --> 2907) face area 0.27 +- 0.13 (0.00-->3.60) mean absolute distance = 0.88 +- 1.15 4034 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=82 using class modes intead of means.... mean inside = 95.9, mean outside = 83.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=89.0, 507 (507) missing vertices, mean dist 0.1 [1.1 (%35.9)->0.8 (%64.1))] %30 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.28 (0.07-->7.70) (max @ vno 299 --> 2907) face area 0.27 +- 0.15 (0.00-->3.52) mean absolute distance = 0.54 +- 0.88 5177 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3423439.5, rms=7.02 001: dt: 0.5000, sse=4751760.5, rms=5.05 002: dt: 0.5000, sse=4903287.5, rms=3.92 003: dt: 0.5000, sse=5175665.0, rms=3.29 004: dt: 0.5000, sse=5239791.5, rms=2.87 005: dt: 0.5000, sse=5342597.5, rms=2.63 006: dt: 0.5000, sse=5381566.5, rms=2.53 007: dt: 0.5000, sse=5435265.0, rms=2.46 rms = 2.42, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5440306.5, rms=2.42 009: dt: 0.2500, sse=3885624.0, rms=1.94 010: dt: 0.2500, sse=3710905.8, rms=1.84 rms = 1.83, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3646126.5, rms=1.83 rms = 1.81, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3605280.2, rms=1.81 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.9, 462 (260) missing vertices, mean dist -0.3 [0.7 (%61.9)->0.3 (%38.1))] %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 0.86 +- 0.27 (0.05-->7.28) (max @ vno 299 --> 2907) face area 0.32 +- 0.17 (0.00-->4.01) mean absolute distance = 0.42 +- 0.58 3861 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3839129.2, rms=3.30 013: dt: 0.5000, sse=4155769.5, rms=2.36 014: dt: 0.5000, sse=4729331.5, rms=2.09 rms = 2.08, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=4708601.0, rms=2.08 016: dt: 0.2500, sse=4122669.2, rms=1.74 017: dt: 0.2500, sse=3983994.0, rms=1.68 rms = 1.66, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3951350.2, rms=1.66 019: dt: 0.1250, sse=3906948.5, rms=1.61 rms = 1.59, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3878566.5, rms=1.59 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.5, 459 (215) missing vertices, mean dist -0.2 [0.5 (%62.6)->0.3 (%37.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.86 +- 0.27 (0.04-->7.22) (max @ vno 299 --> 2907) face area 0.31 +- 0.17 (0.00-->3.97) mean absolute distance = 0.35 +- 0.47 3127 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3972566.5, rms=2.74 021: dt: 0.5000, sse=4299511.0, rms=1.89 022: dt: 0.5000, sse=4855009.5, rms=1.75 rms = 1.85, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4397507.0, rms=1.54 024: dt: 0.2500, sse=4192641.0, rms=1.48 rms = 1.49, time step reduction 2 of 3 to 0.125... rms = 1.47, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4154600.8, rms=1.47 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=93.4, 510 (204) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3 (%43.9))] %72 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/AD01/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4176596.2, rms=1.84 026: dt: 0.5000, sse=5134479.5, rms=1.43 rms = 1.62, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4785070.5, rms=1.25 rms = 1.25, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4642498.5, rms=1.25 029: dt: 0.1250, sse=4625659.0, rms=1.20 rms = 1.18, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4612411.5, rms=1.18 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 1779 vertices erasing segment 1 (vno[0] = 51321) erasing segment 2 (vno[0] = 53316) erasing segment 3 (vno[0] = 77267) erasing segment 4 (vno[0] = 79247) erasing segment 5 (vno[0] = 82065) erasing segment 6 (vno[0] = 82930) erasing segment 7 (vno[0] = 83030) erasing segment 8 (vno[0] = 84802) erasing segment 9 (vno[0] = 85837) erasing segment 10 (vno[0] = 89303) erasing segment 11 (vno[0] = 90931) erasing segment 12 (vno[0] = 116179) writing cortex label to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.cortex.label writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.area vertex spacing 0.86 +- 0.27 (0.05-->7.01) (max @ vno 299 --> 2907) face area 0.31 +- 0.17 (0.00-->3.62) refinement took 4.8 minutes #-------------------------------------------- #@# Smooth2 rh Tue Jul 12 03:50:11 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Jul 12 03:50:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 44.0 mm, total surface area = 65150 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.127 (target=0.015) step 005: RMS=0.092 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.061 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.044 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 249 vertices thresholded to be in k1 ~ [-0.43 0.54], k2 ~ [-0.13 0.13] total integrated curvature = 0.356*4pi (4.480) --> 1 handles ICI = 1.3, FI = 7.9, variation=137.859 157 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 138 vertices thresholded to be in [-0.20 0.21] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.024 done. #-------------------------------------------- #@# Sphere rh Tue Jul 12 03:52:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 0.94 hours scaling brain by 0.355... pass 1: epoch 1 of 3 starting distance error %20.63 pass 1: epoch 2 of 3 starting distance error %20.56 unfolding complete - removing small folds... starting distance error %20.40 removing remaining folds... final distance error %20.44 #-------------------------------------------- #@# Surf Reg rh Tue Jul 12 04:48:28 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.571 curvature mean = 0.043, std = 0.937 curvature mean = 0.029, std = 0.875 curvature mean = 0.008, std = 0.968 curvature mean = 0.011, std = 0.946 curvature mean = 0.006, std = 0.981 curvature mean = 0.004, std = 0.976 curvature mean = 0.004, std = 0.985 curvature mean = 0.001, std = 0.989 curvature mean = -0.051, std = 0.548 curvature mean = 0.006, std = 0.070 curvature mean = 0.060, std = 0.200 curvature mean = 0.005, std = 0.085 curvature mean = 0.039, std = 0.300 curvature mean = 0.005, std = 0.092 curvature mean = 0.024, std = 0.386 curvature mean = 0.004, std = 0.095 curvature mean = 0.010, std = 0.477 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Jul 12 05:24:05 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Jul 12 05:24:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Jul 12 05:24:09 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1027 labels changed using aseg relabeling using gibbs priors... 000: 2570 changed, 116754 examined... 001: 583 changed, 11056 examined... 002: 141 changed, 3238 examined... 003: 51 changed, 833 examined... 004: 21 changed, 314 examined... 005: 7 changed, 120 examined... 006: 6 changed, 47 examined... 007: 1 changed, 25 examined... 008: 1 changed, 7 examined... 009: 0 changed, 12 examined... 143 labels changed using aseg 000: 118 total segments, 79 labels (524 vertices) changed 001: 40 total segments, 1 labels (1 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1692 vertices marked for relabeling... 1692 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 45 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Jul 12 05:24:54 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD01 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 10970 bright wm thresholded. 1109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.3 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 61.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 76.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=82 using class modes intead of means.... mean inside = 95.9, mean outside = 83.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->7.83) (max @ vno 299 --> 2907) face area 0.27 +- 0.13 (0.00-->3.60) mean absolute distance = 0.89 +- 1.15 4158 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 327 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown mean border=89.0, 508 (508) missing vertices, mean dist 0.1 [1.1 (%35.9)->0.8 (%64.1))] %30 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.28 (0.07-->7.70) (max @ vno 299 --> 2907) face area 0.27 +- 0.14 (0.00-->3.51) mean absolute distance = 0.54 +- 0.88 5244 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3428877.8, rms=7.02 001: dt: 0.5000, sse=4761059.5, rms=5.05 002: dt: 0.5000, sse=4913447.5, rms=3.91 003: dt: 0.5000, sse=5186319.0, rms=3.29 004: dt: 0.5000, sse=5252860.0, rms=2.87 005: dt: 0.5000, sse=5357253.0, rms=2.63 006: dt: 0.5000, sse=5395241.0, rms=2.53 007: dt: 0.5000, sse=5446918.0, rms=2.46 rms = 2.42, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5455361.5, rms=2.42 009: dt: 0.2500, sse=3894952.0, rms=1.94 010: dt: 0.2500, sse=3722342.8, rms=1.85 rms = 1.83, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3657640.2, rms=1.83 rms = 1.81, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3615873.8, rms=1.81 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 38 points - only 5.26% unknown removing 2 vertex label from ripped group deleting segment 4 with 14 points - only 0.00% unknown deleting segment 6 with 206 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 131 points - only 30.53% unknown deleting segment 10 with 14 points - only 0.00% unknown mean border=90.9, 477 (265) missing vertices, mean dist -0.3 [0.7 (%61.8)->0.3 (%38.2))] %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 0.86 +- 0.27 (0.05-->7.28) (max @ vno 299 --> 2907) face area 0.32 +- 0.17 (0.00-->4.01) mean absolute distance = 0.42 +- 0.58 3904 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3865579.0, rms=3.30 013: dt: 0.5000, sse=4185955.8, rms=2.36 014: dt: 0.5000, sse=4761582.0, rms=2.09 rms = 2.08, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=4740584.5, rms=2.08 016: dt: 0.2500, sse=4152354.5, rms=1.75 017: dt: 0.2500, sse=4012557.8, rms=1.68 rms = 1.66, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3976453.0, rms=1.66 019: dt: 0.1250, sse=3932312.5, rms=1.61 rms = 1.59, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3904147.0, rms=1.59 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 50 points - only 4.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 14 points - only 0.00% unknown deleting segment 8 with 219 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 145 points - only 34.48% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown mean border=92.5, 489 (221) missing vertices, mean dist -0.2 [0.5 (%62.6)->0.3 (%37.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.86 +- 0.27 (0.04-->7.22) (max @ vno 299 --> 2907) face area 0.31 +- 0.17 (0.00-->3.97) mean absolute distance = 0.36 +- 0.47 3172 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4001028.0, rms=2.74 021: dt: 0.5000, sse=4333778.5, rms=1.89 022: dt: 0.5000, sse=4891057.5, rms=1.76 rms = 1.85, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4431279.0, rms=1.55 024: dt: 0.2500, sse=4227120.5, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... rms = 1.47, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4188801.0, rms=1.47 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 60 points - only 3.33% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 292 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown deleting segment 4 with 148 points - only 33.78% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown mean border=93.4, 536 (205) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3 (%43.9))] %72 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4210810.0, rms=1.85 026: dt: 0.5000, sse=5181921.5, rms=1.43 rms = 1.63, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4830413.0, rms=1.26 rms = 1.26, time step reduction 2 of 3 to 0.125... rms = 1.23, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4790067.5, rms=1.23 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=70.8, 461 (461) missing vertices, mean dist 2.1 [2.4 (%0.0)->2.4 (%100.0))] %44 local maxima, %40 large gradients and %11 min vals, 785 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=14190003.0, rms=23.23 001: dt: 0.5000, sse=11859767.0, rms=20.79 002: dt: 0.5000, sse=9941935.0, rms=18.55 003: dt: 0.5000, sse=8581238.0, rms=16.57 004: dt: 0.5000, sse=7783324.0, rms=14.82 005: dt: 0.5000, sse=7197922.0, rms=13.27 006: dt: 0.5000, sse=6781655.0, rms=11.88 007: dt: 0.5000, sse=6455491.0, rms=10.62 008: dt: 0.5000, sse=6192907.0, rms=9.41 009: dt: 0.5000, sse=5970331.5, rms=8.28 010: dt: 0.5000, sse=5855844.0, rms=7.28 011: dt: 0.5000, sse=5832601.0, rms=6.44 012: dt: 0.5000, sse=5799666.5, rms=5.79 013: dt: 0.5000, sse=5849949.0, rms=5.30 014: dt: 0.5000, sse=5870124.0, rms=4.96 015: dt: 0.5000, sse=5880813.5, rms=4.70 016: dt: 0.5000, sse=5900181.0, rms=4.53 017: dt: 0.5000, sse=5917720.5, rms=4.42 018: dt: 0.5000, sse=5920998.0, rms=4.34 019: dt: 0.5000, sse=5944981.5, rms=4.28 020: dt: 0.5000, sse=5959566.5, rms=4.22 rms = 4.17, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=5934343.5, rms=4.17 022: dt: 0.2500, sse=3996821.8, rms=3.36 023: dt: 0.2500, sse=3771678.2, rms=3.14 rms = 3.10, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3630768.8, rms=3.10 025: dt: 0.1250, sse=3486648.0, rms=2.99 rms = 2.98, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3458032.5, rms=2.98 positioning took 2.4 minutes mean border=67.4, 624 (62) missing vertices, mean dist 0.3 [0.2 (%33.2)->0.5 (%66.8))] %67 local maxima, %23 large gradients and % 5 min vals, 270 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=4199464.0, rms=5.81 027: dt: 0.5000, sse=4360579.0, rms=4.48 028: dt: 0.5000, sse=5297006.0, rms=4.34 rms = 4.36, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4395995.5, rms=3.59 030: dt: 0.2500, sse=4049385.2, rms=3.26 031: dt: 0.2500, sse=3985025.0, rms=3.17 032: dt: 0.2500, sse=3952497.2, rms=3.11 rms = 3.08, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3946805.2, rms=3.08 034: dt: 0.1250, sse=3825322.5, rms=2.96 rms = 2.93, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3807559.5, rms=2.93 positioning took 0.9 minutes mean border=65.7, 855 (46) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.3 (%63.4))] %73 local maxima, %16 large gradients and % 5 min vals, 290 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=3954045.0, rms=3.81 rms = 3.98, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3822820.8, rms=3.29 037: dt: 0.2500, sse=3840469.8, rms=3.00 038: dt: 0.2500, sse=3960102.8, rms=2.91 rms = 2.87, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3975267.5, rms=2.87 040: dt: 0.1250, sse=3869279.2, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3861913.8, rms=2.74 positioning took 0.6 minutes mean border=65.0, 1424 (43) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.3 (%56.0))] %75 local maxima, %14 large gradients and % 5 min vals, 260 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/AD01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3881526.2, rms=2.92 rms = 3.38, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=3831360.8, rms=2.71 043: dt: 0.2500, sse=3948796.0, rms=2.64 rms = 2.64, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4003365.0, rms=2.64 045: dt: 0.1250, sse=3932530.8, rms=2.55 rms = 2.52, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=3928178.5, rms=2.52 positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.area.pial vertex spacing 0.96 +- 0.43 (0.03-->9.78) (max @ vno 90117 --> 89309) face area 0.37 +- 0.30 (0.00-->9.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 116754 vertices processed 25000 of 116754 vertices processed 50000 of 116754 vertices processed 75000 of 116754 vertices processed 100000 of 116754 vertices processed 0 of 116754 vertices processed 25000 of 116754 vertices processed 50000 of 116754 vertices processed 75000 of 116754 vertices processed 100000 of 116754 vertices processed thickness calculation complete, 776:1368 truncations. 49285 vertices at 0 distance 64138 vertices at 1 distance 57800 vertices at 2 distance 29977 vertices at 3 distance 12429 vertices at 4 distance 4732 vertices at 5 distance 1930 vertices at 6 distance 844 vertices at 7 distance 444 vertices at 8 distance 296 vertices at 9 distance 181 vertices at 10 distance 116 vertices at 11 distance 104 vertices at 12 distance 73 vertices at 13 distance 63 vertices at 14 distance 49 vertices at 15 distance 36 vertices at 16 distance 25 vertices at 17 distance 19 vertices at 18 distance 19 vertices at 19 distance 24 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.thickness positioning took 9.8 minutes #-------------------------------------------- #@# Surf Volume rh Tue Jul 12 05:34:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Tue Jul 12 05:34:44 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab AD01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 838 542 1400 2.515 0.815 0.151 0.067 19 2.4 bankssts 876 549 1854 3.169 0.790 0.146 0.047 21 1.7 caudalanteriorcingulate 3559 2109 5512 2.341 0.585 0.160 0.184 270 21.0 caudalmiddlefrontal 1747 1093 2552 2.128 0.638 0.184 0.276 71 9.5 cuneus 562 351 1968 3.202 1.044 0.195 0.136 21 3.2 entorhinal 3643 2337 6136 2.343 0.688 0.172 0.197 207 17.6 fusiform 4901 3103 7783 2.207 0.658 0.172 0.117 196 23.9 inferiorparietal 3065 1963 5915 2.488 0.924 0.177 0.128 181 13.6 inferiortemporal 1356 837 1805 2.068 0.724 0.178 0.160 45 6.7 isthmuscingulate 7075 4437 11540 2.338 0.705 0.185 0.216 645 39.2 lateraloccipital 3426 2136 5898 2.415 0.926 0.180 0.369 210 14.7 lateralorbitofrontal 4257 2642 5449 1.883 0.542 0.177 0.142 127 21.3 lingual 2323 1481 3960 2.210 0.879 0.182 0.189 170 24.4 medialorbitofrontal 3571 2336 7948 2.585 0.760 0.172 0.266 287 16.6 middletemporal 789 522 1369 2.209 0.689 0.133 0.081 11 3.2 parahippocampal 2185 1246 3423 2.634 0.647 0.165 1.684 165 16.2 paracentral 2440 1523 4092 2.340 0.605 0.169 0.142 269 13.1 parsopercularis 962 605 1965 2.454 0.728 0.190 0.361 268 4.6 parsorbitalis 1670 1064 2913 2.452 0.600 0.178 0.148 67 10.3 parstriangularis 1760 1115 1915 1.801 0.546 0.196 0.222 407 15.1 pericalcarine 4911 2997 6899 2.080 0.743 0.154 0.102 161 19.8 postcentral 1339 807 2369 2.724 0.775 0.162 0.103 54 4.2 posteriorcingulate 7612 4631 11666 2.423 0.713 0.165 0.832 1296 50.1 precentral 4647 2824 6316 2.092 0.607 0.153 0.117 158 21.3 precuneus 670 397 1717 3.488 0.927 0.146 0.065 11 1.8 rostralanteriorcingulate 7049 4253 10709 2.216 0.593 0.175 0.238 306 41.1 rostralmiddlefrontal 10679 6261 16917 2.487 0.673 0.180 0.223 871 81.0 superiorfrontal 8153 4804 11414 2.093 0.590 0.174 0.259 577 55.7 superiorparietal 3942 2631 7212 2.344 0.616 0.152 0.171 141 15.3 superiortemporal 4165 2613 7024 2.452 0.648 0.156 0.087 84 15.0 supramarginal 400 235 665 2.251 0.923 0.200 0.124 13 2.1 frontalpole 635 416 2407 3.614 0.882 0.183 0.115 18 2.9 temporalpole 514 293 877 2.454 0.454 0.158 0.113 22 2.6 transversetemporal 3421 2162 7136 3.116 0.992 0.170 0.219 453 23.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Jul 12 05:34:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 11 labels changed using aseg relabeling using gibbs priors... 000: 8633 changed, 116754 examined... 001: 2076 changed, 33079 examined... 002: 647 changed, 10744 examined... 003: 292 changed, 3620 examined... 004: 142 changed, 1635 examined... 005: 57 changed, 781 examined... 006: 29 changed, 337 examined... 007: 19 changed, 156 examined... 008: 18 changed, 114 examined... 009: 5 changed, 88 examined... 010: 2 changed, 34 examined... 011: 0 changed, 9 examined... 3 labels changed using aseg 000: 300 total segments, 215 labels (2342 vertices) changed 001: 100 total segments, 15 labels (82 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 112 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1310 vertices marked for relabeling... 1310 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 51 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jul 12 05:35:49 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab AD01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1082 639 1574 2.194 0.703 0.180 0.102 25 4.8 G_and_S_frontomargin 1510 934 2575 2.274 0.692 0.180 0.172 169 9.0 G_and_S_occipital_inf 1119 622 1415 2.075 0.634 0.185 3.193 106 10.7 G_and_S_paracentral 1284 826 2672 2.911 0.736 0.178 0.102 28 5.4 G_and_S_subcentral 834 479 1485 2.300 0.660 0.183 0.152 40 5.5 G_and_S_transv_frontopol 2070 1286 3878 2.672 0.882 0.141 0.066 31 5.5 G_and_S_cingul-Ant 1284 822 2669 2.946 0.705 0.157 0.068 33 3.4 G_and_S_cingul-Mid-Ant 1451 882 2577 2.719 0.682 0.162 0.109 72 6.1 G_and_S_cingul-Mid-Post 430 261 936 2.685 0.789 0.204 0.130 14 2.3 G_cingul-Post-dorsal 244 132 412 2.260 0.652 0.196 0.386 13 1.5 G_cingul-Post-ventral 1644 979 2291 2.059 0.658 0.191 0.291 73 9.2 G_cuneus 1470 894 3087 2.601 0.642 0.183 0.173 253 9.3 G_front_inf-Opercular 348 213 727 2.638 0.567 0.207 0.192 16 3.0 G_front_inf-Orbital 985 594 1963 2.624 0.561 0.204 0.203 55 8.4 G_front_inf-Triangul 3637 1987 5944 2.312 0.608 0.185 0.396 327 30.5 G_front_middle 7335 4071 12015 2.529 0.698 0.202 0.284 710 71.6 G_front_sup 616 365 1507 3.251 0.889 0.209 0.244 69 7.5 G_Ins_lg_and_S_cent_ins 532 331 1617 3.417 1.058 0.232 0.315 35 5.8 G_insular_short 1395 865 3187 2.874 0.665 0.205 0.196 161 10.4 G_occipital_middle 2002 1097 2880 2.167 0.559 0.194 0.287 186 27.2 G_occipital_sup 1532 936 2607 2.284 0.626 0.190 0.245 144 10.2 G_oc-temp_lat-fusifor 2747 1668 3853 1.920 0.585 0.190 0.180 88 15.9 G_oc-temp_med-Lingual 1291 818 3201 3.074 1.015 0.167 0.777 376 6.3 G_oc-temp_med-Parahip 2466 1470 4819 2.405 0.954 0.196 0.233 341 14.0 G_orbital 2150 1320 4165 2.406 0.686 0.194 0.156 95 15.7 G_pariet_inf-Angular 1926 1147 3957 2.724 0.579 0.166 0.098 44 7.6 G_pariet_inf-Supramar 2793 1588 4062 2.135 0.600 0.173 0.151 172 14.9 G_parietal_sup 1845 1020 2724 2.094 0.598 0.174 0.147 119 10.3 G_postcentral 3055 1639 4830 2.413 0.767 0.190 1.956 1222 32.1 G_precentral 2250 1277 3204 2.109 0.599 0.161 0.135 108 11.9 G_precuneus 711 431 1450 2.383 0.919 0.169 0.118 20 2.4 G_rectus 297 198 543 2.597 1.164 0.356 0.874 129 17.7 G_subcallosal 369 199 721 2.638 0.408 0.163 0.130 21 2.1 G_temp_sup-G_T_transv 1492 953 3522 2.652 0.582 0.205 0.376 110 10.6 G_temp_sup-Lateral 378 264 970 3.048 0.913 0.139 0.084 11 1.3 G_temp_sup-Plan_polar 425 283 692 2.189 0.520 0.122 0.042 4 0.7 G_temp_sup-Plan_tempo 1544 951 3212 2.581 1.095 0.191 0.136 58 7.7 G_temporal_inf 2421 1530 5965 2.749 0.726 0.188 0.124 87 13.3 G_temporal_middle 248 173 341 2.187 0.545 0.140 0.057 3 0.6 Lat_Fis-ant-Horizont 164 116 207 2.148 0.533 0.122 0.042 1 0.3 Lat_Fis-ant-Vertical 1383 886 1686 2.196 0.591 0.130 0.066 25 3.7 Lat_Fis-post 3265 2109 5043 2.196 0.680 0.202 0.163 271 20.2 Pole_occipital 1977 1264 5753 3.037 0.852 0.201 0.171 181 12.4 Pole_temporal 2309 1445 2383 1.880 0.553 0.182 0.182 421 17.3 S_calcarine 2668 1760 3219 2.063 0.786 0.138 0.056 26 6.5 S_central 1262 812 1856 2.420 0.706 0.128 0.047 14 2.5 S_cingul-Marginalis 373 241 657 2.933 0.703 0.178 0.120 10 1.5 S_circular_insula_ant 1223 862 2095 2.705 0.965 0.106 0.041 8 2.1 S_circular_insula_inf 1168 762 1793 2.735 0.553 0.125 0.071 17 4.5 S_circular_insula_sup 731 503 1201 2.218 0.793 0.144 0.053 10 1.8 S_collat_transv_ant 540 347 547 2.013 0.636 0.162 0.074 8 1.8 S_collat_transv_post 1658 1085 2575 2.256 0.562 0.154 0.065 24 4.5 S_front_inf 1647 1059 2371 2.224 0.635 0.166 0.167 54 7.5 S_front_middle 2827 1793 3721 2.229 0.560 0.142 0.159 229 14.1 S_front_sup 312 208 345 1.814 0.403 0.143 0.059 3 0.8 S_interm_prim-Jensen 3037 1906 4105 2.080 0.567 0.158 0.356 197 11.0 S_intrapariet_and_P_trans 784 505 981 1.978 0.496 0.147 0.057 9 2.0 S_oc_middle_and_Lunatus 1440 922 1936 2.068 0.573 0.152 0.427 152 4.7 S_oc_sup_and_transversal 540 355 635 2.177 0.443 0.154 0.066 7 1.5 S_occipital_ant 525 333 976 2.630 0.635 0.169 0.399 14 1.9 S_oc-temp_lat 1617 1101 2021 2.040 0.541 0.123 0.042 14 2.9 S_oc-temp_med_and_Lingual 314 207 382 2.013 0.471 0.154 0.055 4 0.7 S_orbital_lateral 672 473 944 1.956 1.000 0.132 0.049 8 1.2 S_orbital_med-olfact 1591 1015 2404 2.260 0.714 0.174 0.242 89 6.4 S_orbital-H_Shaped 1222 817 1624 2.023 0.555 0.133 0.051 16 2.5 S_parieto_occipital 1579 942 1844 2.454 0.957 0.150 0.090 40 5.3 S_pericallosal 2042 1328 2549 1.984 0.547 0.144 0.069 34 6.2 S_postcentral 2202 1420 3055 2.279 0.545 0.145 0.087 36 9.6 S_precentral-inf-part 1599 1044 2074 2.243 0.563 0.157 0.123 71 9.3 S_precentral-sup-part 277 188 351 1.892 0.601 0.133 0.049 3 0.5 S_suborbital 771 492 1203 2.145 0.825 0.154 0.152 21 4.8 S_subparietal 595 409 795 2.224 0.564 0.130 0.049 6 1.4 S_temporal_inf 3321 2269 4783 2.132 0.678 0.141 0.231 231 8.1 S_temporal_sup 295 191 361 1.949 0.520 0.133 0.039 2 0.6 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 12 05:36:03 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD01 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 = 0 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Jul 12 05:45:09 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD01 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD01 sysname Linux hostname compute-0-15 machine x86_64 user fdu0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 195846 rh white matter volume 181785 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 224989.173834, pTot = 390891.538501 c = 165902.364668 rh surface-based volumes (mm3): wTot = 205541.309966, pTot = 382658.264416 c = 177116.954451 Computing SupraTentVolCor SupraTentVolCor = 54454.000 SupraTentVol = 828003.803 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 16925 16925 4 5 Left-Inf-Lat-Vent 1092 1092 5 7 Left-Cerebellum-White-Matter 12121 12121 6 8 Left-Cerebellum-Cortex 46991 46991 7 10 Left-Thalamus-Proper 5656 5656 8 11 Left-Caudate 2902 2902 9 12 Left-Putamen 4883 4883 10 13 Left-Pallidum 1619 1619 11 14 3rd-Ventricle 1695 1695 12 15 4th-Ventricle 1572 1572 13 16 Brain-Stem 20901 20901 14 17 Left-Hippocampus 3352 3352 15 18 Left-Amygdala 1232 1232 16 24 CSF 1828 1828 17 26 Left-Accumbens-area 295 295 18 28 Left-VentralDC 3232 3232 19 30 Left-vessel 13 13 20 31 Left-choroid-plexus 2407 2407 23 43 Right-Lateral-Ventricle 12572 12572 24 44 Right-Inf-Lat-Vent 491 491 25 46 Right-Cerebellum-White-Matter 11228 11228 26 47 Right-Cerebellum-Cortex 46619 46619 27 49 Right-Thalamus-Proper 6077 6077 28 50 Right-Caudate 3172 3172 29 51 Right-Putamen 4148 4148 30 52 Right-Pallidum 1430 1430 31 53 Right-Hippocampus 3492 3492 32 54 Right-Amygdala 1119 1119 33 58 Right-Accumbens-area 316 316 34 60 Right-VentralDC 3333 3333 35 62 Right-vessel 7 7 36 63 Right-choroid-plexus 2437 2437 37 72 5th-Ventricle 0 38 77 WM-hypointensities 2940 2940 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 21 21 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 276 276 45 251 CC_Posterior 604 604 46 252 CC_Mid_Posterior 353 353 47 253 CC_Central 452 452 48 254 CC_Mid_Anterior 388 388 49 255 CC_Anterior 704 704 Reporting on 45 segmentations SubCortGrayVol = 160769 #----------------------------------------- #@# AParc-to-ASeg Tue Jul 12 05:55:05 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 335779 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 335779 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Jul 12 05:57:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --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 AD01 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/AD01/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7851 vertices from left hemi Ripped 7612 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/AD01/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 692247 Used brute-force search on 63 voxels Fixing Parahip LH WM Found 5 clusters 0 k 978.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 2.000000 Fixing Parahip RH WM Found 7 clusters 0 k 1.000000 1 k 1095.000000 2 k 1.000000 3 k 6.000000 4 k 2.000000 5 k 2.000000 6 k 5.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD01 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD01 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-15 machine x86_64 user fdu0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 195846 rh white matter volume 181785 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1362929 # brainmaskvolume 1362929.0 # nbrainsegvoxels 225779 # brainsegvolume 225779.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 1939 1939 2 3002 wm-lh-caudalanteriorcingulate 2819 2819 3 3003 wm-lh-caudalmiddlefrontal 6146 6146 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2128 2128 6 3006 wm-lh-entorhinal 706 706 7 3007 wm-lh-fusiform 4735 4735 8 3008 wm-lh-inferiorparietal 6394 6394 9 3009 wm-lh-inferiortemporal 4288 4288 10 3010 wm-lh-isthmuscingulate 3170 3170 11 3011 wm-lh-lateraloccipital 9842 9842 12 3012 wm-lh-lateralorbitofrontal 5607 5607 13 3013 wm-lh-lingual 5970 5970 14 3014 wm-lh-medialorbitofrontal 3809 3809 15 3015 wm-lh-middletemporal 3154 3154 16 3016 wm-lh-parahippocampal 1102 1102 17 3017 wm-lh-paracentral 3258 3258 18 3018 wm-lh-parsopercularis 3788 3788 19 3019 wm-lh-parsorbitalis 726 726 20 3020 wm-lh-parstriangularis 2828 2828 21 3021 wm-lh-pericalcarine 2916 2916 22 3022 wm-lh-postcentral 5800 5800 23 3023 wm-lh-posteriorcingulate 3650 3650 24 3024 wm-lh-precentral 13678 13678 25 3025 wm-lh-precuneus 6146 6146 26 3026 wm-lh-rostralanteriorcingulate 2223 2223 27 3027 wm-lh-rostralmiddlefrontal 10660 10660 28 3028 wm-lh-superiorfrontal 15212 15212 29 3029 wm-lh-superiorparietal 10631 10631 30 3030 wm-lh-superiortemporal 6150 6150 31 3031 wm-lh-supramarginal 5488 5488 32 3032 wm-lh-frontalpole 273 273 33 3033 wm-lh-temporalpole 703 703 34 3034 wm-lh-transversetemporal 575 575 35 3035 wm-lh-insula 7676 7676 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 1660 1660 120 4002 wm-rh-caudalanteriorcingulate 2392 2392 121 4003 wm-rh-caudalmiddlefrontal 5179 5179 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1691 1691 124 4006 wm-rh-entorhinal 531 531 125 4007 wm-rh-fusiform 4565 4565 126 4008 wm-rh-inferiorparietal 7060 7060 127 4009 wm-rh-inferiortemporal 4483 4483 128 4010 wm-rh-isthmuscingulate 2886 2886 129 4011 wm-rh-lateraloccipital 8500 8500 130 4012 wm-rh-lateralorbitofrontal 5316 5316 131 4013 wm-rh-lingual 4418 4418 132 4014 wm-rh-medialorbitofrontal 2743 2743 133 4015 wm-rh-middletemporal 3735 3735 134 4016 wm-rh-parahippocampal 1220 1220 135 4017 wm-rh-paracentral 3197 3197 136 4018 wm-rh-parsopercularis 3295 3295 137 4019 wm-rh-parsorbitalis 975 975 138 4020 wm-rh-parstriangularis 2348 2348 139 4021 wm-rh-pericalcarine 2261 2261 140 4022 wm-rh-postcentral 5014 5014 141 4023 wm-rh-posteriorcingulate 3259 3259 142 4024 wm-rh-precentral 12999 12999 143 4025 wm-rh-precuneus 7056 7056 144 4026 wm-rh-rostralanteriorcingulate 1654 1654 145 4027 wm-rh-rostralmiddlefrontal 8907 8907 146 4028 wm-rh-superiorfrontal 14373 14373 147 4029 wm-rh-superiorparietal 9476 9476 148 4030 wm-rh-superiortemporal 4624 4624 149 4031 wm-rh-supramarginal 6188 6188 150 4032 wm-rh-frontalpole 316 316 151 4033 wm-rh-temporalpole 566 566 152 4034 wm-rh-transversetemporal 540 540 153 4035 wm-rh-insula 7824 7824 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 23235 23235 237 5002 Right-UnsegmentedWhiteMatter 23441 23441 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label #-------------------------------------------- #@# BA Labels lh Tue Jul 12 06:13:54 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD01 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD01 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label Linux compute-0-15 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AD01 exited with ERRORS at Tue Jul 12 06:13:54 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jul 12 10:55:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 /autofs/space/plato_002/users/freesurfer/bin/recon-all -balabels -no-isrunning -subjid AD01 subjid AD01 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-29 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 3510340 29366912 4 13416 332284 -/+ buffers/cache: 3164640 29712612 Swap: 67108860 489436 66619424 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:09-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:10-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-14:55:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-29 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label #-------------------------------------------- #@# BA Labels lh Tue Jul 12 10:55:13 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD01 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD01 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label Linux compute-0-29 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AD01 exited with ERRORS at Tue Jul 12 10:55:13 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jul 12 12:07:16 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 /autofs/space/plato_002/users/freesurfer/bin/recon-all -autorecon3 -no-isrunning -subjid AD01 subjid AD01 setenv SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Actual FREESURFER_HOME /autofs/space/plato_002/users/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux compute-0-60 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 128305 total used free shared buffers cached Mem: 32877252 19599192 13278060 8 168880 11895500 -/+ buffers/cache: 7534812 25342440 Swap: 67108860 37184 67071676 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:19-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:20-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:20-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:20-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:20-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:21-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/07/12-16:07:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fdu0 Machine: compute-0-60 Platform: Linux PlatformVersion: 2.6.32-573.18.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /autofs/space/plato_002/users/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /autofs/space/plato_002/users/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Sphere lh Tue Jul 12 12:07:24 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.11 hours scaling brain by 0.349... pass 1: epoch 1 of 3 starting distance error %20.39 pass 1: epoch 2 of 3 starting distance error %20.37 unfolding complete - removing small folds... starting distance error %20.30 removing remaining folds... final distance error %20.32 #-------------------------------------------- #@# Surf Reg lh Tue Jul 12 13:14:02 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv ../surf/lh.sphere /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.575 curvature mean = 0.033, std = 0.933 curvature mean = 0.027, std = 0.875 curvature mean = -0.011, std = 0.964 curvature mean = 0.009, std = 0.948 curvature mean = -0.013, std = 0.978 curvature mean = 0.004, std = 0.977 curvature mean = -0.013, std = 0.982 curvature mean = 0.001, std = 0.990 curvature mean = -0.040, std = 0.440 curvature mean = 0.003, std = 0.067 curvature mean = 0.055, std = 0.242 curvature mean = 0.002, std = 0.079 curvature mean = 0.032, std = 0.367 curvature mean = 0.002, std = 0.086 curvature mean = 0.021, std = 0.467 curvature mean = 0.002, std = 0.088 curvature mean = 0.007, std = 0.563 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Jul 12 13:54:11 EDT 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Jul 12 13:54:13 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jul 12 13:54:15 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1081 labels changed using aseg relabeling using gibbs priors... 000: 2726 changed, 119299 examined... 001: 631 changed, 11799 examined... 002: 158 changed, 3436 examined... 003: 52 changed, 934 examined... 004: 9 changed, 312 examined... 005: 4 changed, 61 examined... 006: 3 changed, 23 examined... 007: 2 changed, 19 examined... 008: 0 changed, 6 examined... 186 labels changed using aseg 000: 130 total segments, 79 labels (254 vertices) changed 001: 55 total segments, 13 labels (26 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1769 vertices marked for relabeling... 1769 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jul 12 13:55:07 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD01 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 11342 bright wm thresholded. 1184 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.3 +- 6.5 [70.0 --> 110.0] GM (86.0) : 82.8 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.2 (was 70) setting MAX_BORDER_WHITE to 104.5 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 52.3 (was 40) setting MAX_GRAY to 91.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 71.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=98, GM=78 using class modes intead of means.... mean inside = 93.9, mean outside = 80.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->4.76) (max @ vno 118894 --> 118895) face area 0.27 +- 0.13 (0.00-->6.34) mean absolute distance = 0.83 +- 1.07 3997 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 540 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 20 points - only 5.00% unknown deleting segment 8 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown mean border=86.5, 503 (501) missing vertices, mean dist 0.1 [0.9 (%38.5)->0.8 (%61.5))] %34 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.28 (0.04-->5.19) (max @ vno 103994 --> 118918) face area 0.27 +- 0.14 (0.00-->5.02) mean absolute distance = 0.60 +- 0.93 5887 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3798159.0, rms=8.16 001: dt: 0.5000, sse=4955813.5, rms=6.06 002: dt: 0.5000, sse=5203011.5, rms=4.83 003: dt: 0.5000, sse=5576064.0, rms=4.15 004: dt: 0.5000, sse=5669829.5, rms=3.73 005: dt: 0.5000, sse=5836718.0, rms=3.44 006: dt: 0.5000, sse=5846223.5, rms=3.22 007: dt: 0.5000, sse=5953561.0, rms=3.09 008: dt: 0.5000, sse=5916808.5, rms=2.98 009: dt: 0.5000, sse=5984281.0, rms=2.89 010: dt: 0.5000, sse=5930242.0, rms=2.83 rms = 2.80, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=6000951.0, rms=2.80 012: dt: 0.2500, sse=4047062.0, rms=2.27 013: dt: 0.2500, sse=3841012.0, rms=2.19 rms = 2.18, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3761698.8, rms=2.18 rms = 2.13, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3706842.2, rms=2.13 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 4.35% unknown deleting segment 4 with 316 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 86 points - only 53.49% unknown deleting segment 9 with 53 points - only 49.06% unknown removing 3 vertex label from ripped group deleting segment 11 with 27 points - only 0.00% unknown mean border=88.6, 308 (165) missing vertices, mean dist -0.4 [0.8 (%61.2)->0.3 (%38.8))] %47 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 0.87 +- 0.27 (0.05-->5.10) (max @ vno 103994 --> 118918) face area 0.33 +- 0.17 (0.00-->5.97) mean absolute distance = 0.49 +- 0.61 4560 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4034540.5, rms=3.88 016: dt: 0.5000, sse=4333050.0, rms=2.90 017: dt: 0.5000, sse=5026546.5, rms=2.58 rms = 2.57, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=5128315.5, rms=2.57 019: dt: 0.2500, sse=4332240.5, rms=2.19 020: dt: 0.2500, sse=4188347.0, rms=2.11 rms = 2.06, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4146061.5, rms=2.06 022: dt: 0.1250, sse=4091290.2, rms=2.01 rms = 1.96, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4071290.8, rms=1.96 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 4.35% unknown deleting segment 1 with 324 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 13 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 111 points - only 41.44% unknown deleting segment 8 with 75 points - only 34.67% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 25 points - only 0.00% unknown mean border=90.4, 320 (112) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %62 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 0.86 +- 0.27 (0.07-->4.96) (max @ vno 103994 --> 118918) face area 0.32 +- 0.17 (0.00-->5.54) mean absolute distance = 0.39 +- 0.47 3882 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4218662.5, rms=3.34 024: dt: 0.5000, sse=4533102.0, rms=2.35 025: dt: 0.5000, sse=5195987.5, rms=2.17 rms = 2.23, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4657222.0, rms=1.92 027: dt: 0.2500, sse=4402116.0, rms=1.82 rms = 1.81, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4341471.0, rms=1.81 029: dt: 0.1250, sse=4296945.0, rms=1.75 rms = 1.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4266340.5, rms=1.73 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 2 with 486 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 105 points - only 43.81% unknown deleting segment 6 with 21 points - only 4.76% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=91.3, 329 (88) missing vertices, mean dist -0.1 [0.5 (%57.3)->0.3 (%42.7))] %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4300530.5, rms=2.21 031: dt: 0.5000, sse=5462467.0, rms=1.74 rms = 1.94, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5000690.0, rms=1.54 rms = 1.56, time step reduction 2 of 3 to 0.125... rms = 1.50, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4949529.0, rms=1.50 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 3 with 6 points - only 16.67% unknown smoothing surface for 5 iterations... mean border=66.2, 404 (404) missing vertices, mean dist 2.0 [0.1 (%0.0)->2.4 (%100.0))] %38 local maxima, %41 large gradients and %16 min vals, 684 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=17153128.0, rms=25.66 001: dt: 0.5000, sse=14299946.0, rms=23.05 002: dt: 0.5000, sse=11890635.0, rms=20.62 003: dt: 0.5000, sse=10105376.0, rms=18.42 004: dt: 0.5000, sse=8883289.0, rms=16.40 005: dt: 0.5000, sse=7961107.0, rms=14.51 006: dt: 0.5000, sse=7312941.0, rms=12.78 007: dt: 0.5000, sse=6809855.5, rms=11.17 008: dt: 0.5000, sse=6538200.5, rms=9.71 009: dt: 0.5000, sse=6294898.0, rms=8.39 010: dt: 0.5000, sse=6165020.5, rms=7.26 011: dt: 0.5000, sse=6091233.0, rms=6.43 012: dt: 0.5000, sse=6148091.5, rms=5.85 013: dt: 0.5000, sse=6168502.0, rms=5.48 014: dt: 0.5000, sse=6224654.5, rms=5.21 015: dt: 0.5000, sse=6226509.5, rms=5.01 016: dt: 0.5000, sse=6244095.5, rms=4.86 017: dt: 0.5000, sse=6235825.5, rms=4.76 018: dt: 0.5000, sse=6259684.5, rms=4.66 019: dt: 0.5000, sse=6259045.5, rms=4.60 020: dt: 0.5000, sse=6240822.5, rms=4.53 rms = 4.50, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6256413.5, rms=4.50 022: dt: 0.2500, sse=3984543.2, rms=3.49 023: dt: 0.2500, sse=3717991.0, rms=3.20 024: dt: 0.2500, sse=3544957.8, rms=3.12 rms = 3.09, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3487125.2, rms=3.09 026: dt: 0.1250, sse=3315250.5, rms=2.96 rms = 2.94, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3281904.2, rms=2.94 positioning took 2.8 minutes mean border=63.9, 647 (62) missing vertices, mean dist 0.2 [0.2 (%41.5)->0.5 (%58.5))] %61 local maxima, %25 large gradients and % 9 min vals, 246 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=3818396.2, rms=5.04 028: dt: 0.5000, sse=4305168.5, rms=4.47 rms = 4.47, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=5356072.0, rms=4.47 030: dt: 0.2500, sse=3951207.2, rms=3.42 031: dt: 0.2500, sse=3961248.5, rms=3.15 032: dt: 0.2500, sse=3844638.0, rms=3.10 033: dt: 0.2500, sse=3851122.2, rms=3.04 rms = 3.02, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=3803146.2, rms=3.02 035: dt: 0.1250, sse=3665328.0, rms=2.88 rms = 2.86, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=3646802.5, rms=2.86 positioning took 0.9 minutes mean border=62.6, 884 (44) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.4 (%56.1))] %70 local maxima, %16 large gradients and % 9 min vals, 243 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=3774872.2, rms=3.66 rms = 4.10, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=3660802.2, rms=3.14 038: dt: 0.2500, sse=3710392.2, rms=2.93 rms = 2.89, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3805691.8, rms=2.89 040: dt: 0.1250, sse=3687806.5, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3694458.5, rms=2.74 positioning took 0.6 minutes mean border=61.8, 1576 (42) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.3 (%51.7))] %72 local maxima, %13 large gradients and % 9 min vals, 246 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/AD01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3731838.5, rms=3.05 rms = 3.65, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=3673808.8, rms=2.79 043: dt: 0.2500, sse=3807186.2, rms=2.72 rms = 2.71, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=3856092.8, rms=2.71 045: dt: 0.1250, sse=3785131.8, rms=2.60 rms = 2.57, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=3786205.2, rms=2.57 positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.area.pial vertex spacing 0.93 +- 0.40 (0.03-->6.26) (max @ vno 103607 --> 102862) face area 0.36 +- 0.28 (0.00-->6.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119299 vertices processed 25000 of 119299 vertices processed 50000 of 119299 vertices processed 75000 of 119299 vertices processed 100000 of 119299 vertices processed 0 of 119299 vertices processed 25000 of 119299 vertices processed 50000 of 119299 vertices processed 75000 of 119299 vertices processed 100000 of 119299 vertices processed thickness calculation complete, 1085:1127 truncations. 54979 vertices at 0 distance 73194 vertices at 1 distance 55217 vertices at 2 distance 26143 vertices at 3 distance 10850 vertices at 4 distance 4107 vertices at 5 distance 1564 vertices at 6 distance 679 vertices at 7 distance 326 vertices at 8 distance 207 vertices at 9 distance 132 vertices at 10 distance 70 vertices at 11 distance 54 vertices at 12 distance 42 vertices at 13 distance 35 vertices at 14 distance 23 vertices at 15 distance 23 vertices at 16 distance 14 vertices at 17 distance 10 vertices at 18 distance 9 vertices at 19 distance 16 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.thickness positioning took 11.4 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jul 12 14:06:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Jul 12 14:06:31 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab AD01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 974 681 1262 1.950 0.497 0.113 0.031 6 1.4 bankssts 902 599 1920 3.653 0.698 0.164 0.060 21 2.2 caudalanteriorcingulate 3428 2062 3993 1.973 0.557 0.170 0.167 311 24.5 caudalmiddlefrontal 1982 1226 2554 1.940 0.531 0.181 0.108 66 9.4 cuneus 552 360 1977 3.825 0.586 0.158 0.077 10 1.6 entorhinal 3319 2260 6955 2.652 0.742 0.190 0.105 103 14.5 fusiform 4827 2915 5634 1.780 0.536 0.172 0.109 141 23.5 inferiorparietal 3560 2342 7398 2.460 0.946 0.214 0.163 204 21.4 inferiortemporal 1585 932 1714 1.839 0.604 0.156 0.131 109 9.4 isthmuscingulate 7424 4564 10778 2.212 0.656 0.180 0.149 293 38.4 lateraloccipital 3465 2284 6497 2.601 0.855 0.173 0.139 91 14.4 lateralorbitofrontal 4950 3194 6087 1.841 0.613 0.174 0.106 129 24.3 lingual 2550 1658 4578 2.590 1.061 0.187 0.167 211 20.1 medialorbitofrontal 3067 1884 5887 2.394 0.913 0.193 0.367 802 27.6 middletemporal 696 473 1552 2.666 0.901 0.150 0.058 15 1.5 parahippocampal 2041 1182 3395 2.754 0.686 0.166 0.172 135 19.3 paracentral 2701 1646 3972 2.235 0.688 0.162 0.112 69 13.2 parsopercularis 790 479 1583 2.469 0.745 0.169 0.123 21 4.5 parsorbitalis 1883 1231 3217 2.367 0.556 0.165 0.098 41 8.1 parstriangularis 1846 1212 1738 1.539 0.439 0.180 0.092 41 6.9 pericalcarine 4962 3006 6497 1.978 0.656 0.158 0.096 122 21.2 postcentral 1397 869 2333 2.674 0.788 0.157 0.087 29 4.9 posteriorcingulate 7874 4834 10754 2.242 0.673 0.180 0.164 513 58.4 precentral 4361 2633 4958 1.780 0.582 0.156 0.165 118 20.3 precuneus 1114 719 2636 3.439 0.956 0.173 0.106 25 5.0 rostralanteriorcingulate 7869 4847 10670 2.031 0.591 0.179 0.989 1793 43.8 rostralmiddlefrontal 10399 6378 15088 2.264 0.670 0.175 0.145 596 62.1 superiorfrontal 7465 4562 8756 1.803 0.546 0.163 0.092 164 29.7 superiorparietal 4697 3069 8125 2.353 0.714 0.162 0.108 192 22.8 superiortemporal 4015 2437 5459 2.093 0.644 0.174 0.195 248 31.5 supramarginal 428 243 702 2.235 0.634 0.218 0.178 15 2.9 frontalpole 538 414 1963 3.225 0.841 0.212 0.100 15 2.6 temporalpole 648 347 1006 2.488 0.441 0.153 0.090 14 2.3 transversetemporal 3139 1981 6102 3.067 0.942 0.161 0.161 153 21.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jul 12 14:06:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 lh ../surf/lh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 21 labels changed using aseg relabeling using gibbs priors... 000: 8405 changed, 119299 examined... 001: 2019 changed, 32375 examined... 002: 616 changed, 10440 examined... 003: 272 changed, 3400 examined... 004: 131 changed, 1481 examined... 005: 76 changed, 710 examined... 006: 44 changed, 431 examined... 007: 30 changed, 248 examined... 008: 17 changed, 167 examined... 009: 8 changed, 92 examined... 010: 5 changed, 57 examined... 011: 3 changed, 32 examined... 012: 0 changed, 10 examined... 6 labels changed using aseg 000: 245 total segments, 160 labels (1444 vertices) changed 001: 90 total segments, 5 labels (14 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 96 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 980 vertices marked for relabeling... 980 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jul 12 14:07:50 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab AD01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1092 705 1572 2.087 0.626 0.191 0.134 35 7.0 G_and_S_frontomargin 2068 1259 2995 2.116 0.670 0.182 0.122 64 10.9 G_and_S_occipital_inf 1448 798 2176 2.386 0.778 0.172 0.162 78 11.6 G_and_S_paracentral 1297 799 2248 2.398 0.677 0.186 0.162 144 9.8 G_and_S_subcentral 818 467 1341 2.268 0.552 0.189 0.127 29 4.2 G_and_S_transv_frontopol 1687 1153 3452 2.907 0.924 0.167 0.090 30 6.5 G_and_S_cingul-Ant 1414 946 2666 2.967 0.633 0.162 0.116 49 3.7 G_and_S_cingul-Mid-Ant 1044 701 1925 2.804 0.597 0.161 0.072 19 3.3 G_and_S_cingul-Mid-Post 433 215 573 2.147 0.576 0.160 0.204 15 4.7 G_cingul-Post-dorsal 386 232 415 1.647 0.554 0.161 0.096 13 1.7 G_cingul-Post-ventral 1912 1147 2650 2.035 0.520 0.178 0.106 47 8.4 G_cuneus 1468 818 2424 2.331 0.677 0.166 0.147 49 9.1 G_front_inf-Opercular 292 160 724 2.909 0.586 0.189 0.178 11 2.7 G_front_inf-Orbital 1448 912 2708 2.368 0.612 0.186 0.130 45 8.5 G_front_inf-Triangul 4194 2401 5682 1.975 0.553 0.198 1.667 1888 35.9 G_front_middle 7274 4226 11331 2.378 0.721 0.187 0.175 561 58.4 G_front_sup 411 253 990 3.617 0.568 0.197 0.185 27 2.4 G_Ins_lg_and_S_cent_ins 716 393 1960 3.771 1.028 0.201 0.292 59 9.9 G_insular_short 1547 878 2620 2.326 0.643 0.195 0.248 127 12.0 G_occipital_middle 1879 1158 2832 2.157 0.652 0.168 0.103 41 7.8 G_occipital_sup 1323 868 2832 2.678 0.660 0.199 0.124 50 6.9 G_oc-temp_lat-fusifor 3639 2289 4628 1.822 0.605 0.187 0.122 113 20.9 G_oc-temp_med-Lingual 943 614 2995 3.444 0.882 0.159 0.070 22 2.7 G_oc-temp_med-Parahip 2339 1426 4780 2.561 0.931 0.181 0.199 93 13.6 G_orbital 2127 1165 2402 1.801 0.565 0.188 0.146 95 13.3 G_pariet_inf-Angular 2135 1234 2988 2.142 0.660 0.186 0.269 201 23.7 G_pariet_inf-Supramar 2912 1696 3364 1.782 0.494 0.162 0.102 75 12.8 G_parietal_sup 1949 1043 2675 2.110 0.589 0.172 0.142 71 12.3 G_postcentral 2896 1623 4206 2.231 0.766 0.196 0.242 227 31.3 G_precentral 2050 1142 2550 1.860 0.581 0.172 0.120 66 10.9 G_precuneus 817 542 1383 2.061 0.896 0.189 0.122 29 3.8 G_rectus 434 278 886 2.864 1.087 0.269 0.391 106 8.3 G_subcallosal 457 223 751 2.551 0.423 0.145 0.078 10 1.4 G_temp_sup-G_T_transv 1928 1210 3985 2.521 0.717 0.191 0.140 76 11.2 G_temp_sup-Lateral 663 444 1388 2.633 0.796 0.194 0.209 96 7.4 G_temp_sup-Plan_polar 776 511 1269 2.126 0.483 0.142 0.065 12 1.9 G_temp_sup-Plan_tempo 2050 1344 4726 2.599 1.001 0.236 0.203 155 14.3 G_temporal_inf 2117 1235 3937 2.350 0.871 0.194 0.214 148 22.5 G_temporal_middle 266 173 335 2.283 0.381 0.118 0.040 2 0.4 Lat_Fis-ant-Horizont 247 174 359 2.373 0.539 0.166 0.079 3 0.9 Lat_Fis-ant-Vertical 1102 746 1378 2.169 0.556 0.136 0.059 13 2.7 Lat_Fis-post 2159 1345 3197 2.216 0.657 0.195 0.118 63 11.3 Pole_occipital 1458 1069 5253 3.212 0.856 0.221 0.526 676 9.5 Pole_temporal 2752 1816 2791 1.692 0.590 0.159 0.179 53 9.2 S_calcarine 3243 2198 3593 1.877 0.667 0.166 0.094 131 13.6 S_central 974 668 1270 1.995 0.632 0.111 0.032 7 1.5 S_cingul-Marginalis 405 292 776 3.084 0.613 0.151 0.090 5 1.1 S_circular_insula_ant 1366 932 2053 2.522 0.845 0.121 0.080 35 4.6 S_circular_insula_inf 1512 1056 2290 2.628 0.612 0.126 0.051 17 3.5 S_circular_insula_sup 672 453 1176 2.517 0.819 0.163 0.065 18 2.0 S_collat_transv_ant 527 363 590 2.095 0.532 0.155 0.070 6 1.4 S_collat_transv_post 2785 1795 3316 1.959 0.561 0.155 0.072 46 9.1 S_front_inf 1255 801 1491 1.948 0.475 0.157 0.561 50 4.1 S_front_middle 2826 1823 3077 1.810 0.542 0.160 0.133 87 15.6 S_front_sup 39 25 31 1.385 0.228 0.149 0.048 0 0.1 S_interm_prim-Jensen 2470 1566 2532 1.653 0.467 0.160 0.081 45 8.6 S_intrapariet_and_P_trans 897 590 1084 1.922 0.485 0.147 0.061 11 2.3 S_oc_middle_and_Lunatus 1076 657 1260 1.924 0.594 0.162 0.094 24 4.5 S_oc_sup_and_transversal 719 449 888 2.373 0.580 0.167 0.254 41 3.5 S_occipital_ant 450 316 558 1.927 0.498 0.165 0.101 7 1.6 S_oc-temp_lat 1361 989 2041 2.313 0.623 0.169 0.072 25 4.1 S_oc-temp_med_and_Lingual 278 188 387 2.474 0.620 0.155 0.084 4 0.7 S_orbital_lateral 905 580 1416 2.574 1.155 0.154 0.091 22 3.0 S_orbital_med-olfact 1275 876 2199 2.577 0.690 0.169 0.078 21 4.1 S_orbital-H_Shaped 1842 1225 1922 1.657 0.517 0.155 0.098 61 8.8 S_parieto_occipital 1277 754 1626 2.892 1.302 0.152 0.104 89 4.9 S_pericallosal 1516 988 1770 1.901 0.566 0.143 0.060 19 3.7 S_postcentral 1722 1106 1986 1.965 0.439 0.149 0.102 52 6.9 S_precentral-inf-part 1654 1070 1996 2.411 0.461 0.161 0.089 33 6.6 S_precentral-sup-part 552 355 996 2.917 0.981 0.164 0.146 53 4.8 S_suborbital 561 334 576 1.643 0.530 0.165 0.078 20 2.0 S_subparietal 1015 669 1554 2.105 0.887 0.190 0.110 34 4.5 S_temporal_inf 3510 2317 4480 1.992 0.649 0.144 0.069 57 10.6 S_temporal_sup 397 257 465 2.149 0.528 0.146 0.063 5 1.2 S_temporal_transverse #-------------------------------------------- #@# Sphere rh Tue Jul 12 14:08:06 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.09 hours scaling brain by 0.355... pass 1: epoch 1 of 3 starting distance error %20.63 pass 1: epoch 2 of 3 starting distance error %20.56 unfolding complete - removing small folds... starting distance error %20.40 removing remaining folds... final distance error %20.44 #-------------------------------------------- #@# Surf Reg rh Tue Jul 12 15:13:47 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_register -curv ../surf/rh.sphere /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.571 curvature mean = 0.043, std = 0.937 curvature mean = 0.029, std = 0.875 curvature mean = 0.008, std = 0.968 curvature mean = 0.011, std = 0.946 curvature mean = 0.006, std = 0.981 curvature mean = 0.004, std = 0.976 curvature mean = 0.004, std = 0.985 curvature mean = 0.001, std = 0.989 curvature mean = -0.051, std = 0.548 curvature mean = 0.006, std = 0.070 curvature mean = 0.060, std = 0.200 curvature mean = 0.005, std = 0.085 curvature mean = 0.039, std = 0.300 curvature mean = 0.005, std = 0.092 curvature mean = 0.024, std = 0.386 curvature mean = 0.004, std = 0.095 curvature mean = 0.010, std = 0.477 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Jul 12 15:55:54 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Jul 12 15:55:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mrisp_paint -a 5 /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/space/plato_002/users/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Jul 12 15:56:01 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1027 labels changed using aseg relabeling using gibbs priors... 000: 2570 changed, 116754 examined... 001: 583 changed, 11056 examined... 002: 141 changed, 3238 examined... 003: 51 changed, 833 examined... 004: 21 changed, 314 examined... 005: 7 changed, 120 examined... 006: 6 changed, 47 examined... 007: 1 changed, 25 examined... 008: 1 changed, 7 examined... 009: 0 changed, 12 examined... 143 labels changed using aseg 000: 118 total segments, 79 labels (524 vertices) changed 001: 40 total segments, 1 labels (1 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1692 vertices marked for relabeling... 1692 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 57 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Jul 12 15:56:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs AD01 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... 10970 bright wm thresholded. 1109 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.orig... computing class statistics... border white: 248743 voxels (1.48%) border gray 259599 voxels (1.55%) WM (95.0): 96.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.3 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 61.0 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 76.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=82 using class modes intead of means.... mean inside = 95.9, mean outside = 83.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.01-->7.83) (max @ vno 299 --> 2907) face area 0.27 +- 0.13 (0.00-->3.60) mean absolute distance = 0.89 +- 1.15 4158 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 327 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown mean border=89.0, 508 (508) missing vertices, mean dist 0.1 [1.1 (%35.9)->0.8 (%64.1))] %30 local maxima, %64 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.28 (0.07-->7.70) (max @ vno 299 --> 2907) face area 0.27 +- 0.14 (0.00-->3.51) mean absolute distance = 0.54 +- 0.88 5244 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3428877.8, rms=7.02 001: dt: 0.5000, sse=4761059.5, rms=5.05 002: dt: 0.5000, sse=4913447.5, rms=3.91 003: dt: 0.5000, sse=5186319.0, rms=3.29 004: dt: 0.5000, sse=5252860.0, rms=2.87 005: dt: 0.5000, sse=5357253.0, rms=2.63 006: dt: 0.5000, sse=5395241.0, rms=2.53 007: dt: 0.5000, sse=5446918.0, rms=2.46 rms = 2.42, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5455361.5, rms=2.42 009: dt: 0.2500, sse=3894952.0, rms=1.94 010: dt: 0.2500, sse=3722342.8, rms=1.85 rms = 1.83, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3657640.2, rms=1.83 rms = 1.81, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3615873.8, rms=1.81 positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 38 points - only 5.26% unknown removing 2 vertex label from ripped group deleting segment 4 with 14 points - only 0.00% unknown deleting segment 6 with 206 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 131 points - only 30.53% unknown deleting segment 10 with 14 points - only 0.00% unknown mean border=90.9, 477 (265) missing vertices, mean dist -0.3 [0.7 (%61.8)->0.3 (%38.2))] %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 0.86 +- 0.27 (0.05-->7.28) (max @ vno 299 --> 2907) face area 0.32 +- 0.17 (0.00-->4.01) mean absolute distance = 0.42 +- 0.58 3904 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3865579.0, rms=3.30 013: dt: 0.5000, sse=4185955.8, rms=2.36 014: dt: 0.5000, sse=4761582.0, rms=2.09 rms = 2.08, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=4740584.5, rms=2.08 016: dt: 0.2500, sse=4152354.5, rms=1.75 017: dt: 0.2500, sse=4012557.8, rms=1.68 rms = 1.66, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3976453.0, rms=1.66 019: dt: 0.1250, sse=3932312.5, rms=1.61 rms = 1.59, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3904147.0, rms=1.59 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 50 points - only 4.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 14 points - only 0.00% unknown deleting segment 8 with 219 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 145 points - only 34.48% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown mean border=92.5, 489 (221) missing vertices, mean dist -0.2 [0.5 (%62.6)->0.3 (%37.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.86 +- 0.27 (0.04-->7.22) (max @ vno 299 --> 2907) face area 0.31 +- 0.17 (0.00-->3.97) mean absolute distance = 0.36 +- 0.47 3172 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4001028.0, rms=2.74 021: dt: 0.5000, sse=4333778.5, rms=1.89 022: dt: 0.5000, sse=4891057.5, rms=1.76 rms = 1.85, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4431279.0, rms=1.55 024: dt: 0.2500, sse=4227120.5, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... rms = 1.47, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4188801.0, rms=1.47 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 60 points - only 3.33% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 292 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown deleting segment 4 with 148 points - only 33.78% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown mean border=93.4, 536 (205) missing vertices, mean dist -0.1 [0.4 (%56.1)->0.3 (%43.9))] %72 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4210810.0, rms=1.85 026: dt: 0.5000, sse=5181921.5, rms=1.43 rms = 1.63, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4830413.0, rms=1.26 rms = 1.26, time step reduction 2 of 3 to 0.125... rms = 1.23, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4790067.5, rms=1.23 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=70.8, 461 (461) missing vertices, mean dist 2.1 [2.4 (%0.0)->2.4 (%100.0))] %44 local maxima, %40 large gradients and %11 min vals, 785 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=14190003.0, rms=23.23 001: dt: 0.5000, sse=11859767.0, rms=20.79 002: dt: 0.5000, sse=9941935.0, rms=18.55 003: dt: 0.5000, sse=8581238.0, rms=16.57 004: dt: 0.5000, sse=7783324.0, rms=14.82 005: dt: 0.5000, sse=7197922.0, rms=13.27 006: dt: 0.5000, sse=6781655.0, rms=11.88 007: dt: 0.5000, sse=6455491.0, rms=10.62 008: dt: 0.5000, sse=6192907.0, rms=9.41 009: dt: 0.5000, sse=5970331.5, rms=8.28 010: dt: 0.5000, sse=5855844.0, rms=7.28 011: dt: 0.5000, sse=5832601.0, rms=6.44 012: dt: 0.5000, sse=5799666.5, rms=5.79 013: dt: 0.5000, sse=5849949.0, rms=5.30 014: dt: 0.5000, sse=5870124.0, rms=4.96 015: dt: 0.5000, sse=5880813.5, rms=4.70 016: dt: 0.5000, sse=5900181.0, rms=4.53 017: dt: 0.5000, sse=5917720.5, rms=4.42 018: dt: 0.5000, sse=5920998.0, rms=4.34 019: dt: 0.5000, sse=5944981.5, rms=4.28 020: dt: 0.5000, sse=5959566.5, rms=4.22 rms = 4.17, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=5934343.5, rms=4.17 022: dt: 0.2500, sse=3996821.8, rms=3.36 023: dt: 0.2500, sse=3771678.2, rms=3.14 rms = 3.10, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3630768.8, rms=3.10 025: dt: 0.1250, sse=3486648.0, rms=2.99 rms = 2.98, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3458032.5, rms=2.98 positioning took 2.6 minutes mean border=67.4, 624 (62) missing vertices, mean dist 0.3 [0.2 (%33.2)->0.5 (%66.8))] %67 local maxima, %23 large gradients and % 5 min vals, 270 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=4199464.0, rms=5.81 027: dt: 0.5000, sse=4360579.0, rms=4.48 028: dt: 0.5000, sse=5297006.0, rms=4.34 rms = 4.36, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4395995.5, rms=3.59 030: dt: 0.2500, sse=4049385.2, rms=3.26 031: dt: 0.2500, sse=3985025.0, rms=3.17 032: dt: 0.2500, sse=3952497.2, rms=3.11 rms = 3.08, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3946805.2, rms=3.08 034: dt: 0.1250, sse=3825322.5, rms=2.96 rms = 2.93, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3807559.5, rms=2.93 positioning took 1.0 minutes mean border=65.7, 855 (46) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.3 (%63.4))] %73 local maxima, %16 large gradients and % 5 min vals, 290 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=3954045.0, rms=3.81 rms = 3.98, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3822820.8, rms=3.29 037: dt: 0.2500, sse=3840469.8, rms=3.00 038: dt: 0.2500, sse=3960102.8, rms=2.91 rms = 2.87, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3975267.5, rms=2.87 040: dt: 0.1250, sse=3869279.2, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3861913.8, rms=2.74 positioning took 0.6 minutes mean border=65.0, 1424 (43) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.3 (%56.0))] %75 local maxima, %14 large gradients and % 5 min vals, 260 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/AD01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3881526.2, rms=2.92 rms = 3.38, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=3831360.8, rms=2.71 043: dt: 0.2500, sse=3948796.0, rms=2.64 rms = 2.64, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4003365.0, rms=2.64 045: dt: 0.1250, sse=3932530.8, rms=2.55 rms = 2.52, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=3928178.5, rms=2.52 positioning took 0.5 minutes writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.area.pial vertex spacing 0.96 +- 0.43 (0.03-->9.78) (max @ vno 90117 --> 89309) face area 0.37 +- 0.30 (0.00-->9.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 116754 vertices processed 25000 of 116754 vertices processed 50000 of 116754 vertices processed 75000 of 116754 vertices processed 100000 of 116754 vertices processed 0 of 116754 vertices processed 25000 of 116754 vertices processed 50000 of 116754 vertices processed 75000 of 116754 vertices processed 100000 of 116754 vertices processed thickness calculation complete, 776:1368 truncations. 49285 vertices at 0 distance 64138 vertices at 1 distance 57800 vertices at 2 distance 29977 vertices at 3 distance 12429 vertices at 4 distance 4732 vertices at 5 distance 1930 vertices at 6 distance 844 vertices at 7 distance 444 vertices at 8 distance 296 vertices at 9 distance 181 vertices at 10 distance 116 vertices at 11 distance 104 vertices at 12 distance 73 vertices at 13 distance 63 vertices at 14 distance 49 vertices at 15 distance 36 vertices at 16 distance 25 vertices at 17 distance 19 vertices at 18 distance 19 vertices at 19 distance 24 vertices at 20 distance writing curvature file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.thickness positioning took 10.7 minutes #-------------------------------------------- #@# Surf Volume rh Tue Jul 12 16:07:40 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Tue Jul 12 16:07:42 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab AD01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 838 542 1400 2.515 0.815 0.151 0.067 19 2.4 bankssts 876 549 1854 3.169 0.790 0.146 0.047 21 1.7 caudalanteriorcingulate 3559 2109 5512 2.341 0.585 0.160 0.184 270 21.0 caudalmiddlefrontal 1747 1093 2552 2.128 0.638 0.184 0.276 71 9.5 cuneus 562 351 1968 3.202 1.044 0.195 0.136 21 3.2 entorhinal 3643 2337 6136 2.343 0.688 0.172 0.197 207 17.6 fusiform 4901 3103 7783 2.207 0.658 0.172 0.117 196 23.9 inferiorparietal 3065 1963 5915 2.488 0.924 0.177 0.128 181 13.6 inferiortemporal 1356 837 1805 2.068 0.724 0.178 0.160 45 6.7 isthmuscingulate 7075 4437 11540 2.338 0.705 0.185 0.216 645 39.2 lateraloccipital 3426 2136 5898 2.415 0.926 0.180 0.369 210 14.7 lateralorbitofrontal 4257 2642 5449 1.883 0.542 0.177 0.142 127 21.3 lingual 2323 1481 3960 2.210 0.879 0.182 0.189 170 24.4 medialorbitofrontal 3571 2336 7948 2.585 0.760 0.172 0.266 287 16.6 middletemporal 789 522 1369 2.209 0.689 0.133 0.081 11 3.2 parahippocampal 2185 1246 3423 2.634 0.647 0.165 1.684 165 16.2 paracentral 2440 1523 4092 2.340 0.605 0.169 0.142 269 13.1 parsopercularis 962 605 1965 2.454 0.728 0.190 0.361 268 4.6 parsorbitalis 1670 1064 2913 2.452 0.600 0.178 0.148 67 10.3 parstriangularis 1760 1115 1915 1.801 0.546 0.196 0.222 407 15.1 pericalcarine 4911 2997 6899 2.080 0.743 0.154 0.102 161 19.8 postcentral 1339 807 2369 2.724 0.775 0.162 0.103 54 4.2 posteriorcingulate 7612 4631 11666 2.423 0.713 0.165 0.832 1296 50.1 precentral 4647 2824 6316 2.092 0.607 0.153 0.117 158 21.3 precuneus 670 397 1717 3.488 0.927 0.146 0.065 11 1.8 rostralanteriorcingulate 7049 4253 10709 2.216 0.593 0.175 0.238 306 41.1 rostralmiddlefrontal 10679 6261 16917 2.487 0.673 0.180 0.223 871 81.0 superiorfrontal 8153 4804 11414 2.093 0.590 0.174 0.259 577 55.7 superiorparietal 3942 2631 7212 2.344 0.616 0.152 0.171 141 15.3 superiortemporal 4165 2613 7024 2.452 0.648 0.156 0.087 84 15.0 supramarginal 400 235 665 2.251 0.923 0.200 0.124 13 2.1 frontalpole 635 416 2407 3.614 0.882 0.183 0.115 18 2.9 temporalpole 514 293 877 2.454 0.454 0.158 0.113 22 2.6 transversetemporal 3421 2162 7136 3.116 0.992 0.170 0.219 453 23.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Jul 12 16:07:58 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 AD01 rh ../surf/rh.sphere.reg /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /autofs/space/plato_002/users/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 11 labels changed using aseg relabeling using gibbs priors... 000: 8633 changed, 116754 examined... 001: 2076 changed, 33079 examined... 002: 647 changed, 10744 examined... 003: 292 changed, 3620 examined... 004: 142 changed, 1635 examined... 005: 57 changed, 781 examined... 006: 29 changed, 337 examined... 007: 19 changed, 156 examined... 008: 18 changed, 114 examined... 009: 5 changed, 88 examined... 010: 2 changed, 34 examined... 011: 0 changed, 9 examined... 3 labels changed using aseg 000: 300 total segments, 215 labels (2342 vertices) changed 001: 100 total segments, 15 labels (82 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 112 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1310 vertices marked for relabeling... 1310 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 59 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jul 12 16:08:57 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab AD01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/wm.mgz... reading input surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... reading input pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial... reading input white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1082 639 1574 2.194 0.703 0.180 0.102 25 4.8 G_and_S_frontomargin 1510 934 2575 2.274 0.692 0.180 0.172 169 9.0 G_and_S_occipital_inf 1119 622 1415 2.075 0.634 0.185 3.193 106 10.7 G_and_S_paracentral 1284 826 2672 2.911 0.736 0.178 0.102 28 5.4 G_and_S_subcentral 834 479 1485 2.300 0.660 0.183 0.152 40 5.5 G_and_S_transv_frontopol 2070 1286 3878 2.672 0.882 0.141 0.066 31 5.5 G_and_S_cingul-Ant 1284 822 2669 2.946 0.705 0.157 0.068 33 3.4 G_and_S_cingul-Mid-Ant 1451 882 2577 2.719 0.682 0.162 0.109 72 6.1 G_and_S_cingul-Mid-Post 430 261 936 2.685 0.789 0.204 0.130 14 2.3 G_cingul-Post-dorsal 244 132 412 2.260 0.652 0.196 0.386 13 1.5 G_cingul-Post-ventral 1644 979 2291 2.059 0.658 0.191 0.291 73 9.2 G_cuneus 1470 894 3087 2.601 0.642 0.183 0.173 253 9.3 G_front_inf-Opercular 348 213 727 2.638 0.567 0.207 0.192 16 3.0 G_front_inf-Orbital 985 594 1963 2.624 0.561 0.204 0.203 55 8.4 G_front_inf-Triangul 3637 1987 5944 2.312 0.608 0.185 0.396 327 30.5 G_front_middle 7335 4071 12015 2.529 0.698 0.202 0.284 710 71.6 G_front_sup 616 365 1507 3.251 0.889 0.209 0.244 69 7.5 G_Ins_lg_and_S_cent_ins 532 331 1617 3.417 1.058 0.232 0.315 35 5.8 G_insular_short 1395 865 3187 2.874 0.665 0.205 0.196 161 10.4 G_occipital_middle 2002 1097 2880 2.167 0.559 0.194 0.287 186 27.2 G_occipital_sup 1532 936 2607 2.284 0.626 0.190 0.245 144 10.2 G_oc-temp_lat-fusifor 2747 1668 3853 1.920 0.585 0.190 0.180 88 15.9 G_oc-temp_med-Lingual 1291 818 3201 3.074 1.015 0.167 0.777 376 6.3 G_oc-temp_med-Parahip 2466 1470 4819 2.405 0.954 0.196 0.233 341 14.0 G_orbital 2150 1320 4165 2.406 0.686 0.194 0.156 95 15.7 G_pariet_inf-Angular 1926 1147 3957 2.724 0.579 0.166 0.098 44 7.6 G_pariet_inf-Supramar 2793 1588 4062 2.135 0.600 0.173 0.151 172 14.9 G_parietal_sup 1845 1020 2724 2.094 0.598 0.174 0.147 119 10.3 G_postcentral 3055 1639 4830 2.413 0.767 0.190 1.956 1222 32.1 G_precentral 2250 1277 3204 2.109 0.599 0.161 0.135 108 11.9 G_precuneus 711 431 1450 2.383 0.919 0.169 0.118 20 2.4 G_rectus 297 198 543 2.597 1.164 0.356 0.874 129 17.7 G_subcallosal 369 199 721 2.638 0.408 0.163 0.130 21 2.1 G_temp_sup-G_T_transv 1492 953 3522 2.652 0.582 0.205 0.376 110 10.6 G_temp_sup-Lateral 378 264 970 3.048 0.913 0.139 0.084 11 1.3 G_temp_sup-Plan_polar 425 283 692 2.189 0.520 0.122 0.042 4 0.7 G_temp_sup-Plan_tempo 1544 951 3212 2.581 1.095 0.191 0.136 58 7.7 G_temporal_inf 2421 1530 5965 2.749 0.726 0.188 0.124 87 13.3 G_temporal_middle 248 173 341 2.187 0.545 0.140 0.057 3 0.6 Lat_Fis-ant-Horizont 164 116 207 2.148 0.533 0.122 0.042 1 0.3 Lat_Fis-ant-Vertical 1383 886 1686 2.196 0.591 0.130 0.066 25 3.7 Lat_Fis-post 3265 2109 5043 2.196 0.680 0.202 0.163 271 20.2 Pole_occipital 1977 1264 5753 3.037 0.852 0.201 0.171 181 12.4 Pole_temporal 2309 1445 2383 1.880 0.553 0.182 0.182 421 17.3 S_calcarine 2668 1760 3219 2.063 0.786 0.138 0.056 26 6.5 S_central 1262 812 1856 2.420 0.706 0.128 0.047 14 2.5 S_cingul-Marginalis 373 241 657 2.933 0.703 0.178 0.120 10 1.5 S_circular_insula_ant 1223 862 2095 2.705 0.965 0.106 0.041 8 2.1 S_circular_insula_inf 1168 762 1793 2.735 0.553 0.125 0.071 17 4.5 S_circular_insula_sup 731 503 1201 2.218 0.793 0.144 0.053 10 1.8 S_collat_transv_ant 540 347 547 2.013 0.636 0.162 0.074 8 1.8 S_collat_transv_post 1658 1085 2575 2.256 0.562 0.154 0.065 24 4.5 S_front_inf 1647 1059 2371 2.224 0.635 0.166 0.167 54 7.5 S_front_middle 2827 1793 3721 2.229 0.560 0.142 0.159 229 14.1 S_front_sup 312 208 345 1.814 0.403 0.143 0.059 3 0.8 S_interm_prim-Jensen 3037 1906 4105 2.080 0.567 0.158 0.356 197 11.0 S_intrapariet_and_P_trans 784 505 981 1.978 0.496 0.147 0.057 9 2.0 S_oc_middle_and_Lunatus 1440 922 1936 2.068 0.573 0.152 0.427 152 4.7 S_oc_sup_and_transversal 540 355 635 2.177 0.443 0.154 0.066 7 1.5 S_occipital_ant 525 333 976 2.630 0.635 0.169 0.399 14 1.9 S_oc-temp_lat 1617 1101 2021 2.040 0.541 0.123 0.042 14 2.9 S_oc-temp_med_and_Lingual 314 207 382 2.013 0.471 0.154 0.055 4 0.7 S_orbital_lateral 672 473 944 1.956 1.000 0.132 0.049 8 1.2 S_orbital_med-olfact 1591 1015 2404 2.260 0.714 0.174 0.242 89 6.4 S_orbital-H_Shaped 1222 817 1624 2.023 0.555 0.133 0.051 16 2.5 S_parieto_occipital 1579 942 1844 2.454 0.957 0.150 0.090 40 5.3 S_pericallosal 2042 1328 2549 1.984 0.547 0.144 0.069 34 6.2 S_postcentral 2202 1420 3055 2.279 0.545 0.145 0.087 36 9.6 S_precentral-inf-part 1599 1044 2074 2.243 0.563 0.157 0.123 71 9.3 S_precentral-sup-part 277 188 351 1.892 0.601 0.133 0.049 3 0.5 S_suborbital 771 492 1203 2.145 0.825 0.154 0.152 21 4.8 S_subparietal 595 409 795 2.224 0.564 0.130 0.049 6 1.4 S_temporal_inf 3321 2269 4783 2.132 0.678 0.141 0.231 231 8.1 S_temporal_sup 295 191 361 1.949 0.520 0.133 0.039 2 0.6 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 12 16:09:17 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AD01 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 = 0 writing volume /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Jul 12 16:19:39 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD01 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /autofs/space/plato_002/users/freesurfer/ASegStatsLUT.txt --subject AD01 sysname Linux hostname compute-0-60 machine x86_64 user fdu0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 195846 rh white matter volume 181785 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 224989.173834, pTot = 390891.538501 c = 165902.364668 rh surface-based volumes (mm3): wTot = 205541.309966, pTot = 382658.264416 c = 177116.954451 Computing SupraTentVolCor SupraTentVolCor = 54454.000 SupraTentVol = 828003.803 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 16925 16925 4 5 Left-Inf-Lat-Vent 1092 1092 5 7 Left-Cerebellum-White-Matter 12121 12121 6 8 Left-Cerebellum-Cortex 46991 46991 7 10 Left-Thalamus-Proper 5656 5656 8 11 Left-Caudate 2902 2902 9 12 Left-Putamen 4883 4883 10 13 Left-Pallidum 1619 1619 11 14 3rd-Ventricle 1695 1695 12 15 4th-Ventricle 1572 1572 13 16 Brain-Stem 20901 20901 14 17 Left-Hippocampus 3352 3352 15 18 Left-Amygdala 1232 1232 16 24 CSF 1828 1828 17 26 Left-Accumbens-area 295 295 18 28 Left-VentralDC 3232 3232 19 30 Left-vessel 13 13 20 31 Left-choroid-plexus 2407 2407 23 43 Right-Lateral-Ventricle 12572 12572 24 44 Right-Inf-Lat-Vent 491 491 25 46 Right-Cerebellum-White-Matter 11228 11228 26 47 Right-Cerebellum-Cortex 46619 46619 27 49 Right-Thalamus-Proper 6077 6077 28 50 Right-Caudate 3172 3172 29 51 Right-Putamen 4148 4148 30 52 Right-Pallidum 1430 1430 31 53 Right-Hippocampus 3492 3492 32 54 Right-Amygdala 1119 1119 33 58 Right-Accumbens-area 316 316 34 60 Right-VentralDC 3333 3333 35 62 Right-vessel 7 7 36 63 Right-choroid-plexus 2437 2437 37 72 5th-Ventricle 0 38 77 WM-hypointensities 2940 2940 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 21 21 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 276 276 45 251 CC_Posterior 604 604 46 252 CC_Mid_Posterior 353 353 47 253 CC_Central 452 452 48 254 CC_Mid_Anterior 388 388 49 255 CC_Anterior 704 704 Reporting on 45 segmentations SubCortGrayVol = 160769 #----------------------------------------- #@# AParc-to-ASeg Tue Jul 12 16:30:11 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 335779 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --volmask --a2009s SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc subject AD01 outvol /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/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/AD01/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 335779 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Jul 12 16:32:43 EDT 2016 /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_aparc2aseg --s AD01 --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 AD01 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/AD01/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.white Reading lh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/lh.pial Loading lh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.white Reading rh pial surface /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/surf/rh.pial Loading rh annotations from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/ribbon.mgz Loading filled from /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7851 vertices from left hemi Ripped 7612 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/AD01/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 692247 Used brute-force search on 63 voxels Fixing Parahip LH WM Found 5 clusters 0 k 978.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 2.000000 Fixing Parahip RH WM Found 7 clusters 0 k 1.000000 1 k 1095.000000 2 k 1.000000 3 k 6.000000 4 k 2.000000 5 k 2.000000 6 k 5.000000 Writing output aseg to mri/wmparc.mgz /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD01 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject AD01 --surf-wm-vol --ctab /autofs/space/plato_002/users/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-60 machine x86_64 user fdu0 atlas_icv (eTIV) = 1321820 mm^3 (det: 1.473805 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 195846 rh white matter volume 181785 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1362929 # brainmaskvolume 1362929.0 # nbrainsegvoxels 225779 # brainsegvolume 225779.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 1939 1939 2 3002 wm-lh-caudalanteriorcingulate 2819 2819 3 3003 wm-lh-caudalmiddlefrontal 6146 6146 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2128 2128 6 3006 wm-lh-entorhinal 706 706 7 3007 wm-lh-fusiform 4735 4735 8 3008 wm-lh-inferiorparietal 6394 6394 9 3009 wm-lh-inferiortemporal 4288 4288 10 3010 wm-lh-isthmuscingulate 3170 3170 11 3011 wm-lh-lateraloccipital 9842 9842 12 3012 wm-lh-lateralorbitofrontal 5607 5607 13 3013 wm-lh-lingual 5970 5970 14 3014 wm-lh-medialorbitofrontal 3809 3809 15 3015 wm-lh-middletemporal 3154 3154 16 3016 wm-lh-parahippocampal 1102 1102 17 3017 wm-lh-paracentral 3258 3258 18 3018 wm-lh-parsopercularis 3788 3788 19 3019 wm-lh-parsorbitalis 726 726 20 3020 wm-lh-parstriangularis 2828 2828 21 3021 wm-lh-pericalcarine 2916 2916 22 3022 wm-lh-postcentral 5800 5800 23 3023 wm-lh-posteriorcingulate 3650 3650 24 3024 wm-lh-precentral 13678 13678 25 3025 wm-lh-precuneus 6146 6146 26 3026 wm-lh-rostralanteriorcingulate 2223 2223 27 3027 wm-lh-rostralmiddlefrontal 10660 10660 28 3028 wm-lh-superiorfrontal 15212 15212 29 3029 wm-lh-superiorparietal 10631 10631 30 3030 wm-lh-superiortemporal 6150 6150 31 3031 wm-lh-supramarginal 5488 5488 32 3032 wm-lh-frontalpole 273 273 33 3033 wm-lh-temporalpole 703 703 34 3034 wm-lh-transversetemporal 575 575 35 3035 wm-lh-insula 7676 7676 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 1660 1660 120 4002 wm-rh-caudalanteriorcingulate 2392 2392 121 4003 wm-rh-caudalmiddlefrontal 5179 5179 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1691 1691 124 4006 wm-rh-entorhinal 531 531 125 4007 wm-rh-fusiform 4565 4565 126 4008 wm-rh-inferiorparietal 7060 7060 127 4009 wm-rh-inferiortemporal 4483 4483 128 4010 wm-rh-isthmuscingulate 2886 2886 129 4011 wm-rh-lateraloccipital 8500 8500 130 4012 wm-rh-lateralorbitofrontal 5316 5316 131 4013 wm-rh-lingual 4418 4418 132 4014 wm-rh-medialorbitofrontal 2743 2743 133 4015 wm-rh-middletemporal 3735 3735 134 4016 wm-rh-parahippocampal 1220 1220 135 4017 wm-rh-paracentral 3197 3197 136 4018 wm-rh-parsopercularis 3295 3295 137 4019 wm-rh-parsorbitalis 975 975 138 4020 wm-rh-parstriangularis 2348 2348 139 4021 wm-rh-pericalcarine 2261 2261 140 4022 wm-rh-postcentral 5014 5014 141 4023 wm-rh-posteriorcingulate 3259 3259 142 4024 wm-rh-precentral 12999 12999 143 4025 wm-rh-precuneus 7056 7056 144 4026 wm-rh-rostralanteriorcingulate 1654 1654 145 4027 wm-rh-rostralmiddlefrontal 8907 8907 146 4028 wm-rh-superiorfrontal 14373 14373 147 4029 wm-rh-superiorparietal 9476 9476 148 4030 wm-rh-superiortemporal 4624 4624 149 4031 wm-rh-supramarginal 6188 6188 150 4032 wm-rh-frontalpole 316 316 151 4033 wm-rh-temporalpole 566 566 152 4034 wm-rh-transversetemporal 540 540 153 4035 wm-rh-insula 7824 7824 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 23235 23235 237 5002 Right-UnsegmentedWhiteMatter 23441 23441 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/AD01/label #-------------------------------------------- #@# BA Labels lh Tue Jul 12 16:51:04 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label --trgsubject AD01 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srclabel = /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = AD01 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc FREESURFER_HOME /autofs/space/plato_002/users/freesurfer Loading source label. Invalid argument ERROR reading /autofs/cluster/sperling/Centiloid_New/50-70_Data/FreeSurferProc/fsaverage/label/lh.BA1.label Linux compute-0-60 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AD01 exited with ERRORS at Tue Jul 12 16:51:04 EDT 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting