Sun Dec 20 20:04:09 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/recon-all -s MRM_003_w_070655_171011_0000FD62 -i /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE00C688 -all -hippocampal-subfields-T1 -brainstem-structures subjid MRM_003_w_070655_171011_0000FD62 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Actual FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 122880 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 27033600 kbytes descriptors 1024 memorylocked 301989888 kbytes maxproc 191984 total used free shared buffers cached Mem: 24594348 3049952 21544396 0 124188 279100 -/+ buffers/cache: 2646664 21947684 Swap: 50331640 52972 50278668 ######################################## program versions used $Id: recon-all,v 1.515.2.24 2015/10/01 21:23:52 greve 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: $ TimeStamp: 2015/12/20-20:04:09-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.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: 2015/12/20-20:04:11-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/20-20:04:11-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize.c,v 1.84.2.1 2015/08/13 17:12:10 zkaufman Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:12-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_watershed.cpp,v 1.100.2.1 2015/07/10 18:57:54 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:12-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:12-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:13-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:13-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_em_register.c,v 1.101.2.1 2015/06/24 20:18:26 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:14-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_normalize.c,v 1.62.2.1 2015/06/24 20:18:24 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:14-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_register.c,v 1.92.2.1 2015/06/24 20:18:25 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:14-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_label.c,v 1.108 2014/11/24 20:09:20 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:15-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:15-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_concatenate_lta.c,v 1.13.2.2 2015/08/19 16:36:35 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:17-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:17-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:17-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:18-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:18-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:19-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:19-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:19-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/20-20:04:20-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_make_surfaces.c,v 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:20-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:21-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:21-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_anatomical_stats.c,v 1.76.2.2 2015/07/06 21:59:22 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature_stats.c,v 1.64.4.1 2015/06/04 21:12:38 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_calc.c,v 1.51.2.2 2015/06/04 21:12:37 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:25-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2015/12/20-20:04:25-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_relabel_hypointensities.c,v 1.11.2.1 2015/05/15 18:45:54 nicks Exp $ User: s1158296 Machine: eddie423 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_convert /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE00C688 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig/001.mgz mri_convert /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE00C688 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig/001.mgz $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE00C688... Getting Series No INFO: Found 162 files in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62 INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 19 INFO: sorting. WARNING: file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE282DA4 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (240 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW FileName /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/AD_MRM_3D_T1_MRI/MRM_003_w_070655_171011_0000FD62/EE282DA4 Identification NumarisVer syngo MR B18P ScannerModel Biograph_mMR PatientName Anonymous Female 1955 Date and time StudyDate 20111017 StudyTime 132631.000000 SeriesTime 134535.921000 AcqTime 134032.085000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol anonymous PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.98 InversionTime 900 RepetitionTime 2300 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 19 SeriesNo 20 ImageNo 1 NImageRows 256 NImageCols 240 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 68.8477 146.3787 123.0421 VolRes 1.0000 1.0000 1.0000 VolDim 240 256 160 Vc 0.0802 -0.9968 -0.0000 Vr -0.0365 -0.0029 -0.9993 Vs -0.9961 -0.0801 0.0366 VolCenter -5.8922 19.9798 -1.9430 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (0.0801721, -0.996781, -9.71902e-09) j_ras = (-0.0364963, -0.00293542, -0.99933) k_ras = (-0.996113, -0.0801183, 0.0366141) writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Dec 20 20:04:44 GMT 2015 Found 1 runs /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig/001.mgz /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_convert /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz --conform mri_convert /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz --conform $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (0.0801721, -0.996781, -9.71902e-09) j_ras = (-0.0364963, -0.00293542, -0.99933) k_ras = (-0.996113, -0.0801183, 0.0366141) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz... mri_add_xform_to_header -c /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/talairach.xfm /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Dec 20 20:04:55 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 nIters 1 $Id: mri_nu_correct.mni,v 1.20.2.3 2015/06/18 00:23:55 nicks Exp $ Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux Sun Dec 20 20:04:55 GMT 2015 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 tmpdir is ./tmp.mri_nu_correct.mni.23112 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23112/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23112/nu0.mnc -odt float $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from orig.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, -7.45058e-09, 3.72529e-09) j_ras = (-3.72529e-09, 0, -1) k_ras = (0, 1, 2.32831e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.23112/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Dec 20 20:04:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.23112/nu0.mnc ./tmp.mri_nu_correct.mni.23112/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23112/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 [s1158296@eddie423:/exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/] [2015-12-20 20:04:57] running: /exports/work/mcm_cric_nas/Kaiming/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 2 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23112/0/ ./tmp.mri_nu_correct.mni.23112/nu0.mnc ./tmp.mri_nu_correct.mni.23112/nu1.imp Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done 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Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Number of iterations: 87 CV of field change: 9.92174e-05 mri_convert ./tmp.mri_nu_correct.mni.23112/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.23112/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from ./tmp.mri_nu_correct.mni.23112/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.45058e-09, 3.72529e-09) j_ras = (-3.72529e-09, 0, -1) k_ras = (0, 1, 2.32831e-10) 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... Sun Dec 20 20:10:54 GMT 2015 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... cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Dec 20 20:11:37 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7887, pval=0.8469 >= threshold=0.0050) awk -f /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/extract_talairach_avi_QA.awk /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/talairach_avi.log tal_QC_AZS /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/talairach_avi.log TalAviQA: 0.97543 z-score: 0 #-------------------------------------------- #@# Intensity Normalization Sun Dec 20 20:11:37 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_normalize -g 1 orig_nu.mgz T1.mgz using max gradient = 1.000 reading from orig_nu.mgz... normalizing image... talairach transform 1.02530 0.09862 -0.07282 4.49567; -0.04698 1.08642 0.19528 -33.14877; 0.06669 -0.22801 1.21864 -22.71928; 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 = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 69 (69), valley at 36 (36) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 36 (36) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 27 seconds. #-------------------------------------------- #@# Skull Stripping Sun Dec 20 20:14:05 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_em_register -skull orig_nu.mgz /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_withskull_2014-08-21.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 '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'orig_nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (46, 18, 31) --> (208, 255, 225) using (100, 97, 128) as brain centroid... mean wm in atlas = 118, using box (80,68,104) --> (119, 126,151) to find MRI wm before smoothing, mri peak at 136 after smoothing, mri peak at 137, scaling input intensities by 0.861 scaling channel 0 by 0.861314 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.477043 @ (9.091, 9.091, -9.091) max log p = -4.381739 @ (-4.545, 4.545, -4.545) max log p = -4.334674 @ (-6.818, 2.273, 6.818) max log p = -4.318799 @ (1.136, 1.136, 1.136) max log p = -4.316393 @ (0.568, 0.568, -0.568) max log p = -4.316106 @ (0.284, -0.852, 0.284) Found translation: (-0.3, 16.8, -6.0): log p = -4.316 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.3 (thresh=-4.3) 1.04563 -0.11969 -0.15460 24.89130; 0.15998 1.21794 0.13910 -36.14070; 0.15011 -0.14882 1.13041 -23.50506; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.04563 -0.11969 -0.15460 24.89130; 0.15998 1.21794 0.13910 -36.14070; 0.15011 -0.14882 1.13041 -23.50506; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.07845 -0.04377 -0.10869 9.32192; 0.10231 1.26284 0.19275 -39.54340; 0.10549 -0.17455 1.08805 -12.22201; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07845 -0.04377 -0.10869 9.32192; 0.10231 1.26284 0.19275 -39.54340; 0.10549 -0.17455 1.08805 -12.22201; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07667 -0.05267 -0.11918 11.68746; 0.11100 1.26097 0.19156 -40.76248; 0.11402 -0.17449 1.08458 -13.35989; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.8 (old=-4.7) transform before final EM align: 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.07667 -0.05267 -0.11918 11.68746; 0.11061 1.25654 0.19088 -40.17142; 0.11389 -0.17429 1.08331 -13.21691; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 55 seconds. mri_watershed -T1 -brain_atlas /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=96 z=118 r=88 first estimation of the main basin volume: 2950731 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=148, y=94, z=77, Imax=255 CSF=17, 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=12609463440 voxels, voxel volume =1.000 = 12609463440 mmm3 = 12609463.296 cm3 done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=125,y=101, z=113, r=9456 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=9, CSF_MAX=37 , nb = 44864 RIGHT_CER CSF_MIN=1, CSF_intensity=9, CSF_MAX=33 , nb = -1039664033 LEFT_CER CSF_MIN=0, CSF_intensity=11, CSF_MAX=45 , nb = 1082819751 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=39 , nb = -1067161667 LEFT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=34 , nb = 1076466468 OTHER CSF_MIN=0, CSF_intensity=5, CSF_MAX=21 , nb = 1073089220 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 37, 32, 24, 71 after analyzing : 25, 32, 32, 41 RIGHT_CER before analyzing : 33, 39, 48, 81 after analyzing : 33, 45, 48, 54 LEFT_CER before analyzing : 45, 46, 47, 75 after analyzing : 45, 46, 47, 53 RIGHT_BRAIN before analyzing : 39, 33, 25, 71 after analyzing : 26, 33, 33, 42 LEFT_BRAIN before analyzing : 34, 30, 23, 69 after analyzing : 24, 30, 30, 39 OTHER before analyzing : 21, 20, 19, 40 after analyzing : 20, 23, 25, 27 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 66.893, std = 6.947 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.68, sigma = 5.41 after rotation: sse = 3.68, sigma = 5.41 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.24, its var is 5.22 before Erosion-Dilatation 1.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...38 iterations mri_strip_skull: done peeling brain Brain Size = 1437480 voxels, voxel volume = 1.000 mm3 = 1437480 mmm3 = 1437.480 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Dec 20 20:32:27 GMT 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 nIters 1 $Id: mri_nu_correct.mni,v 1.20.2.3 2015/06/18 00:23:55 nicks Exp $ Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux Sun Dec 20 20:32:27 GMT 2015 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 tmpdir is ./tmp.mri_nu_correct.mni.24639 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24639/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24639/nu0.mnc -odt float $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from orig.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, -7.45058e-09, 3.72529e-09) j_ras = (-3.72529e-09, 0, -1) k_ras = (0, 1, 2.32831e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24639/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Dec 20 20:32:29 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.24639/nu0.mnc ./tmp.mri_nu_correct.mni.24639/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24639/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 [s1158296@eddie423:/exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/] [2015-12-20 20:32:29] running: /exports/work/mcm_cric_nas/Kaiming/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 2 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24639/0/ 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Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Number of iterations: 87 CV of field change: 9.92174e-05 mri_binarize --i ./tmp.mri_nu_correct.mni.24639/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24639/ones.mgz $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24639/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24639/ones.mgz sysname Linux hostname eddie423 machine x86_64 user s1158296 input ./tmp.mri_nu_correct.mni.24639/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24639/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.24639/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24639/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24639/input.mean.dat $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24639/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24639/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24639/input.mean.dat sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24639/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.24639/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24639/ones.mgz --i ./tmp.mri_nu_correct.mni.24639/nu1.mnc --sum ./tmp.mri_nu_correct.mni.24639/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24639/output.mean.dat $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24639/ones.mgz --i ./tmp.mri_nu_correct.mni.24639/nu1.mnc --sum ./tmp.mri_nu_correct.mni.24639/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24639/output.mean.dat sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24639/ones.mgz Loading ./tmp.mri_nu_correct.mni.24639/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.24639/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.24639/nu1.mnc ./tmp.mri_nu_correct.mni.24639/nu1.mnc mul 1.00870564422177812128 Saving result to './tmp.mri_nu_correct.mni.24639/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.24639/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24639/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from ./tmp.mri_nu_correct.mni.24639/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -7.45058e-09, 3.72529e-09) j_ras = (-3.72529e-09, 0, -1) k_ras = (0, 1, 2.32831e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 8, 121) to ( 3, 110) Sun Dec 20 20:38:56 GMT 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #------------------------------------- #@# EM Registration Sun Dec 20 20:38:57 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.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 '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca'... average std = 7.4 using min determinant for regularization = 5.4 0 singular and 937 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.2 or > 452.2 total sample mean = 78.8 (1019 zeros) ************************************************ spacing=8, using 2854 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2854, passno 0, spacing 8 resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (58, 42, 40) --> (194, 152, 199) using (103, 79, 120) as brain centroid... mean wm in atlas = 105, using box (86,66,100) --> (119, 92,139) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 0.991 scaling channel 0 by 0.990566 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.093777 @ (-9.091, 27.273, -9.091) max log p = -3.843191 @ (13.636, -13.636, -4.545) max log p = -3.806953 @ (-2.273, 6.818, 2.273) max log p = -3.761224 @ (-1.136, -5.682, -1.136) max log p = -3.761224 @ (0.000, 0.000, 0.000) max log p = -3.757277 @ (-1.420, 0.284, 0.284) Found translation: (-0.3, 15.1, -12.2): log p = -3.757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8) 0.98296 -0.13372 -0.15102 33.90000; 0.13912 1.21183 0.16189 -36.77850; 0.14032 -0.11896 1.06209 -17.49685; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.98296 -0.13372 -0.15102 33.90000; 0.13912 1.21183 0.16189 -36.77850; 0.14032 -0.11896 1.06209 -17.49685; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.01238 -0.06283 -0.10062 17.46450; 0.08452 1.23112 0.24030 -40.54432; 0.09950 -0.18735 1.03343 -4.16591; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97442 -0.06048 -0.09684 21.59921; 0.08452 1.23112 0.24030 -40.54432; 0.10323 -0.19438 1.07218 -8.31024; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97442 -0.06048 -0.09684 21.59921; 0.08452 1.23112 0.24030 -40.54432; 0.10323 -0.19438 1.07218 -8.31024; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97672 -0.06071 -0.09679 21.32567; 0.08458 1.23257 0.24054 -40.72405; 0.10261 -0.19373 1.06844 -7.87333; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97550 -0.07959 -0.10932 24.78552; 0.09884 1.23444 0.22127 -40.53741; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2854 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; nsamples 2854 Quasinewton: input matrix 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.3 (old=-4.3) transform before final EM align: 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314792 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; nsamples 314792 Quasinewton: input matrix 0.97550 -0.07959 -0.10932 24.78552; 0.09919 1.23878 0.22205 -41.10395; 0.11183 -0.17382 1.07015 -11.22433; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 012: -log(p) = 3.8 after pass:transform: ( 0.98, -0.08, -0.11, 24.79) ( 0.10, 1.24, 0.22, -41.10) ( 0.11, -0.17, 1.07, -11.22) dfp_em_step_func: 013: -log(p) = 3.8 after pass:transform: ( 0.98, -0.08, -0.11, 24.79) ( 0.10, 1.24, 0.22, -41.10) ( 0.11, -0.17, 1.07, -11.22) dfp_em_step_func: 014: -log(p) = 3.8 after pass:transform: ( 0.98, -0.08, -0.11, 24.79) ( 0.10, 1.24, 0.22, -41.10) ( 0.11, -0.17, 1.07, -11.22) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 016: -log(p) = 3.8 tol 0.000000 final transform: 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10395; 0.11181 -0.17378 1.07020 -11.22433; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 58 seconds. #-------------------------------------- #@# CA Normalize Sun Dec 20 21:00:56 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.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 '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=20.0 skull bounding box = (58, 42, 40) --> (194, 152, 199) using (103, 79, 120) as brain centroid... mean wm in atlas = 105, using box (86,66,100) --> (119, 92,139) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 0.991 scaling channel 0 by 0.990566 using 245868 sample points... INFO: compute sample coordinates transform 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10395; 0.11181 -0.17378 1.07020 -11.22433; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (118, 46, 40) --> (193, 136, 192) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 220.0 1 of 130 (0.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (59, 48, 44) --> (130, 140, 194) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 220.0 0 of 134 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (125, 118, 64) --> (176, 150, 113) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 220.0 0 of 13 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (81, 119, 67) --> (125, 154, 118) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 220.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (110, 108, 97) --> (146, 164, 126) Brain_Stem: limiting intensities to 96.0 --> 220.0 0 of 15 (0.0%) samples deleted using 303 total control points for intensity normalization... bias field = 0.963 +- 0.064 0 of 302 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (118, 46, 40) --> (193, 136, 192) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 194.0 0 of 170 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (59, 48, 44) --> (130, 140, 194) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 194.0 0 of 191 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (125, 118, 64) --> (176, 150, 113) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 194.0 0 of 37 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (81, 119, 67) --> (125, 154, 118) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 194.0 0 of 39 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (110, 108, 97) --> (146, 164, 126) Brain_Stem: limiting intensities to 77.0 --> 194.0 0 of 84 (0.0%) samples deleted using 521 total control points for intensity normalization... bias field = 0.983 +- 0.060 0 of 521 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (118, 46, 40) --> (193, 136, 192) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 185.0 0 of 232 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (59, 48, 44) --> (130, 140, 194) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 185.0 0 of 224 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (125, 118, 64) --> (176, 150, 113) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 185.0 0 of 65 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (81, 119, 67) --> (125, 154, 118) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 185.0 0 of 84 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (110, 108, 97) --> (146, 164, 126) Brain_Stem: limiting intensities to 72.0 --> 185.0 0 of 134 (0.0%) samples deleted using 739 total control points for intensity normalization... bias field = 0.994 +- 0.047 2 of 739 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 47 seconds. #-------------------------------------- #@# CA Reg Sun Dec 20 21:02:43 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.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 '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.35 (predicted orig area = 5.9) 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=0.860, neg=0, invalid=3294 0001: dt=223.042611, rms=0.766 (10.957%), neg=0, invalid=3294 0002: dt=192.000000, rms=0.741 (3.339%), neg=0, invalid=3294 0003: dt=221.952000, rms=0.726 (1.957%), neg=0, invalid=3294 0004: dt=148.093023, rms=0.719 (1.044%), neg=0, invalid=3294 0005: dt=369.920000, rms=0.710 (1.223%), neg=0, invalid=3294 0006: dt=110.976000, rms=0.704 (0.799%), neg=0, invalid=3294 0007: dt=887.808000, rms=0.694 (1.482%), neg=0, invalid=3294 0008: dt=92.480000, rms=0.690 (0.545%), neg=0, invalid=3294 0009: dt=1183.744000, rms=0.684 (0.798%), neg=0, invalid=3294 0010: dt=129.472000, rms=0.680 (0.590%), neg=0, invalid=3294 0011: dt=129.472000, rms=0.680 (0.084%), neg=0, invalid=3294 0012: dt=129.472000, rms=0.679 (0.124%), neg=0, invalid=3294 0013: dt=129.472000, rms=0.678 (0.183%), neg=0, invalid=3294 0014: dt=129.472000, rms=0.676 (0.239%), neg=0, invalid=3294 0015: dt=129.472000, rms=0.674 (0.286%), neg=0, invalid=3294 0016: dt=129.472000, rms=0.672 (0.346%), neg=0, invalid=3294 0017: dt=129.472000, rms=0.669 (0.353%), neg=0, invalid=3294 0018: dt=129.472000, rms=0.667 (0.342%), neg=0, invalid=3294 0019: dt=129.472000, rms=0.665 (0.330%), neg=0, invalid=3294 0020: dt=129.472000, rms=0.663 (0.333%), neg=0, invalid=3294 0021: dt=129.472000, rms=0.661 (0.296%), neg=0, invalid=3294 0022: dt=129.472000, rms=0.659 (0.257%), neg=0, invalid=3294 0023: dt=129.472000, rms=0.658 (0.226%), neg=0, invalid=3294 0024: dt=129.472000, rms=0.656 (0.205%), neg=0, invalid=3294 0025: dt=129.472000, rms=0.655 (0.201%), neg=0, invalid=3294 0026: dt=129.472000, rms=0.654 (0.193%), neg=0, invalid=3294 0027: dt=129.472000, rms=0.653 (0.156%), neg=0, invalid=3294 0028: dt=129.472000, rms=0.652 (0.138%), neg=0, invalid=3294 0029: dt=129.472000, rms=0.651 (0.142%), neg=0, invalid=3294 0030: dt=129.472000, rms=0.650 (0.142%), neg=0, invalid=3294 0031: dt=129.472000, rms=0.649 (0.122%), neg=0, invalid=3294 0032: dt=129.472000, rms=0.648 (0.103%), neg=0, invalid=3294 0033: dt=32.368000, rms=0.648 (0.002%), neg=0, invalid=3294 0034: dt=32.368000, rms=0.648 (0.003%), neg=0, invalid=3294 0035: dt=32.368000, rms=0.648 (0.002%), neg=0, invalid=3294 0036: dt=32.368000, rms=0.648 (0.004%), neg=0, invalid=3294 0037: dt=32.368000, rms=0.648 (0.005%), neg=0, invalid=3294 0038: dt=32.368000, rms=0.648 (0.007%), neg=0, invalid=3294 0039: dt=32.368000, rms=0.648 (0.014%), neg=0, invalid=3294 0040: dt=32.368000, rms=0.648 (0.014%), neg=0, invalid=3294 0041: dt=32.368000, rms=0.648 (0.009%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=3294 0042: dt=221.952000, rms=0.647 (0.230%), neg=0, invalid=3294 0043: dt=517.888000, rms=0.646 (0.209%), neg=0, invalid=3294 0044: dt=517.888000, rms=0.646 (-1.401%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=3294 0045: dt=112.040712, rms=0.646 (0.803%), neg=0, invalid=3294 0046: dt=116.023392, rms=0.640 (1.038%), neg=0, invalid=3294 0047: dt=63.058824, rms=0.636 (0.558%), neg=0, invalid=3294 0048: dt=158.446602, rms=0.631 (0.771%), neg=0, invalid=3294 0049: dt=57.212121, rms=0.628 (0.476%), neg=0, invalid=3294 0050: dt=166.787879, rms=0.625 (0.554%), neg=0, invalid=3294 0051: dt=53.527273, rms=0.623 (0.337%), neg=0, invalid=3294 0052: dt=145.152000, rms=0.620 (0.409%), neg=0, invalid=3294 0053: dt=36.288000, rms=0.619 (0.184%), neg=0, invalid=3294 0054: dt=36.288000, rms=0.618 (0.102%), neg=0, invalid=3294 0055: dt=36.288000, rms=0.617 (0.164%), neg=0, invalid=3294 0056: dt=36.288000, rms=0.616 (0.236%), neg=0, invalid=3294 0057: dt=36.288000, rms=0.614 (0.283%), neg=0, invalid=3294 0058: dt=36.288000, rms=0.612 (0.304%), neg=0, invalid=3294 0059: dt=36.288000, rms=0.610 (0.312%), neg=0, invalid=3294 0060: dt=36.288000, rms=0.608 (0.309%), neg=0, invalid=3294 0061: dt=36.288000, rms=0.606 (0.303%), neg=0, invalid=3294 0062: dt=36.288000, rms=0.605 (0.306%), neg=0, invalid=3294 0063: dt=36.288000, rms=0.603 (0.273%), neg=0, invalid=3294 0064: dt=36.288000, rms=0.601 (0.249%), neg=0, invalid=3294 0065: dt=36.288000, rms=0.600 (0.221%), neg=0, invalid=3294 0066: dt=36.288000, rms=0.599 (0.201%), neg=0, invalid=3294 0067: dt=36.288000, rms=0.598 (0.204%), neg=0, invalid=3294 0068: dt=36.288000, rms=0.597 (0.181%), neg=0, invalid=3294 0069: dt=36.288000, rms=0.596 (0.174%), neg=0, invalid=3294 0070: dt=36.288000, rms=0.595 (0.147%), neg=0, invalid=3294 0071: dt=36.288000, rms=0.594 (0.127%), neg=0, invalid=3294 0072: dt=18.144000, rms=0.594 (0.016%), neg=0, invalid=3294 0073: dt=4.536000, rms=0.594 (-0.002%), neg=0, invalid=3294 0074: dt=6.480000, rms=0.594 (0.002%), neg=0, invalid=3294 0075: dt=0.141750, rms=0.594 (-0.002%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.595, neg=0, invalid=3294 0076: dt=0.141750, rms=0.594 (0.123%), neg=0, invalid=3294 0077: dt=0.008859, rms=0.594 (0.000%), neg=0, invalid=3294 0078: dt=0.004430, rms=0.594 (0.001%), neg=0, invalid=3294 0079: dt=0.001107, rms=0.594 (0.000%), neg=0, invalid=3294 0080: dt=0.000554, rms=0.594 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=3294 0081: dt=6.400000, rms=0.615 (0.187%), neg=0, invalid=3294 0082: dt=2.800000, rms=0.615 (0.008%), neg=0, invalid=3294 0083: dt=2.800000, rms=0.615 (0.006%), neg=0, invalid=3294 0084: dt=2.800000, rms=0.615 (-0.025%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=3294 0085: dt=2.800000, rms=0.615 (0.138%), neg=0, invalid=3294 0086: dt=2.800000, rms=0.615 (0.006%), neg=0, invalid=3294 0087: dt=2.800000, rms=0.615 (-0.002%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.669, neg=0, invalid=3294 0088: dt=4.509259, rms=0.660 (1.360%), neg=0, invalid=3294 0089: dt=1.008000, rms=0.660 (0.016%), neg=0, invalid=3294 0090: dt=1.008000, rms=0.660 (-0.010%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.660, neg=0, invalid=3294 0091: dt=0.000000, rms=0.660 (0.089%), neg=0, invalid=3294 0092: dt=0.000000, rms=0.660 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=3294 0093: dt=1.280000, rms=0.726 (0.666%), neg=0, invalid=3294 0094: dt=1.792000, rms=0.723 (0.401%), neg=0, invalid=3294 0095: dt=0.448000, rms=0.723 (0.047%), neg=0, invalid=3294 0096: dt=0.448000, rms=0.723 (0.031%), neg=0, invalid=3294 0097: dt=0.448000, rms=0.723 (0.010%), neg=0, invalid=3294 0098: dt=0.448000, rms=0.723 (-0.055%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=3294 0099: dt=1.280000, rms=0.722 (0.193%), neg=0, invalid=3294 0100: dt=0.028000, rms=0.722 (0.003%), neg=0, invalid=3294 0101: dt=0.028000, rms=0.722 (-0.002%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.660, neg=0, invalid=3294 0102: dt=0.979098, rms=0.636 (3.685%), neg=0, invalid=3294 0103: dt=0.080000, rms=0.635 (0.181%), neg=0, invalid=3294 0104: dt=0.080000, rms=0.635 (-0.072%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=3294 0105: dt=0.028000, rms=0.634 (0.122%), neg=0, invalid=3294 0106: dt=0.005000, rms=0.634 (-0.001%), neg=0, invalid=3294 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12974 (17) mri peak = 0.09615 (16) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1565 voxels, overlap=0.645) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1565 voxels, peak = 14), gca=13.7 gca peak = 0.13808 (16) mri peak = 0.10741 (17) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (989 voxels, overlap=0.712) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (989 voxels, peak = 14), gca=13.8 gca peak = 0.25042 (96) mri peak = 0.10405 (98) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (690 voxels, overlap=0.964) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (690 voxels, peak = 99), gca=99.4 gca peak = 0.22986 (96) mri peak = 0.11721 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (673 voxels, overlap=0.533) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (673 voxels, peak = 100), gca=100.3 gca peak = 0.21624 (56) mri peak = 0.07346 (65) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (545 voxels, overlap=0.577) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (545 voxels, peak = 64), gca=63.6 gca peak = 0.29672 (58) mri peak = 0.07918 (64) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (401 voxels, overlap=0.965) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (401 voxels, peak = 64), gca=63.5 gca peak = 0.11066 (101) mri peak = 0.11248 (104) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (53430 voxels, overlap=0.688) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (53430 voxels, peak = 106), gca=105.5 gca peak = 0.10944 (101) mri peak = 0.11063 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52795 voxels, overlap=0.611) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52795 voxels, peak = 107), gca=106.6 gca peak = 0.14864 (59) mri peak = 0.02948 (63) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (21546 voxels, overlap=0.439) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (21546 voxels, peak = 65), gca=64.6 gca peak = 0.16234 (58) mri peak = 0.03419 (63) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20441 voxels, overlap=0.729) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20441 voxels, peak = 64), gca=63.5 gca peak = 0.14764 (67) mri peak = 0.09743 (72) Right_Caudate (50): linear fit = 1.09 x + 0.0 (391 voxels, overlap=0.749) Right_Caudate (50): linear fit = 1.09 x + 0.0 (391 voxels, peak = 73), gca=72.7 gca peak = 0.15152 (71) mri peak = 0.10323 (78) Left_Caudate (11): linear fit = 1.03 x + 0.0 (695 voxels, overlap=0.804) Left_Caudate (11): linear fit = 1.03 x + 0.0 (695 voxels, peak = 73), gca=73.5 gca peak = 0.12476 (59) mri peak = 0.04188 (61) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20191 voxels, overlap=0.793) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20191 voxels, peak = 63), gca=63.4 gca peak = 0.13886 (58) mri peak = 0.04194 (63) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (21943 voxels, overlap=0.842) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (21943 voxels, peak = 64), gca=63.5 gca peak = 0.19332 (88) mri peak = 0.09656 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6585 voxels, overlap=0.593) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6585 voxels, peak = 95), gca=94.6 gca peak = 0.19182 (87) mri peak = 0.10419 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5932 voxels, overlap=0.644) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5932 voxels, peak = 94), gca=93.5 gca peak = 0.19349 (58) mri peak = 0.09492 (69) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (207 voxels, overlap=0.380) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (207 voxels, peak = 67), gca=67.0 gca peak = 0.32581 (57) mri peak = 0.08876 (70) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (339 voxels, overlap=0.052) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (339 voxels, peak = 69), gca=68.7 gca peak = 0.09144 (86) mri peak = 0.05421 (92) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3820 voxels, overlap=0.855) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3820 voxels, peak = 92), gca=91.6 gca peak = 0.10273 (84) mri peak = 0.05522 (93) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3412 voxels, overlap=0.536) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3412 voxels, peak = 94), gca=94.5 gca peak = 0.13860 (78) mri peak = 0.05288 (84) Left_Putamen (12): linear fit = 1.11 x + 0.0 (1911 voxels, overlap=0.667) Left_Putamen (12): linear fit = 1.11 x + 0.0 (1911 voxels, peak = 86), gca=86.2 gca peak = 0.12691 (78) mri peak = 0.06019 (83) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1810 voxels, overlap=0.956) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1810 voxels, peak = 82), gca=81.5 gca peak = 0.11764 (82) mri peak = 0.09797 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10043 voxels, overlap=0.521) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10043 voxels, peak = 90), gca=89.8 gca peak = 0.10015 (86) mri peak = 0.09385 (98) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (810 voxels, overlap=0.121) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (810 voxels, peak = 98), gca=98.5 gca peak = 0.11151 (90) mri peak = 0.07439 (98) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1154 voxels, overlap=0.335) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1154 voxels, peak = 99), gca=99.5 gca peak = 0.19608 (23) mri peak = 0.18987 (19) Third_Ventricle (14): linear fit = 0.79 x + 0.0 (75 voxels, overlap=0.582) Third_Ventricle (14): linear fit = 0.79 x + 0.0 (75 voxels, peak = 18), gca=18.1 gca peak = 0.13512 (19) mri peak = 0.13661 (18) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (277 voxels, overlap=0.467) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (277 voxels, peak = 15), gca=14.7 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.12743 (29) gca peak Left_Thalamus = 0.71074 (95) gca peak CSF = 0.17789 (37) gca peak Left_Accumbens_area = 0.50032 (62) gca peak Left_undetermined = 0.97690 (28) gca peak Left_vessel = 0.36001 (53) gca peak Left_choroid_plexus = 0.12300 (45) gca peak Right_Inf_Lat_Vent = 0.21149 (25) gca peak Right_Accumbens_area = 0.31737 (65) gca peak Right_vessel = 0.50186 (52) gca peak Right_choroid_plexus = 0.10991 (44) gca peak Fifth_Ventricle = 0.55462 (35) gca peak WM_hypointensities = 0.10555 (76) gca peak non_WM_hypointensities = 0.08508 (48) gca peak Optic_Chiasm = 0.30852 (73) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.13 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.81 x + 0.0 saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** 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=0.650, neg=0, invalid=3294 0107: dt=84.841499, rms=0.642 (1.262%), neg=0, invalid=3294 0108: dt=130.865672, rms=0.639 (0.406%), neg=0, invalid=3294 0109: dt=443.904000, rms=0.634 (0.791%), neg=0, invalid=3294 0110: dt=110.976000, rms=0.633 (0.230%), neg=0, invalid=3294 0111: dt=110.976000, rms=0.631 (0.192%), neg=0, invalid=3294 0112: dt=110.976000, rms=0.630 (0.254%), neg=0, invalid=3294 0113: dt=110.976000, rms=0.628 (0.306%), neg=0, invalid=3294 0114: dt=110.976000, rms=0.626 (0.259%), neg=0, invalid=3294 0115: dt=110.976000, rms=0.625 (0.258%), neg=0, invalid=3294 0116: dt=110.976000, rms=0.623 (0.209%), neg=0, invalid=3294 0117: dt=110.976000, rms=0.622 (0.187%), neg=0, invalid=3294 0118: dt=110.976000, rms=0.621 (0.171%), neg=0, invalid=3294 0119: dt=110.976000, rms=0.620 (0.168%), neg=0, invalid=3294 0120: dt=110.976000, rms=0.619 (0.184%), neg=0, invalid=3294 0121: dt=110.976000, rms=0.618 (0.186%), neg=0, invalid=3294 0122: dt=110.976000, rms=0.617 (0.192%), neg=0, invalid=3294 0123: dt=110.976000, rms=0.615 (0.182%), neg=0, invalid=3294 0124: dt=110.976000, rms=0.614 (0.171%), neg=0, invalid=3294 0125: dt=110.976000, rms=0.613 (0.158%), neg=0, invalid=3294 0126: dt=110.976000, rms=0.613 (0.148%), neg=0, invalid=3294 0127: dt=110.976000, rms=0.612 (0.135%), neg=0, invalid=3294 0128: dt=110.976000, rms=0.611 (0.135%), neg=0, invalid=3294 0129: dt=110.976000, rms=0.610 (0.128%), neg=0, invalid=3294 0130: dt=110.976000, rms=0.609 (0.115%), neg=0, invalid=3294 0131: dt=110.976000, rms=0.609 (0.103%), neg=0, invalid=3294 0132: dt=369.920000, rms=0.609 (0.032%), neg=0, invalid=3294 0133: dt=369.920000, rms=0.609 (-0.222%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=3294 0134: dt=129.472000, rms=0.607 (0.379%), neg=0, invalid=3294 0135: dt=295.936000, rms=0.606 (0.159%), neg=0, invalid=3294 0136: dt=295.936000, rms=0.606 (-0.058%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.608, neg=0, invalid=3294 0137: dt=95.036789, rms=0.603 (0.953%), neg=0, invalid=3294 0138: dt=103.125506, rms=0.597 (0.898%), neg=0, invalid=3294 0139: dt=52.884211, rms=0.593 (0.655%), neg=0, invalid=3294 0140: dt=84.638436, rms=0.591 (0.420%), neg=0, invalid=3294 0141: dt=76.800000, rms=0.588 (0.376%), neg=0, invalid=3294 0142: dt=36.288000, rms=0.587 (0.335%), neg=0, invalid=3294 0143: dt=995.328000, rms=0.573 (2.359%), neg=0, invalid=3294 0144: dt=36.288000, rms=0.570 (0.421%), neg=0, invalid=3294 0145: dt=82.944000, rms=0.569 (0.159%), neg=0, invalid=3294 0146: dt=82.944000, rms=0.569 (0.068%), neg=0, invalid=3294 0147: dt=82.944000, rms=0.568 (0.156%), neg=0, invalid=3294 0148: dt=82.944000, rms=0.568 (0.098%), neg=0, invalid=3294 0149: dt=82.944000, rms=0.567 (0.130%), neg=0, invalid=3294 0150: dt=82.944000, rms=0.566 (0.140%), neg=0, invalid=3294 0151: dt=82.944000, rms=0.565 (0.192%), neg=0, invalid=3294 0152: dt=82.944000, rms=0.563 (0.256%), neg=0, invalid=3294 0153: dt=82.944000, rms=0.562 (0.293%), neg=0, invalid=3294 0154: dt=82.944000, rms=0.560 (0.300%), neg=0, invalid=3294 0155: dt=82.944000, rms=0.559 (0.287%), neg=0, invalid=3294 0156: dt=82.944000, rms=0.557 (0.233%), neg=0, invalid=3294 0157: dt=82.944000, rms=0.556 (0.249%), neg=0, invalid=3294 0158: dt=82.944000, rms=0.555 (0.158%), neg=0, invalid=3294 0159: dt=82.944000, rms=0.554 (0.177%), neg=0, invalid=3294 0160: dt=82.944000, rms=0.553 (0.096%), neg=0, invalid=3294 0161: dt=82.944000, rms=0.553 (0.108%), neg=0, invalid=3294 0162: dt=82.944000, rms=0.552 (0.085%), neg=0, invalid=3294 0163: dt=36.288000, rms=0.552 (0.017%), neg=0, invalid=3294 0164: dt=36.288000, rms=0.552 (0.007%), neg=0, invalid=3294 0165: dt=36.288000, rms=0.552 (0.007%), neg=0, invalid=3294 0166: dt=36.288000, rms=0.552 (0.009%), neg=0, invalid=3294 0167: dt=36.288000, rms=0.552 (0.011%), neg=0, invalid=3294 0168: dt=36.288000, rms=0.552 (0.005%), neg=0, invalid=3294 0169: dt=36.288000, rms=0.552 (0.004%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=3294 0170: dt=89.121495, rms=0.550 (0.411%), neg=0, invalid=3294 0171: dt=62.208000, rms=0.550 (0.054%), neg=0, invalid=3294 0172: dt=62.208000, rms=0.550 (0.017%), neg=0, invalid=3294 0173: dt=62.208000, rms=0.550 (0.012%), neg=0, invalid=3294 0174: dt=62.208000, rms=0.550 (-0.015%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=3294 0175: dt=4.800000, rms=0.562 (0.141%), neg=0, invalid=3294 0176: dt=1.600000, rms=0.562 (0.004%), neg=0, invalid=3294 0177: dt=1.600000, rms=0.562 (-0.001%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=3294 0178: dt=0.700000, rms=0.562 (0.105%), neg=0, invalid=3294 0179: dt=0.500000, rms=0.562 (0.001%), neg=0, invalid=3294 0180: dt=0.500000, rms=0.562 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=3294 0181: dt=3.512915, rms=0.590 (1.159%), neg=0, invalid=3294 0182: dt=0.576000, rms=0.590 (0.012%), neg=0, invalid=3294 0183: dt=0.576000, rms=0.590 (-0.007%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=3294 0184: dt=0.000000, rms=0.590 (0.084%), neg=0, invalid=3294 0185: dt=0.000000, rms=0.590 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.632, neg=0, invalid=3294 0186: dt=0.849785, rms=0.628 (0.523%), neg=0, invalid=3294 0187: dt=0.448000, rms=0.628 (0.062%), neg=0, invalid=3294 0188: dt=0.448000, rms=0.628 (-0.011%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.628, neg=0, invalid=3294 0189: dt=0.448000, rms=0.628 (0.142%), neg=0, invalid=3294 0190: dt=0.112000, rms=0.628 (0.006%), neg=0, invalid=3294 0191: dt=0.112000, rms=0.627 (0.004%), neg=0, invalid=3294 0192: dt=0.112000, rms=0.627 (-0.005%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.587, neg=0, invalid=3294 0193: dt=0.930496, rms=0.566 (3.688%), neg=0, invalid=3294 0194: dt=0.080000, rms=0.565 (0.159%), neg=0, invalid=3294 0195: dt=0.080000, rms=0.565 (-0.143%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=3294 0196: dt=0.016000, rms=0.565 (0.095%), neg=0, invalid=3294 0197: dt=0.000000, rms=0.565 (0.000%), neg=0, invalid=3294 0198: dt=0.050000, rms=0.565 (-0.048%), neg=0, invalid=3294 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 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.552, neg=0, invalid=3294 0199: dt=18.496000, rms=0.552 (0.007%), neg=0, invalid=3294 0200: dt=6.936000, rms=0.552 (0.001%), neg=0, invalid=3294 0201: dt=6.936000, rms=0.552 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=3294 0202: dt=221.952000, rms=0.551 (0.203%), neg=0, invalid=3294 0203: dt=129.472000, rms=0.550 (0.091%), neg=0, invalid=3294 0204: dt=129.472000, rms=0.550 (0.054%), neg=0, invalid=3294 0205: dt=129.472000, rms=0.550 (0.087%), neg=0, invalid=3294 0206: dt=129.472000, rms=0.549 (0.106%), neg=0, invalid=3294 0207: dt=129.472000, rms=0.549 (0.093%), neg=0, invalid=3294 0208: dt=129.472000, rms=0.548 (0.086%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.548, neg=0, invalid=3294 0209: dt=72.094862, rms=0.546 (0.489%), neg=0, invalid=3294 0210: dt=145.152000, rms=0.541 (0.914%), neg=0, invalid=3294 0211: dt=77.847953, rms=0.539 (0.208%), neg=0, invalid=3294 0212: dt=77.847953, rms=0.538 (0.314%), neg=0, invalid=3294 0213: dt=77.847953, rms=0.536 (0.397%), neg=0, invalid=3294 0214: dt=77.847953, rms=0.534 (0.334%), neg=0, invalid=3294 0215: dt=77.847953, rms=0.532 (0.340%), neg=0, invalid=3294 0216: dt=77.847953, rms=0.530 (0.299%), neg=0, invalid=3294 0217: dt=77.847953, rms=0.529 (0.295%), neg=0, invalid=3294 0218: dt=77.847953, rms=0.528 (0.219%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0219: dt=77.847953, rms=0.527 (0.207%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0220: dt=77.847953, rms=0.526 (0.169%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0221: dt=77.847953, rms=0.525 (0.174%), neg=0, invalid=3294 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0222: dt=77.847953, rms=0.524 (0.147%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0223: dt=77.847953, rms=0.524 (0.107%), neg=0, invalid=3294 0224: dt=77.847953, rms=0.523 (0.091%), neg=0, invalid=3294 0225: dt=124.416000, rms=0.523 (0.060%), neg=0, invalid=3294 0226: dt=124.416000, rms=0.523 (-0.087%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=3294 0227: dt=89.971014, rms=0.521 (0.406%), neg=0, invalid=3294 0228: dt=36.288000, rms=0.520 (0.112%), neg=0, invalid=3294 0229: dt=36.288000, rms=0.520 (0.046%), neg=0, invalid=3294 0230: dt=36.288000, rms=0.519 (0.071%), neg=0, invalid=3294 0231: dt=36.288000, rms=0.519 (0.074%), neg=0, invalid=3294 0232: dt=36.288000, rms=0.519 (0.063%), neg=0, invalid=3294 0233: dt=36.288000, rms=0.518 (0.048%), neg=0, invalid=3294 0234: dt=248.832000, rms=0.518 (0.052%), neg=0, invalid=3294 0235: dt=103.680000, rms=0.518 (0.024%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.523, neg=0, invalid=3294 0236: dt=11.200000, rms=0.522 (0.188%), neg=0, invalid=3294 0237: dt=11.200000, rms=0.521 (0.095%), neg=0, invalid=3294 0238: dt=11.200000, rms=0.521 (0.069%), neg=0, invalid=3294 0239: dt=11.200000, rms=0.521 (0.063%), neg=0, invalid=3294 0240: dt=11.200000, rms=0.520 (0.024%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=3294 0241: dt=38.400000, rms=0.518 (0.533%), neg=0, invalid=3294 0242: dt=38.400000, rms=0.517 (0.130%), neg=0, invalid=3294 0243: dt=38.400000, rms=0.516 (0.146%), neg=0, invalid=3294 0244: dt=38.400000, rms=0.515 (0.266%), neg=0, invalid=3294 0245: dt=38.400000, rms=0.514 (0.250%), neg=0, invalid=3294 0246: dt=38.400000, rms=0.512 (0.300%), neg=0, invalid=3294 0247: dt=38.400000, rms=0.511 (0.304%), neg=0, invalid=3294 0248: dt=38.400000, rms=0.509 (0.225%), neg=0, invalid=3294 0249: dt=38.400000, rms=0.509 (0.129%), neg=0, invalid=3294 0250: dt=38.400000, rms=0.508 (0.084%), neg=0, invalid=3294 0251: dt=38.400000, rms=0.508 (0.025%), neg=0, invalid=3294 0252: dt=11.200000, rms=0.508 (0.009%), neg=0, invalid=3294 0253: dt=11.200000, rms=0.508 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=3294 0254: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=3294 0255: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=3294 0256: dt=0.024000, rms=0.535 (0.001%), neg=0, invalid=3294 0257: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=3294 0258: dt=0.064000, rms=0.535 (0.005%), neg=0, invalid=3294 0259: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.506, neg=0, invalid=3294 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0260: dt=0.818431, rms=0.492 (2.912%), neg=0, invalid=3294 0261: dt=0.028000, rms=0.491 (0.068%), neg=0, invalid=3294 0262: dt=0.028000, rms=0.491 (0.012%), neg=0, invalid=3294 0263: dt=0.028000, rms=0.491 (-0.099%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=3294 0264: dt=0.007000, rms=0.491 (0.002%), neg=0, invalid=3294 0265: dt=0.001500, rms=0.491 (0.000%), neg=0, invalid=3294 0266: dt=0.001500, rms=0.491 (-0.000%), neg=0, invalid=3294 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 37 minutes and 50 seconds. #-------------------------------------- #@# Remove Neck Sun Dec 20 22:40:32 GMT 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 5.90 removing structures at least 25 mm from brain... 11641328 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 24 seconds. #-------------------------------------- #@# SkullLTA Sun Dec 20 22:41:57 GMT 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (45, 22, 26) --> (204, 194, 218) using (98, 79, 122) as brain centroid... mean wm in atlas = 118, using box (78,58,98) --> (117, 100,145) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.124 scaling channel 0 by 1.12381 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.03791 -0.08455 -0.11616 18.28364; 0.09932 1.23889 0.22222 -41.10395; 0.11181 -0.17378 1.07020 -11.22433; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.03791 -0.08455 -0.11616 18.28364; 0.09932 1.23889 0.22222 -41.10395; 0.11181 -0.17378 1.07020 -11.22433; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.06011 -0.04479 -0.11086 12.56383; 0.06408 1.21772 0.22167 -34.37098; 0.11383 -0.17691 1.08951 -13.38756; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07925 -0.04560 -0.11286 10.50266; 0.06408 1.21772 0.22167 -34.37098; 0.11383 -0.17691 1.08951 -13.38756; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07925 -0.04560 -0.11286 10.50266; 0.06408 1.21772 0.22167 -34.37098; 0.11383 -0.17691 1.08951 -13.38756; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.07619 -0.05547 -0.11411 11.12982; 0.07283 1.21587 0.22056 -34.64309; 0.11394 -0.17743 1.09339 -13.32873; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 19 minutes and 58 seconds. #-------------------------------------- #@# SubCort Seg Sun Dec 20 23:01:55 GMT 2015 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz sysname Linux hostname eddie423 machine x86_64 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca... reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 5.90 Atlas used for the 3D morph was /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/RB_all_2015-08-04.gca average std = 7.4 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16337 (20) mri peak = 0.10318 (16) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (2499 voxels, overlap=0.837) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (2499 voxels, peak = 15), gca=15.3 gca peak = 0.19190 (13) mri peak = 0.09171 (17) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (2278 voxels, overlap=0.875) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (2278 voxels, peak = 14), gca=14.5 gca peak = 0.24200 (96) mri peak = 0.11901 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (563 voxels, overlap=0.762) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (563 voxels, peak = 100), gca=100.3 gca peak = 0.14904 (91) mri peak = 0.12648 (99) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (591 voxels, overlap=0.583) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (591 voxels, peak = 96), gca=96.0 gca peak = 0.25211 (57) mri peak = 0.09461 (65) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (756 voxels, overlap=0.384) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (756 voxels, peak = 64), gca=63.6 gca peak = 0.31987 (57) mri peak = 0.07622 (63) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (662 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (662 voxels, peak = 61), gca=61.3 gca peak = 0.08094 (102) mri peak = 0.12030 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33709 voxels, overlap=0.649) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33709 voxels, peak = 104), gca=103.5 gca peak = 0.08600 (104) mri peak = 0.11710 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37125 voxels, overlap=0.588) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (37125 voxels, peak = 106), gca=105.6 gca peak = 0.09612 (57) mri peak = 0.03194 (68) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (23552 voxels, overlap=0.540) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (23552 voxels, peak = 66), gca=66.4 gca peak = 0.11462 (58) mri peak = 0.03134 (63) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (20664 voxels, overlap=0.555) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (20664 voxels, peak = 69), gca=69.3 gca peak = 0.25255 (66) mri peak = 0.09051 (75) Right_Caudate (50): linear fit = 1.12 x + 0.0 (685 voxels, overlap=0.393) Right_Caudate (50): linear fit = 1.12 x + 0.0 (685 voxels, peak = 74), gca=74.2 gca peak = 0.18480 (77) mri peak = 0.10765 (76) Left_Caudate (11): linear fit = 1.04 x + 0.0 (768 voxels, overlap=0.897) Left_Caudate (11): linear fit = 1.04 x + 0.0 (768 voxels, peak = 80), gca=80.5 gca peak = 0.12729 (58) mri peak = 0.05234 (61) Left_Cerebellum_Cortex (8): linear fit = 1.10 x + 0.0 (20267 voxels, overlap=0.928) Left_Cerebellum_Cortex (8): linear fit = 1.10 x + 0.0 (20267 voxels, peak = 64), gca=63.5 gca peak = 0.12622 (58) mri peak = 0.05333 (63) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (21297 voxels, overlap=0.895) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (21297 voxels, peak = 64), gca=63.5 gca peak = 0.15410 (88) mri peak = 0.11233 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5381 voxels, overlap=0.690) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5381 voxels, peak = 92), gca=92.0 gca peak = 0.15661 (88) mri peak = 0.12848 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5468 voxels, overlap=0.723) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5468 voxels, peak = 93), gca=92.8 gca peak = 0.30376 (59) mri peak = 0.09239 (69) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (393 voxels, overlap=0.054) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (393 voxels, peak = 68), gca=67.6 gca peak = 0.35132 (58) mri peak = 0.09943 (70) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (349 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (349 voxels, peak = 69), gca=68.7 gca peak = 0.10548 (89) mri peak = 0.05889 (89) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3695 voxels, overlap=0.853) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3695 voxels, peak = 92), gca=92.1 gca peak = 0.10706 (82) mri peak = 0.06740 (91) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3580 voxels, overlap=0.577) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3580 voxels, peak = 90), gca=89.8 gca peak = 0.08512 (74) mri peak = 0.05751 (78) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1614 voxels, overlap=0.747) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1614 voxels, peak = 80), gca=80.3 gca peak = 0.08440 (78) mri peak = 0.06475 (84) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1355 voxels, overlap=0.858) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1355 voxels, peak = 83), gca=83.1 gca peak = 0.07263 (80) mri peak = 0.08992 (88) Brain_Stem (16): linear fit = 1.09 x + 0.0 (10897 voxels, overlap=0.615) Brain_Stem (16): linear fit = 1.09 x + 0.0 (10897 voxels, peak = 87), gca=86.8 gca peak = 0.13309 (90) mri peak = 0.07821 (98) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1322 voxels, overlap=0.079) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1322 voxels, peak = 99), gca=99.5 gca peak = 0.15558 (86) mri peak = 0.07279 (100) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1558 voxels, overlap=0.323) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1558 voxels, peak = 98), gca=98.5 gca peak = 0.17913 (26) mri peak = 0.11377 (19) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (332 voxels, overlap=0.441) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (332 voxels, peak = 18), gca=18.3 gca peak = 0.17310 (16) mri peak = 0.14340 (18) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (265 voxels, overlap=0.761) Fourth_Ventricle (15): linear fit = 0.82 x + 0.0 (265 voxels, peak = 13), gca=13.2 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.21424 (27) gca peak Left_Thalamus = 1.00000 (95) gca peak CSF = 0.22008 (37) gca peak Left_Accumbens_area = 0.78455 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09096 (57) gca peak Right_Inf_Lat_Vent = 0.24233 (28) gca peak Right_Accumbens_area = 0.41783 (64) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (33) gca peak WM_hypointensities = 0.10945 (75) gca peak non_WM_hypointensities = 0.07381 (29) gca peak Optic_Chiasm = 0.66945 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.15 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.85 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.18820 (15) mri peak = 0.10318 (16) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (2499 voxels, overlap=0.981) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (2499 voxels, peak = 17), gca=16.6 gca peak = 0.17166 (14) mri peak = 0.09171 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (2278 voxels, overlap=0.790) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (2278 voxels, peak = 14), gca=14.5 gca peak = 0.21032 (97) mri peak = 0.11901 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (563 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (563 voxels, peak = 97), gca=97.5 gca peak = 0.14490 (96) mri peak = 0.12648 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (591 voxels, overlap=0.995) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (591 voxels, peak = 96), gca=95.5 gca peak = 0.23865 (63) mri peak = 0.09461 (65) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (756 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (756 voxels, peak = 64), gca=63.9 gca peak = 0.23075 (61) mri peak = 0.07622 (63) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (662 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (662 voxels, peak = 64), gca=64.4 gca peak = 0.08164 (105) mri peak = 0.12030 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33709 voxels, overlap=0.717) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33709 voxels, peak = 104), gca=104.5 gca peak = 0.08538 (105) mri peak = 0.11710 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37125 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37125 voxels, peak = 105), gca=105.0 gca peak = 0.08649 (67) mri peak = 0.03194 (68) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23552 voxels, overlap=0.865) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (23552 voxels, peak = 66), gca=66.0 gca peak = 0.09543 (69) mri peak = 0.03134 (63) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (20664 voxels, overlap=0.929) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (20664 voxels, peak = 67), gca=67.3 gca peak = 0.22812 (74) mri peak = 0.09051 (75) Right_Caudate (50): linear fit = 1.00 x + 0.0 (685 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (685 voxels, peak = 74), gca=74.0 gca peak = 0.17534 (81) mri peak = 0.10765 (76) Left_Caudate (11): linear fit = 0.99 x + 0.0 (768 voxels, overlap=1.001) Left_Caudate (11): linear fit = 0.99 x + 0.0 (768 voxels, peak = 80), gca=79.8 gca peak = 0.12059 (63) mri peak = 0.05234 (61) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (20267 voxels, overlap=0.991) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (20267 voxels, peak = 61), gca=60.8 gca peak = 0.12416 (62) mri peak = 0.05333 (63) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (21297 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (21297 voxels, peak = 61), gca=61.1 gca peak = 0.14575 (92) mri peak = 0.11233 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5381 voxels, overlap=0.901) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5381 voxels, peak = 92), gca=91.5 gca peak = 0.15582 (93) mri peak = 0.12848 (91) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5468 voxels, overlap=0.930) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5468 voxels, peak = 92), gca=91.6 gca peak = 0.32104 (67) mri peak = 0.09239 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (393 voxels, overlap=1.019) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (393 voxels, peak = 67), gca=67.0 gca peak = 0.38887 (68) mri peak = 0.09943 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (349 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (349 voxels, peak = 68), gca=68.0 gca peak = 0.10420 (92) mri peak = 0.05889 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3695 voxels, overlap=0.954) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3695 voxels, peak = 92), gca=91.5 gca peak = 0.11508 (90) mri peak = 0.06740 (91) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3580 voxels, overlap=0.966) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3580 voxels, peak = 90), gca=89.6 gca peak = 0.09085 (81) mri peak = 0.05751 (78) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1614 voxels, overlap=0.985) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1614 voxels, peak = 81), gca=80.6 gca peak = 0.08707 (80) mri peak = 0.06475 (84) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1355 voxels, overlap=1.000) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1355 voxels, peak = 79), gca=78.8 gca peak = 0.07075 (87) mri peak = 0.08992 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10897 voxels, overlap=0.867) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10897 voxels, peak = 87), gca=87.0 gca peak = 0.10741 (99) mri peak = 0.07821 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1322 voxels, overlap=0.786) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1322 voxels, peak = 99), gca=99.5 gca peak = 0.14454 (99) mri peak = 0.07279 (100) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1558 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1558 voxels, peak = 98), gca=97.5 gca peak = 0.23143 (18) mri peak = 0.11377 (19) Third_Ventricle (14): linear fit = 1.08 x + 0.0 (332 voxels, overlap=1.008) Third_Ventricle (14): linear fit = 1.08 x + 0.0 (332 voxels, peak = 19), gca=19.4 gca peak = 0.15527 (15) mri peak = 0.14340 (18) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (265 voxels, overlap=0.862) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (265 voxels, peak = 17), gca=16.6 gca peak Unknown = 0.94960 ( 0) gca peak Left_Inf_Lat_Vent = 0.18281 (29) gca peak Left_Thalamus = 0.35898 (109) gca peak CSF = 0.19690 (32) gca peak Left_Accumbens_area = 0.73942 (65) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.08943 (44) gca peak Right_Inf_Lat_Vent = 0.23889 (26) gca peak Right_Accumbens_area = 0.40544 (72) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (28) gca peak WM_hypointensities = 0.12206 (76) gca peak non_WM_hypointensities = 0.08334 (44) gca peak Optic_Chiasm = 0.66405 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.08 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 55318 voxels changed in iteration 0 of unlikely voxel relabeling 119 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 42194 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 404 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 54013 changed. image ll: -2.090, PF=0.500 pass 2: 14215 changed. image ll: -2.090, PF=0.500 pass 3: 4104 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 34 minutes and 9 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/cc_up.lta MRM_003_w_070655_171011_0000FD62 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/transforms/cc_up.lta reading aseg from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aseg.auto_noCCseg.mgz reading norm from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/norm.mgz 48442 voxels in left wm, 51012 in right wm, xrange [116, 132] searching rotation angles z=[-5 9], y=[-13 1] 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 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 global minimum found at slice 124.2, rotations (-5.97, 2.43) final transformation (x=124.2, yr=-5.970, zr=2.430): 0.99368 -0.04240 -0.10392 20.71012; 0.04217 0.99910 -0.00441 34.36650; 0.10401 0.00000 0.99458 -3.27456; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 89 119 eigenvectors: 0.00122 0.00555 0.99998; -0.07349 -0.99728 0.00563; 0.99730 -0.07350 -0.00081; error in mid anterior detected - correcting... writing aseg with callosum to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.1 minutes #-------------------------------------- #@# Merge ASeg Sun Dec 20 23:37:13 GMT 2015 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Dec 20 23:37:13 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1825 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 71 (71), valley at 46 (46) csf peak at 17, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 46 (46) csf peak at 17, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 36 seconds. #-------------------------------------------- #@# Mask BFS Sun Dec 20 23:40:50 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1434350 voxels in mask (pct= 8.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Dec 20 23:40:53 GMT 2015 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.2 +- 5.4 [80.0 --> 125.0] GM (72.0) : 70.1 +- 10.7 [30.0 --> 96.0] setting bottom of white matter range to 80.7 setting top of gray matter range to 91.4 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... 4647 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4112 filled 949 bright non-wm voxels segmented. 2704 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... 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 0.54 minutes reading wm segmentation from wm.seg.mgz... 86 voxels added to wm to prevent paths from MTL structures to cortex 2362 additional wm voxels added 0 additional wm voxels added SEG EDIT: 46720 voxels turned on, 39571 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 15 found - 15 modified | TOTAL: 25 pass 2 (xy-): 0 found - 15 modified | TOTAL: 25 pass 1 (yz+): 21 found - 21 modified | TOTAL: 46 pass 2 (yz+): 0 found - 21 modified | TOTAL: 46 pass 1 (yz-): 12 found - 12 modified | TOTAL: 58 pass 2 (yz-): 0 found - 12 modified | TOTAL: 58 pass 1 (xz+): 15 found - 15 modified | TOTAL: 73 pass 2 (xz+): 0 found - 15 modified | TOTAL: 73 pass 1 (xz-): 11 found - 11 modified | TOTAL: 84 pass 2 (xz-): 0 found - 11 modified | TOTAL: 84 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 11 found - 11 modified | TOTAL: 21 pass 2 (+++): 0 found - 11 modified | TOTAL: 21 pass 1 (+++): 6 found - 6 modified | TOTAL: 27 pass 2 (+++): 0 found - 6 modified | TOTAL: 27 Iteration Number : 1 pass 1 (++): 87 found - 87 modified | TOTAL: 87 pass 2 (++): 0 found - 87 modified | TOTAL: 87 pass 1 (+-): 68 found - 68 modified | TOTAL: 155 pass 2 (+-): 0 found - 68 modified | TOTAL: 155 pass 1 (--): 70 found - 70 modified | TOTAL: 225 pass 2 (--): 0 found - 70 modified | TOTAL: 225 pass 1 (-+): 48 found - 48 modified | TOTAL: 273 pass 2 (-+): 0 found - 48 modified | TOTAL: 273 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 0 found - 0 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 396 (out of 496478: 0.079762) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Dec 20 23:43:09 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10394; 0.11181 -0.17378 1.07020 -11.22430; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10394; 0.11181 -0.17378 1.07020 -11.22430; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1157 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (125, 119, 152), TAL = (3.0, 24.0, 9.0) talairach voxel to voxel transform 1.00713 0.07679 0.08681 -20.83151; -0.06011 0.77975 -0.16805 31.65449; -0.11498 0.11859 0.89805 17.80442; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 119, 152) --> (3.0, 24.0, 9.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, 24.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 24.00, 9.00) SRC: (109.27, 92.47, 156.12) search lh wm seed point around talairach space (-15.00, 24.00, 9.00), SRC: (145.52, 90.31, 151.98) 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 Sun Dec 20 23:43:56 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 4 found - 4 modified | TOTAL: 9 pass 2 (yz-): 0 found - 4 modified | TOTAL: 9 pass 1 (xz+): 2 found - 2 modified | TOTAL: 11 pass 2 (xz+): 0 found - 2 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 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 (+-): 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 = 14 (out of 242553: 0.005772) 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ slice 50: 2429 vertices, 2575 faces slice 60: 9033 vertices, 9285 faces slice 70: 17784 vertices, 18140 faces slice 80: 28335 vertices, 28668 faces slice 90: 38933 vertices, 39245 faces slice 100: 49796 vertices, 50198 faces slice 110: 60922 vertices, 61290 faces slice 120: 71359 vertices, 71761 faces slice 130: 81843 vertices, 82241 faces slice 140: 92111 vertices, 92480 faces slice 150: 101147 vertices, 101460 faces slice 160: 109100 vertices, 109385 faces slice 170: 115636 vertices, 115866 faces slice 180: 121047 vertices, 121238 faces slice 190: 124386 vertices, 124480 faces slice 200: 124774 vertices, 124804 faces slice 210: 124774 vertices, 124804 faces slice 220: 124774 vertices, 124804 faces slice 230: 124774 vertices, 124804 faces slice 240: 124774 vertices, 124804 faces slice 250: 124774 vertices, 124804 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... 124774 voxel in cpt #1: X=-30 [v=124774,e=374412,f=249608] located at (-24.473303, -16.090403, 36.082397) For the whole surface: X=-30 [v=124774,e=374412,f=249608] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun Dec 20 23:44:03 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 236155: 0.004235) 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ slice 50: 1166 vertices, 1254 faces slice 60: 6349 vertices, 6538 faces slice 70: 14370 vertices, 14685 faces slice 80: 24292 vertices, 24626 faces slice 90: 33735 vertices, 34035 faces slice 100: 43759 vertices, 44119 faces slice 110: 54871 vertices, 55247 faces slice 120: 65369 vertices, 65726 faces slice 130: 75492 vertices, 75866 faces slice 140: 85630 vertices, 85997 faces slice 150: 94716 vertices, 95038 faces slice 160: 102595 vertices, 102871 faces slice 170: 109715 vertices, 109955 faces slice 180: 115522 vertices, 115747 faces slice 190: 119777 vertices, 119895 faces slice 200: 120670 vertices, 120698 faces slice 210: 120670 vertices, 120698 faces slice 220: 120670 vertices, 120698 faces slice 230: 120670 vertices, 120698 faces slice 240: 120670 vertices, 120698 faces slice 250: 120670 vertices, 120698 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... 120670 voxel in cpt #1: X=-28 [v=120670,e=362094,f=241396] located at (31.770746, -12.466810, 33.834839) For the whole surface: X=-28 [v=120670,e=362094,f=241396] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Dec 20 23:44:09 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Sun Dec 20 23:44:14 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Sun Dec 20 23:44:19 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.6 mm, total surface area = 65536 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.153 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Inflation1 rh Sun Dec 20 23:44:53 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.0 mm, total surface area = 63312 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Sun Dec 20 23:45:24 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.57 (0.00-->6.92) (max @ vno 91832 --> 91833) face area 0.03 +- 0.03 (-0.15-->0.91) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.336... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.199, avgs=0 005/300: dt: 0.9000, rms radial error=175.944, avgs=0 010/300: dt: 0.9000, rms radial error=175.395, avgs=0 015/300: dt: 0.9000, rms radial error=174.674, avgs=0 020/300: dt: 0.9000, rms radial error=173.853, avgs=0 025/300: dt: 0.9000, rms radial error=172.971, avgs=0 030/300: dt: 0.9000, rms radial error=172.052, avgs=0 035/300: dt: 0.9000, rms radial error=171.117, avgs=0 040/300: dt: 0.9000, rms radial error=170.174, avgs=0 045/300: dt: 0.9000, rms radial error=169.227, avgs=0 050/300: dt: 0.9000, rms radial error=168.282, avgs=0 055/300: dt: 0.9000, rms radial error=167.339, avgs=0 060/300: dt: 0.9000, rms radial error=166.402, avgs=0 065/300: dt: 0.9000, rms radial error=165.468, avgs=0 070/300: dt: 0.9000, rms radial error=164.539, avgs=0 075/300: dt: 0.9000, rms radial error=163.615, avgs=0 080/300: dt: 0.9000, rms radial error=162.695, avgs=0 085/300: dt: 0.9000, rms radial error=161.780, avgs=0 090/300: dt: 0.9000, rms radial error=160.870, avgs=0 095/300: dt: 0.9000, rms radial error=159.965, avgs=0 100/300: dt: 0.9000, rms radial error=159.065, avgs=0 105/300: dt: 0.9000, rms radial error=158.170, avgs=0 110/300: dt: 0.9000, rms radial error=157.279, avgs=0 115/300: dt: 0.9000, rms radial error=156.394, avgs=0 120/300: dt: 0.9000, rms radial error=155.513, avgs=0 125/300: dt: 0.9000, rms radial error=154.637, avgs=0 130/300: dt: 0.9000, rms radial error=153.766, avgs=0 135/300: dt: 0.9000, rms radial error=152.900, avgs=0 140/300: dt: 0.9000, rms radial error=152.039, avgs=0 145/300: dt: 0.9000, rms radial error=151.182, avgs=0 150/300: dt: 0.9000, rms radial error=150.330, avgs=0 155/300: dt: 0.9000, rms radial error=149.483, avgs=0 160/300: dt: 0.9000, rms radial error=148.640, avgs=0 165/300: dt: 0.9000, rms radial error=147.802, avgs=0 170/300: dt: 0.9000, rms radial error=146.969, avgs=0 175/300: dt: 0.9000, rms radial error=146.140, avgs=0 180/300: dt: 0.9000, rms radial error=145.315, avgs=0 185/300: dt: 0.9000, rms radial error=144.496, avgs=0 190/300: dt: 0.9000, rms radial error=143.680, avgs=0 195/300: dt: 0.9000, rms radial error=142.870, avgs=0 200/300: dt: 0.9000, rms radial error=142.063, avgs=0 205/300: dt: 0.9000, rms radial error=141.262, avgs=0 210/300: dt: 0.9000, rms radial error=140.464, avgs=0 215/300: dt: 0.9000, rms radial error=139.671, avgs=0 220/300: dt: 0.9000, rms radial error=138.883, avgs=0 225/300: dt: 0.9000, rms radial error=138.099, avgs=0 230/300: dt: 0.9000, rms radial error=137.319, avgs=0 235/300: dt: 0.9000, rms radial error=136.543, avgs=0 240/300: dt: 0.9000, rms radial error=135.772, avgs=0 245/300: dt: 0.9000, rms radial error=135.006, avgs=0 250/300: dt: 0.9000, rms radial error=134.243, avgs=0 255/300: dt: 0.9000, rms radial error=133.485, avgs=0 260/300: dt: 0.9000, rms radial error=132.731, avgs=0 265/300: dt: 0.9000, rms radial error=131.981, avgs=0 270/300: dt: 0.9000, rms radial error=131.235, avgs=0 275/300: dt: 0.9000, rms radial error=130.494, avgs=0 280/300: dt: 0.9000, rms radial error=129.756, avgs=0 285/300: dt: 0.9000, rms radial error=129.023, avgs=0 290/300: dt: 0.9000, rms radial error=128.294, avgs=0 295/300: dt: 0.9000, rms radial error=127.569, avgs=0 300/300: dt: 0.9000, rms radial error=126.848, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14176.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2208.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00020 epoch 3 (K=160.0), pass 1, starting sse = 201.53 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01030 epoch 4 (K=640.0), pass 1, starting sse = 11.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/18 = 0.01065 final distance error %24.92 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours #-------------------------------------------- #@# QSphere rh Sun Dec 20 23:49:15 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.58 (0.00-->9.54) (max @ vno 49210 --> 50262) face area 0.03 +- 0.03 (-0.08-->0.80) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.339... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.300, avgs=0 005/300: dt: 0.9000, rms radial error=176.044, avgs=0 010/300: dt: 0.9000, rms radial error=175.492, avgs=0 015/300: dt: 0.9000, rms radial error=174.766, avgs=0 020/300: dt: 0.9000, rms radial error=173.938, avgs=0 025/300: dt: 0.9000, rms radial error=173.052, avgs=0 030/300: dt: 0.9000, rms radial error=172.135, avgs=0 035/300: dt: 0.9000, rms radial error=171.200, avgs=0 040/300: dt: 0.9000, rms radial error=170.258, avgs=0 045/300: dt: 0.9000, rms radial error=169.313, avgs=0 050/300: dt: 0.9000, rms radial error=168.369, avgs=0 055/300: dt: 0.9000, rms radial error=167.428, avgs=0 060/300: dt: 0.9000, rms radial error=166.490, avgs=0 065/300: dt: 0.9000, rms radial error=165.556, avgs=0 070/300: dt: 0.9000, rms radial error=164.627, avgs=0 075/300: dt: 0.9000, rms radial error=163.703, avgs=0 080/300: dt: 0.9000, rms radial error=162.783, avgs=0 085/300: dt: 0.9000, rms radial error=161.869, avgs=0 090/300: dt: 0.9000, rms radial error=160.959, avgs=0 095/300: dt: 0.9000, rms radial error=160.057, avgs=0 100/300: dt: 0.9000, rms radial error=159.159, avgs=0 105/300: dt: 0.9000, rms radial error=158.266, avgs=0 110/300: dt: 0.9000, rms radial error=157.378, avgs=0 115/300: dt: 0.9000, rms radial error=156.495, avgs=0 120/300: dt: 0.9000, rms radial error=155.616, avgs=0 125/300: dt: 0.9000, rms radial error=154.742, avgs=0 130/300: dt: 0.9000, rms radial error=153.873, avgs=0 135/300: dt: 0.9000, rms radial error=153.008, avgs=0 140/300: dt: 0.9000, rms radial error=152.149, avgs=0 145/300: dt: 0.9000, rms radial error=151.294, avgs=0 150/300: dt: 0.9000, rms radial error=150.443, avgs=0 155/300: dt: 0.9000, rms radial error=149.598, avgs=0 160/300: dt: 0.9000, rms radial error=148.756, avgs=0 165/300: dt: 0.9000, rms radial error=147.920, avgs=0 170/300: dt: 0.9000, rms radial error=147.088, avgs=0 175/300: dt: 0.9000, rms radial error=146.261, avgs=0 180/300: dt: 0.9000, rms radial error=145.438, avgs=0 185/300: dt: 0.9000, rms radial error=144.620, avgs=0 190/300: dt: 0.9000, rms radial error=143.806, avgs=0 195/300: dt: 0.9000, rms radial error=142.997, avgs=0 200/300: dt: 0.9000, rms radial error=142.192, avgs=0 205/300: dt: 0.9000, rms radial error=141.392, avgs=0 210/300: dt: 0.9000, rms radial error=140.596, avgs=0 215/300: dt: 0.9000, rms radial error=139.804, avgs=0 220/300: dt: 0.9000, rms radial error=139.017, avgs=0 225/300: dt: 0.9000, rms radial error=138.234, avgs=0 230/300: dt: 0.9000, rms radial error=137.456, avgs=0 235/300: dt: 0.9000, rms radial error=136.681, avgs=0 240/300: dt: 0.9000, rms radial error=135.912, avgs=0 245/300: dt: 0.9000, rms radial error=135.146, avgs=0 250/300: dt: 0.9000, rms radial error=134.385, avgs=0 255/300: dt: 0.9000, rms radial error=133.627, avgs=0 260/300: dt: 0.9000, rms radial error=132.874, avgs=0 265/300: dt: 0.9000, rms radial error=132.126, avgs=0 270/300: dt: 0.9000, rms radial error=131.381, avgs=0 275/300: dt: 0.9000, rms radial error=130.641, avgs=0 280/300: dt: 0.9000, rms radial error=129.905, avgs=0 285/300: dt: 0.9000, rms radial error=129.173, avgs=0 290/300: dt: 0.9000, rms radial error=128.445, avgs=0 295/300: dt: 0.9000, rms radial error=127.721, avgs=0 300/300: dt: 0.9000, rms radial error=127.001, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13674.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2122.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 191.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00952 epoch 4 (K=640.0), pass 1, starting sse = 9.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00820 final distance error %24.74 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours #-------------------------------------------- #@# Fix Topology lh Sun Dec 20 23:52:57 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology rh Sun Dec 20 23:52:57 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MRM_003_w_070655_171011_0000FD62 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-30 (nv=124774, nf=249608, ne=374412, g=16) 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... 2316 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 26 defects to be corrected 0 vertices coincident reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5469 (-4.7735) -vertex loglikelihood: -6.4074 (-3.2037) -normal dot loglikelihood: -3.6008 (-3.6008) -quad curv loglikelihood: -6.5595 (-3.2798) Total Loglikelihood : -26.1147 CORRECTING DEFECT 0 (vertices=44, convex hull=82) After retessellation of defect 0, euler #=-23 (123356,369504,246125) : difference with theory (-23) = 0 CORRECTING DEFECT 1 (vertices=63, convex hull=83) After retessellation of defect 1, euler #=-22 (123383,369621,246216) : difference with theory (-22) = 0 CORRECTING DEFECT 2 (vertices=41, convex hull=61) After retessellation of defect 2, euler #=-21 (123400,369695,246274) : difference with theory (-21) = 0 CORRECTING DEFECT 3 (vertices=50, convex hull=83) After retessellation of defect 3, euler #=-20 (123426,369808,246362) : difference with theory (-20) = 0 CORRECTING DEFECT 4 (vertices=7, convex hull=22) After retessellation of defect 4, euler #=-19 (123429,369820,246372) : difference with theory (-19) = 0 CORRECTING DEFECT 5 (vertices=39, convex hull=77) After retessellation of defect 5, euler #=-18 (123454,369926,246454) : difference with theory (-18) = 0 CORRECTING DEFECT 6 (vertices=19, convex hull=55) After retessellation of defect 6, euler #=-17 (123464,369974,246493) : difference with theory (-17) = 0 CORRECTING DEFECT 7 (vertices=141, convex hull=115) After retessellation of defect 7, euler #=-16 (123502,370143,246625) : difference with theory (-16) = 0 CORRECTING DEFECT 8 (vertices=35, convex hull=51) After retessellation of defect 8, euler #=-15 (123522,370223,246686) : difference with theory (-15) = 0 CORRECTING DEFECT 9 (vertices=21, convex hull=51) After retessellation of defect 9, euler #=-14 (123531,370271,246726) : difference with theory (-14) = 0 CORRECTING DEFECT 10 (vertices=33, convex hull=57) After retessellation of defect 10, euler #=-13 (123545,370335,246777) : difference with theory (-13) = 0 CORRECTING DEFECT 11 (vertices=9, convex hull=31) After retessellation of defect 11, euler #=-12 (123547,370352,246793) : difference with theory (-12) = 0 CORRECTING DEFECT 12 (vertices=69, convex hull=33) After retessellation of defect 12, euler #=-11 (123557,370393,246825) : difference with theory (-11) = 0 CORRECTING DEFECT 13 (vertices=198, convex hull=77) After retessellation of defect 13, euler #=-10 (123577,370484,246897) : difference with theory (-10) = 0 CORRECTING DEFECT 14 (vertices=340, convex hull=107) After retessellation of defect 14, euler #=-9 (123623,370666,247034) : difference with theory (-9) = 0 CORRECTING DEFECT 15 (vertices=85, convex hull=58) After retessellation of defect 15, euler #=-8 (123647,370760,247105) : difference with theory (-8) = 0 CORRECTING DEFECT 16 (vertices=22, convex hull=33) After retessellation of defect 16, euler #=-7 (123648,370778,247123) : difference with theory (-7) = 0 CORRECTING DEFECT 17 (vertices=6, convex hull=29) After retessellation of defect 17, euler #=-6 (123651,370794,247137) : difference with theory (-6) = 0 CORRECTING DEFECT 18 (vertices=57, convex hull=30) After retessellation of defect 18, euler #=-5 (123658,370825,247162) : difference with theory (-5) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=24) After retessellation of defect 19, euler #=-4 (123661,370841,247176) : difference with theory (-4) = 0 CORRECTING DEFECT 20 (vertices=12, convex hull=31) After retessellation of defect 20, euler #=-3 (123665,370866,247198) : difference with theory (-3) = 0 CORRECTING DEFECT 21 (vertices=6, convex hull=17) After retessellation of defect 21, euler #=-2 (123666,370873,247205) : difference with theory (-2) = 0 CORRECTING DEFECT 22 (vertices=58, convex hull=111) After retessellation of defect 22, euler #=-1 (123699,371030,247330) : difference with theory (-1) = 0 CORRECTING DEFECT 23 (vertices=21, convex hull=61) After retessellation of defect 23, euler #=0 (123707,371080,247373) : difference with theory (0) = 0 CORRECTING DEFECT 24 (vertices=14, convex hull=23) After retessellation of defect 24, euler #=1 (123707,371088,247382) : difference with theory (1) = 0 CORRECTING DEFECT 25 (vertices=24, convex hull=72) After retessellation of defect 25, euler #=2 (123724,371166,247444) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.06-->10.40) (max @ vno 50244 --> 56818) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.06-->10.40) (max @ vno 50244 --> 56818) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 91 mutations (38.6%), 145 crossovers (61.4%), 62 vertices were eliminated building final representation... 1050 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123724, nf=247444, ne=371166, g=0) writing corrected surface to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.2 minutes 0 defective edges removing intersecting faces 000: 115 intersecting 001: 5 intersecting mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MRM_003_w_070655_171011_0000FD62 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-28 (nv=120670, nf=241396, ne=362094, g=15) 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... 2146 ambiguous faces found in tessellation segmenting defects... 24 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 8 23 defects to be corrected 0 vertices coincident reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4927 (-4.7464) -vertex loglikelihood: -6.4722 (-3.2361) -normal dot loglikelihood: -3.6481 (-3.6481) -quad curv loglikelihood: -6.5218 (-3.2609) Total Loglikelihood : -26.1348 CORRECTING DEFECT 0 (vertices=30, convex hull=58) After retessellation of defect 0, euler #=-21 (119383,357684,238280) : difference with theory (-20) = 1 CORRECTING DEFECT 1 (vertices=186, convex hull=110) After retessellation of defect 1, euler #=-20 (119444,357914,238450) : difference with theory (-19) = 1 CORRECTING DEFECT 2 (vertices=65, convex hull=101) After retessellation of defect 2, euler #=-19 (119479,358065,238567) : difference with theory (-18) = 1 CORRECTING DEFECT 3 (vertices=9, convex hull=17) After retessellation of defect 3, euler #=-18 (119480,358071,238573) : difference with theory (-17) = 1 CORRECTING DEFECT 4 (vertices=13, convex hull=31) After retessellation of defect 4, euler #=-17 (119483,358090,238590) : difference with theory (-16) = 1 CORRECTING DEFECT 5 (vertices=19, convex hull=18) After retessellation of defect 5, euler #=-16 (119485,358098,238597) : difference with theory (-15) = 1 CORRECTING DEFECT 6 (vertices=34, convex hull=76) After retessellation of defect 6, euler #=-15 (119496,358162,238651) : difference with theory (-14) = 1 CORRECTING DEFECT 7 (vertices=20, convex hull=20) After retessellation of defect 7, euler #=-14 (119500,358177,238663) : difference with theory (-13) = 1 CORRECTING DEFECT 8 (vertices=63, convex hull=94) After retessellation of defect 8, euler #=-12 (119536,358331,238783) : difference with theory (-12) = 0 CORRECTING DEFECT 9 (vertices=24, convex hull=58) After retessellation of defect 9, euler #=-11 (119553,358407,238843) : difference with theory (-11) = 0 CORRECTING DEFECT 10 (vertices=30, convex hull=26) After retessellation of defect 10, euler #=-10 (119560,358435,238865) : difference with theory (-10) = 0 CORRECTING DEFECT 11 (vertices=138, convex hull=46) After retessellation of defect 11, euler #=-9 (119568,358476,238899) : difference with theory (-9) = 0 CORRECTING DEFECT 12 (vertices=46, convex hull=29) After retessellation of defect 12, euler #=-8 (119578,358515,238929) : difference with theory (-8) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=33) After retessellation of defect 13, euler #=-7 (119580,358532,238945) : difference with theory (-7) = 0 CORRECTING DEFECT 14 (vertices=54, convex hull=28) After retessellation of defect 14, euler #=-6 (119589,358567,238972) : difference with theory (-6) = 0 CORRECTING DEFECT 15 (vertices=37, convex hull=55) After retessellation of defect 15, euler #=-5 (119606,358639,239028) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=53, convex hull=37) After retessellation of defect 16, euler #=-4 (119612,358668,239052) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=67, convex hull=104) After retessellation of defect 17, euler #=-3 (119644,358813,239166) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=216, convex hull=44) After retessellation of defect 18, euler #=-2 (119655,358864,239207) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=39, convex hull=72) After retessellation of defect 19, euler #=-1 (119669,358936,239266) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=60, convex hull=71) After retessellation of defect 20, euler #=0 (119695,359045,239350) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=31, convex hull=58) After retessellation of defect 21, euler #=1 (119708,359109,239402) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=46, convex hull=24) After retessellation of defect 22, euler #=2 (119710,359124,239416) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.04-->6.40) (max @ vno 109211 --> 112137) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.04-->6.40) (max @ vno 109211 --> 112137) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (36.3%), 121 crossovers (63.7%), 30 vertices were eliminated building final representation... 960 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119710, nf=239416, ne=359124, g=0) writing corrected surface to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 8.9 minutes 0 defective edges removing intersecting faces 000: 105 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 123724 - 371166 + 247444 = 2 --> 0 holes F =2V-4: 247444 = 247448-4 (0) 2E=3F: 742332 = 742332 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 119710 - 359124 + 239416 = 2 --> 0 holes F =2V-4: 239416 = 239420-4 (0) 2E=3F: 718248 = 718248 (0) total defect index = 0 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 15 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Dec 21 00:14:11 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10753 bright wm thresholded. 1423 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... computing class statistics... border white: 231145 voxels (1.38%) border gray 251358 voxels (1.50%) WM (94.0): 94.7 +- 8.3 [70.0 --> 110.0] GM (81.0) : 78.5 +- 12.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.41) (max @ vno 49087 --> 50244) face area 0.28 +- 0.12 (0.00-->2.18) mean absolute distance = 0.86 +- 1.13 3339 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=67+-10.4 mean inside = 94.0, mean outside = 75.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=79.4, 90 (90) missing vertices, mean dist 0.3 [0.9 (%34.0)->0.8 (%66.0))] %46 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 0.92 +- 0.27 (0.09-->6.40) (max @ vno 49087 --> 50244) face area 0.28 +- 0.13 (0.00-->2.12) mean absolute distance = 0.45 +- 0.87 3655 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5183187.0, rms=11.138 001: dt: 0.5000, sse=5812551.0, rms=8.090 (27.368%) 002: dt: 0.5000, sse=6079757.0, rms=6.186 (23.530%) 003: dt: 0.5000, sse=6379639.0, rms=4.935 (20.227%) 004: dt: 0.5000, sse=6565912.5, rms=4.162 (15.668%) 005: dt: 0.5000, sse=6767800.0, rms=3.739 (10.154%) 006: dt: 0.5000, sse=6857345.5, rms=3.516 (5.962%) 007: dt: 0.5000, sse=6906671.0, rms=3.409 (3.057%) 008: dt: 0.5000, sse=6939957.5, rms=3.337 (2.094%) rms = 3.31, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6942384.0, rms=3.312 (0.769%) 010: dt: 0.2500, sse=4319668.5, rms=2.251 (32.044%) 011: dt: 0.2500, sse=3954039.2, rms=1.957 (13.061%) 012: dt: 0.2500, sse=3790803.0, rms=1.898 (3.013%) rms = 1.86, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3751600.8, rms=1.862 (1.889%) 014: dt: 0.1250, sse=3672439.2, rms=1.808 (2.906%) rms = 1.80, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3646053.8, rms=1.804 (0.207%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.0, 54 (9) missing vertices, mean dist -0.3 [0.6 (%63.0)->0.3 (%37.0))] %54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.26 (0.11-->6.67) (max @ vno 49087 --> 50244) face area 0.35 +- 0.17 (0.00-->3.08) mean absolute distance = 0.34 +- 0.53 2729 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4177482.8, rms=4.547 016: dt: 0.5000, sse=4580163.5, rms=3.034 (33.269%) rms = 3.00, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=5204692.5, rms=3.003 (1.036%) 018: dt: 0.2500, sse=4199985.0, rms=1.902 (36.659%) 019: dt: 0.2500, sse=4032595.0, rms=1.659 (12.767%) 020: dt: 0.2500, sse=3909081.2, rms=1.598 (3.689%) rms = 1.57, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3891672.0, rms=1.567 (1.955%) rms = 1.52, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3826572.2, rms=1.520 (2.996%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.8, 44 (6) missing vertices, mean dist -0.2 [0.4 (%69.0)->0.2 (%31.0))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.10-->6.75) (max @ vno 49087 --> 50244) face area 0.34 +- 0.16 (0.00-->3.37) mean absolute distance = 0.26 +- 0.39 2744 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4130360.0, rms=3.988 023: dt: 0.5000, sse=4418370.0, rms=2.621 (34.273%) rms = 2.89, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4123237.8, rms=1.910 (27.138%) 025: dt: 0.2500, sse=4034705.8, rms=1.525 (20.171%) 026: dt: 0.2500, sse=3986376.8, rms=1.418 (6.970%) rms = 1.42, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3954732.2, rms=1.416 (0.157%) rms = 1.37, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3908004.0, rms=1.367 (3.500%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.1, 36 (3) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3958456.0, rms=2.128 029: dt: 0.5000, sse=5049258.5, rms=2.014 (5.345%) rms = 2.54, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4516626.0, rms=1.342 (33.400%) 031: dt: 0.2500, sse=4272153.0, rms=1.192 (11.185%) 032: dt: 0.2500, sse=4386261.0, rms=1.100 (7.658%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.08, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4372629.5, rms=1.080 (1.809%) positioning took 0.5 minutes generating cortex label... 22 non-cortical segments detected only using segment with 6300 vertices erasing segment 0 (vno[0] = 27952) erasing segment 1 (vno[0] = 33309) erasing segment 2 (vno[0] = 33335) erasing segment 3 (vno[0] = 36567) erasing segment 5 (vno[0] = 54474) erasing segment 6 (vno[0] = 63216) erasing segment 7 (vno[0] = 73853) erasing segment 8 (vno[0] = 78066) erasing segment 9 (vno[0] = 78943) erasing segment 10 (vno[0] = 81011) erasing segment 11 (vno[0] = 82049) erasing segment 12 (vno[0] = 85209) erasing segment 13 (vno[0] = 86045) erasing segment 14 (vno[0] = 88189) erasing segment 15 (vno[0] = 89841) erasing segment 16 (vno[0] = 89936) erasing segment 17 (vno[0] = 91832) erasing segment 18 (vno[0] = 93814) erasing segment 19 (vno[0] = 94760) erasing segment 20 (vno[0] = 94796) erasing segment 21 (vno[0] = 123646) writing cortex label to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label... writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv writing smoothed area to lh.area writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area vertex spacing 0.89 +- 0.26 (0.02-->6.86) (max @ vno 49087 --> 50244) face area 0.34 +- 0.16 (0.00-->3.65) refinement took 4.2 minutes #-------------------------------------------- #@# Make White Surf rh Mon Dec 21 00:18:25 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10209 bright wm thresholded. 1422 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... computing class statistics... border white: 231145 voxels (1.38%) border gray 251358 voxels (1.50%) WM (93.0): 94.5 +- 8.0 [70.0 --> 110.0] GM (81.0) : 78.8 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.2 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.4 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.06) (max @ vno 119439 --> 119444) face area 0.28 +- 0.12 (0.00-->1.86) mean absolute distance = 0.88 +- 1.18 3484 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=69+-11.3 mean inside = 93.5, mean outside = 74.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.9, 51 (51) missing vertices, mean dist 0.1 [1.0 (%38.3)->0.8 (%61.7))] %35 local maxima, %60 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.08-->3.26) (max @ vno 83848 --> 83847) face area 0.28 +- 0.13 (0.00-->1.76) mean absolute distance = 0.47 +- 0.92 3972 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4871417.5, rms=10.883 001: dt: 0.5000, sse=5400089.5, rms=7.473 (31.333%) 002: dt: 0.5000, sse=5726302.0, rms=5.460 (26.938%) 003: dt: 0.5000, sse=6027679.0, rms=4.372 (19.923%) 004: dt: 0.5000, sse=6279683.5, rms=3.758 (14.041%) 005: dt: 0.5000, sse=6443961.5, rms=3.467 (7.754%) 006: dt: 0.5000, sse=6516092.5, rms=3.316 (4.342%) 007: dt: 0.5000, sse=6563349.5, rms=3.262 (1.623%) rms = 3.21, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=6557277.5, rms=3.213 (1.516%) 009: dt: 0.2500, sse=4094736.5, rms=2.168 (32.527%) 010: dt: 0.2500, sse=3749583.0, rms=1.878 (13.383%) 011: dt: 0.2500, sse=3599172.2, rms=1.820 (3.075%) rms = 1.79, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3549226.0, rms=1.788 (1.774%) rms = 1.75, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3482233.0, rms=1.745 (2.379%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.4, 58 (18) missing vertices, mean dist -0.3 [0.6 (%61.7)->0.3 (%38.3))] %44 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.10-->3.34) (max @ vno 45440 --> 45420) face area 0.35 +- 0.16 (0.00-->2.48) mean absolute distance = 0.37 +- 0.58 3061 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3943354.8, rms=4.279 014: dt: 0.5000, sse=4289739.0, rms=2.839 (33.643%) rms = 2.87, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3967596.5, rms=2.317 (18.380%) 016: dt: 0.2500, sse=3799288.5, rms=1.848 (20.245%) 017: dt: 0.2500, sse=3697461.8, rms=1.631 (11.738%) 018: dt: 0.2500, sse=3648412.2, rms=1.545 (5.293%) rms = 1.51, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3620497.5, rms=1.507 (2.439%) rms = 1.47, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3577160.2, rms=1.469 (2.544%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.1, 49 (12) missing vertices, mean dist -0.2 [0.4 (%67.1)->0.2 (%32.9))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->3.50) (max @ vno 45440 --> 45420) face area 0.34 +- 0.16 (0.00-->2.60) mean absolute distance = 0.28 +- 0.43 2767 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3867722.2, rms=3.939 021: dt: 0.5000, sse=4079827.0, rms=2.503 (36.445%) rms = 2.72, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3828715.0, rms=1.871 (25.253%) 023: dt: 0.2500, sse=3758456.2, rms=1.481 (20.850%) 024: dt: 0.2500, sse=3716776.0, rms=1.364 (7.923%) rms = 1.35, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3695891.0, rms=1.351 (0.926%) rms = 1.32, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3654970.8, rms=1.317 (2.503%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.4, 39 (9) missing vertices, mean dist -0.1 [0.3 (%58.6)->0.2 (%41.4))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3705924.0, rms=2.135 027: dt: 0.5000, sse=4628669.5, rms=1.891 (11.392%) rms = 2.41, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4163794.5, rms=1.274 (32.628%) 029: dt: 0.2500, sse=3962562.2, rms=1.130 (11.311%) 030: dt: 0.2500, sse=4047956.2, rms=1.045 (7.493%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4037914.5, rms=1.035 (1.024%) positioning took 0.5 minutes generating cortex label... 30 non-cortical segments detected only using segment with 6384 vertices erasing segment 0 (vno[0] = 27843) erasing segment 2 (vno[0] = 39186) erasing segment 3 (vno[0] = 46606) erasing segment 4 (vno[0] = 49731) erasing segment 5 (vno[0] = 49733) erasing segment 6 (vno[0] = 51878) erasing segment 7 (vno[0] = 51880) erasing segment 8 (vno[0] = 52898) erasing segment 9 (vno[0] = 54174) erasing segment 10 (vno[0] = 57207) erasing segment 11 (vno[0] = 59530) erasing segment 12 (vno[0] = 61498) erasing segment 13 (vno[0] = 65816) erasing segment 14 (vno[0] = 67359) erasing segment 15 (vno[0] = 67725) erasing segment 16 (vno[0] = 67747) erasing segment 17 (vno[0] = 69830) erasing segment 18 (vno[0] = 71490) erasing segment 19 (vno[0] = 78573) erasing segment 20 (vno[0] = 79626) erasing segment 21 (vno[0] = 80734) erasing segment 22 (vno[0] = 81818) erasing segment 23 (vno[0] = 81838) erasing segment 24 (vno[0] = 81906) erasing segment 25 (vno[0] = 83830) erasing segment 26 (vno[0] = 84778) erasing segment 27 (vno[0] = 84923) erasing segment 28 (vno[0] = 85727) erasing segment 29 (vno[0] = 88232) writing cortex label to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label... writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv writing smoothed area to rh.area writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->3.59) (max @ vno 45420 --> 45440) face area 0.33 +- 0.16 (0.00-->2.62) refinement took 3.9 minutes #-------------------------------------------- #@# Smooth2 lh Mon Dec 21 00:22:22 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Mon Dec 21 00:22:27 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Mon Dec 21 00:22:32 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.8 mm, total surface area = 74953 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.5 minutes #-------------------------------------------- #@# Inflation2 rh Mon Dec 21 00:23:05 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.1 mm, total surface area = 71692 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (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 0.5 minutes #-------------------------------------------- #@# Curv .H and .K lh Mon Dec 21 00:23:37 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature -w lh.white total integrated curvature = -2.763*4pi (-34.724) --> 4 handles ICI = 145.6, FI = 1520.8, variation=24048.467 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 135 vertices thresholded to be in k1 ~ [-0.22 0.55], k2 ~ [-0.08 0.08] total integrated curvature = 0.646*4pi (8.119) --> 0 handles ICI = 1.6, FI = 8.4, variation=150.258 96 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 122 vertices thresholded to be in [-0.11 0.26] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #-------------------------------------------- #@# Curv .H and .K rh Mon Dec 21 00:24:58 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature -w rh.white total integrated curvature = 4.345*4pi (54.598) --> -3 handles ICI = 143.2, FI = 1519.9, variation=23823.910 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 147 vertices thresholded to be in k1 ~ [-0.21 0.60], k2 ~ [-0.11 0.17] total integrated curvature = 0.627*4pi (7.880) --> 0 handles ICI = 1.4, FI = 7.7, variation=136.474 110 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 = 0.001 124 vertices thresholded to be in [-0.13 0.30] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Mon Dec 21 00:26:17 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MRM_003_w_070655_171011_0000FD62 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 [ MRM_003_w_070655_171011_0000FD62/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 [ 205 ] Gb_filter = 0 WARN: S lookup min: -0.355253 WARN: S explicit min: 0.000000 vertex = 12 #----------------------------------------- #@# Curvature Stats rh Mon Dec 21 00:26:21 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MRM_003_w_070655_171011_0000FD62 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 [ MRM_003_w_070655_171011_0000FD62/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 [ 209 ] Gb_filter = 0 WARN: S lookup min: -0.030114 WARN: S explicit min: 0.000000 vertex = 937 #-------------------------------------------- #@# Sphere lh Mon Dec 21 00:26:24 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.312... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=eddie, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.15 pass 1: epoch 2 of 3 starting distance error %19.13 unfolding complete - removing small folds... starting distance error %19.08 removing remaining folds... final distance error %19.10 MRISunfold() return, current seed 1234 -01: dt=0.0000, 87 negative triangles 178: dt=0.9900, 87 negative triangles 179: dt=0.9900, 41 negative triangles 180: dt=0.9900, 29 negative triangles 181: dt=0.9900, 23 negative triangles 182: dt=0.9900, 22 negative triangles 183: dt=0.9900, 24 negative triangles 184: dt=0.9900, 21 negative triangles 185: dt=0.9900, 22 negative triangles 186: dt=0.9900, 22 negative triangles 187: dt=0.9900, 22 negative triangles 188: dt=0.9900, 19 negative triangles 189: dt=0.9900, 18 negative triangles 190: dt=0.9900, 15 negative triangles 191: dt=0.9900, 17 negative triangles 192: dt=0.9900, 15 negative triangles 193: dt=0.9900, 19 negative triangles 194: dt=0.9900, 15 negative triangles 195: dt=0.9900, 15 negative triangles 196: dt=0.9900, 14 negative triangles 197: dt=0.9900, 13 negative triangles 198: dt=0.9900, 9 negative triangles 199: dt=0.9900, 9 negative triangles 200: dt=0.9900, 9 negative triangles 201: dt=0.9900, 12 negative triangles 202: dt=0.9900, 10 negative triangles 203: dt=0.9900, 9 negative triangles 204: dt=0.9900, 12 negative triangles 205: dt=0.9900, 6 negative triangles 206: dt=0.9900, 9 negative triangles 207: dt=0.9900, 7 negative triangles 208: dt=0.9900, 8 negative triangles 209: dt=0.9900, 9 negative triangles 210: dt=0.9900, 10 negative triangles 211: dt=0.9900, 10 negative triangles 212: dt=0.9900, 14 negative triangles 213: dt=0.9900, 13 negative triangles 214: dt=0.9900, 3 negative triangles 215: dt=0.9900, 9 negative triangles 216: dt=0.9900, 3 negative triangles 217: dt=0.9900, 11 negative triangles 218: dt=0.9900, 3 negative triangles 219: dt=0.9900, 10 negative triangles 220: dt=0.9900, 3 negative triangles 221: dt=0.9900, 10 negative triangles 222: dt=0.9900, 3 negative triangles 223: dt=0.9900, 7 negative triangles 224: dt=0.9405, 3 negative triangles 225: dt=0.9405, 4 negative triangles 226: dt=0.9405, 6 negative triangles 227: dt=0.9405, 3 negative triangles 228: dt=0.9405, 5 negative triangles 229: dt=0.9405, 3 negative triangles 230: dt=0.9405, 6 negative triangles 231: dt=0.9405, 3 negative triangles 232: dt=0.9405, 2 negative triangles 233: dt=0.9405, 2 negative triangles 234: dt=0.9405, 4 negative triangles 235: dt=0.9405, 2 negative triangles 236: dt=0.9405, 2 negative triangles 237: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.76 hours #-------------------------------------------- #@# Sphere rh Mon Dec 21 01:11:44 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.316... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=eddie, 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.39 pass 1: epoch 2 of 3 starting distance error %19.33 unfolding complete - removing small folds... starting distance error %19.26 removing remaining folds... final distance error %19.28 MRISunfold() return, current seed 1234 -01: dt=0.0000, 69 negative triangles 185: dt=0.9900, 69 negative triangles 186: dt=0.9900, 20 negative triangles 187: dt=0.9900, 9 negative triangles 188: dt=0.9900, 7 negative triangles 189: dt=0.9900, 6 negative triangles 190: dt=0.9900, 3 negative triangles 191: dt=0.9900, 2 negative triangles 192: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.71 hours #-------------------------------------------- #@# Surf Reg lh Mon Dec 21 01:54:26 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_register -curv ../surf/lh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cmdline mris_register -curv ../surf/lh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=eddie, 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=eddie, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.591 curvature mean = 0.034, std = 0.940 curvature mean = 0.020, std = 0.873 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 291647.6, tmin=1.0301 d=32.00 min @ (8.00, 8.00, 0.00) sse = 199336.8, tmin=2.0832 d=16.00 min @ (0.00, 0.00, 4.00) sse = 187510.3, tmin=3.1525 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 185410.6, tmin=4.2321 d=4.00 min @ (1.00, 1.00, 1.00) sse = 182574.4, tmin=5.3227 d=2.00 min @ (0.00, -0.50, 0.00) sse = 182141.5, tmin=6.4180 d=0.50 min @ (0.00, 0.12, -0.12) sse = 182115.0, tmin=8.6029 tol=1.0e+00, sigma=0.5, host=eddie, 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 8.60 min curvature mean = 0.013, std = 0.961 curvature mean = 0.010, std = 0.946 curvature mean = 0.013, std = 0.974 curvature mean = 0.004, std = 0.976 curvature mean = 0.010, std = 0.976 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.025, std = 0.280 curvature mean = 0.004, std = 0.068 curvature mean = 0.062, std = 0.366 curvature mean = 0.003, std = 0.080 curvature mean = 0.029, std = 0.565 curvature mean = 0.003, std = 0.086 curvature mean = 0.015, std = 0.709 curvature mean = 0.004, std = 0.090 curvature mean = 0.005, std = 0.813 MRISregister() return, current seed 0 -01: dt=0.0000, 43 negative triangles 110: dt=0.9900, 43 negative triangles expanding nbhd size to 1 111: dt=0.9900, 68 negative triangles 112: dt=0.9900, 42 negative triangles 113: dt=0.9900, 40 negative triangles 114: dt=0.9900, 39 negative triangles 115: dt=0.9900, 29 negative triangles 116: dt=0.9900, 30 negative triangles 117: dt=0.9900, 29 negative triangles 118: dt=0.9900, 28 negative triangles 119: dt=0.9900, 21 negative triangles 120: dt=0.9900, 26 negative triangles 121: dt=0.9900, 23 negative triangles 122: dt=0.9900, 24 negative triangles 123: dt=0.9900, 26 negative triangles 124: dt=0.9900, 19 negative triangles 125: dt=0.9900, 13 negative triangles 126: dt=0.9900, 13 negative triangles 127: dt=0.9900, 8 negative triangles 128: dt=0.9900, 9 negative triangles 129: dt=0.9900, 9 negative triangles 130: dt=0.9900, 8 negative triangles 131: dt=0.9900, 6 negative triangles 132: dt=0.9900, 5 negative triangles 133: dt=0.9900, 5 negative triangles 134: dt=0.9900, 5 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 3 negative triangles 137: dt=0.9900, 4 negative triangles 138: dt=0.9900, 3 negative triangles 139: dt=0.9900, 2 negative triangles 140: dt=0.9900, 2 negative triangles 141: dt=0.9900, 2 negative triangles 142: dt=0.9900, 1 negative triangles 143: dt=0.9900, 1 negative triangles 144: dt=0.9900, 1 negative triangles 145: dt=0.9900, 1 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.66 hours #-------------------------------------------- #@# Surf Reg rh Mon Dec 21 02:33:49 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_register -curv ../surf/rh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cmdline mris_register -curv ../surf/rh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=eddie, 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=eddie, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.598 curvature mean = 0.028, std = 0.926 curvature mean = 0.025, std = 0.875 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 283774.2, tmin=0.9972 d=32.00 min @ (0.00, 0.00, 8.00) sse = 221111.0, tmin=2.0184 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 215129.4, tmin=3.0490 d=8.00 min @ (0.00, 2.00, 0.00) sse = 206373.6, tmin=4.1126 d=4.00 min @ (1.00, 0.00, 0.00) sse = 205168.4, tmin=5.1848 d=1.00 min @ (0.00, 0.00, 0.25) sse = 205155.2, tmin=7.3358 d=0.50 min @ (0.00, 0.00, -0.12) sse = 205146.0, tmin=8.3962 tol=1.0e+00, sigma=0.5, host=eddie, 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 8.40 min curvature mean = 0.016, std = 0.955 curvature mean = 0.010, std = 0.950 curvature mean = 0.015, std = 0.968 curvature mean = 0.004, std = 0.978 curvature mean = 0.014, std = 0.970 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.029, std = 0.280 curvature mean = 0.006, std = 0.071 curvature mean = 0.069, std = 0.381 curvature mean = 0.006, std = 0.086 curvature mean = 0.028, std = 0.587 curvature mean = 0.006, std = 0.092 curvature mean = 0.015, std = 0.731 curvature mean = 0.006, std = 0.095 curvature mean = 0.004, std = 0.836 MRISregister() return, current seed 0 -01: dt=0.0000, 24 negative triangles 108: dt=0.9900, 24 negative triangles expanding nbhd size to 1 109: dt=0.9900, 31 negative triangles 110: dt=0.9900, 21 negative triangles 111: dt=0.9900, 18 negative triangles 112: dt=0.9900, 19 negative triangles 113: dt=0.9900, 21 negative triangles 114: dt=0.9900, 14 negative triangles 115: dt=0.9900, 13 negative triangles 116: dt=0.9900, 9 negative triangles 117: dt=0.9900, 9 negative triangles 118: dt=0.9900, 10 negative triangles 119: dt=0.9900, 5 negative triangles 120: dt=0.9900, 4 negative triangles 121: dt=0.9900, 4 negative triangles 122: dt=0.9900, 4 negative triangles 123: dt=0.9900, 4 negative triangles 124: dt=0.9900, 3 negative triangles 125: dt=0.9900, 3 negative triangles 126: dt=0.9900, 1 negative triangles 127: dt=0.9900, 2 negative triangles 128: dt=0.9900, 3 negative triangles 129: dt=0.9900, 2 negative triangles 130: dt=0.9900, 1 negative triangles 131: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.75 hours #-------------------------------------------- #@# Jacobian white lh Mon Dec 21 03:18:50 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Mon Dec 21 03:18:52 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Mon Dec 21 03:18:54 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mrisp_paint -a 5 /exports/work/mcm_cric_nas/Kaiming/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Mon Dec 21 03:18:55 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mrisp_paint -a 5 /exports/work/mcm_cric_nas/Kaiming/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Dec 21 03:18:57 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 1043 labels changed using aseg relabeling using gibbs priors... 000: 2802 changed, 123724 examined... 001: 609 changed, 12132 examined... 002: 149 changed, 3389 examined... 003: 38 changed, 888 examined... 004: 16 changed, 228 examined... 005: 9 changed, 102 examined... 006: 4 changed, 45 examined... 007: 1 changed, 28 examined... 008: 0 changed, 5 examined... 190 labels changed using aseg 000: 110 total segments, 70 labels (181 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 30 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1536 vertices marked for relabeling... 1536 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Cortical Parc rh Mon Dec 21 03:19:44 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 960 labels changed using aseg relabeling using gibbs priors... 000: 2578 changed, 119710 examined... 001: 575 changed, 11350 examined... 002: 142 changed, 3247 examined... 003: 40 changed, 875 examined... 004: 16 changed, 244 examined... 005: 4 changed, 89 examined... 006: 1 changed, 30 examined... 007: 1 changed, 7 examined... 008: 0 changed, 5 examined... 148 labels changed using aseg 000: 108 total segments, 70 labels (307 vertices) changed 001: 39 total segments, 1 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1556 vertices marked for relabeling... 1556 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 45 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Dec 21 03:20:29 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10753 bright wm thresholded. 1423 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... computing class statistics... border white: 231145 voxels (1.38%) border gray 251358 voxels (1.50%) WM (94.0): 94.7 +- 8.3 [70.0 --> 110.0] GM (81.0) : 78.5 +- 12.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.9 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=67+-10.4 mean inside = 94.0, mean outside = 75.2 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... 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 0 with 64 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=56.5, 115 (115) missing vertices, mean dist 1.7 [1.9 (%0.1)->2.1 (%99.9))] %29 local maxima, %50 large gradients and %17 min vals, 572 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=26154306.0, rms=30.280 001: dt: 0.5000, sse=19424300.0, rms=25.242 (16.637%) 002: dt: 0.5000, sse=14372339.0, rms=20.838 (17.448%) 003: dt: 0.5000, sse=10729923.0, rms=17.301 (16.971%) 004: dt: 0.5000, sse=8533539.0, rms=14.827 (14.299%) 005: dt: 0.5000, sse=7673764.5, rms=12.848 (13.352%) 006: dt: 0.5000, sse=7067193.5, rms=11.126 (13.402%) 007: dt: 0.5000, sse=6748120.0, rms=9.530 (14.343%) 008: dt: 0.5000, sse=6472918.5, rms=8.143 (14.557%) 009: dt: 0.5000, sse=6425257.0, rms=6.945 (14.705%) 010: dt: 0.5000, sse=6401904.5, rms=6.070 (12.608%) 011: dt: 0.5000, sse=6494290.5, rms=5.432 (10.503%) 012: dt: 0.5000, sse=6551928.5, rms=5.091 (6.282%) 013: dt: 0.5000, sse=6670843.0, rms=4.819 (5.343%) 014: dt: 0.5000, sse=6619061.0, rms=4.693 (2.605%) 015: dt: 0.5000, sse=6723412.0, rms=4.550 (3.045%) rms = 4.53, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=6688047.0, rms=4.527 (0.510%) 017: dt: 0.2500, sse=4479704.5, rms=3.454 (23.717%) 018: dt: 0.2500, sse=4214841.5, rms=3.138 (9.139%) 019: dt: 0.2500, sse=4075735.2, rms=3.062 (2.432%) rms = 3.03, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4029997.2, rms=3.027 (1.144%) 021: dt: 0.1250, sse=3810053.5, rms=2.868 (5.231%) rms = 2.85, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3781705.0, rms=2.849 (0.660%) positioning took 1.7 minutes mean border=53.6, 749 (20) missing vertices, mean dist 0.2 [0.2 (%41.5)->0.4 (%58.5))] %49 local maxima, %34 large gradients and %12 min vals, 191 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, 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=4404758.5, rms=5.444 023: dt: 0.5000, sse=4640914.0, rms=4.298 (21.051%) rms = 4.41, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4242968.0, rms=3.465 (19.392%) 025: dt: 0.2500, sse=4257002.5, rms=3.088 (10.866%) 026: dt: 0.2500, sse=4235920.0, rms=2.943 (4.712%) 027: dt: 0.2500, sse=4249946.0, rms=2.868 (2.542%) rms = 2.83, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4225418.5, rms=2.826 (1.474%) 029: dt: 0.1250, sse=4063627.8, rms=2.648 (6.291%) rms = 2.62, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4046027.5, rms=2.617 (1.153%) positioning took 0.7 minutes mean border=51.2, 906 (15) missing vertices, mean dist 0.1 [0.2 (%36.5)->0.3 (%63.5))] %63 local maxima, %20 large gradients and %12 min vals, 226 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, 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=4293956.5, rms=4.065 rms = 4.28, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4096449.0, rms=3.241 (20.258%) 032: dt: 0.2500, sse=4092254.0, rms=2.836 (12.497%) 033: dt: 0.2500, sse=4246947.5, rms=2.683 (5.411%) rms = 2.65, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4299600.0, rms=2.652 (1.163%) 035: dt: 0.1250, sse=4151574.2, rms=2.472 (6.764%) rms = 2.44, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4144571.8, rms=2.437 (1.419%) positioning took 0.5 minutes mean border=49.9, 1634 (15) missing vertices, mean dist 0.1 [0.2 (%42.9)->0.2 (%57.1))] %67 local maxima, %16 large gradients and %12 min vals, 187 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4199762.5, rms=2.878 rms = 3.87, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4090471.8, rms=2.519 (12.489%) 038: dt: 0.2500, sse=4219676.0, rms=2.449 (2.784%) rms = 2.41, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4261042.0, rms=2.411 (1.552%) 040: dt: 0.1250, sse=4187669.8, rms=2.281 (5.394%) rms = 2.26, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4176337.8, rms=2.259 (0.941%) positioning took 0.4 minutes writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial vertex spacing 0.99 +- 0.40 (0.06-->7.07) (max @ vno 49087 --> 50244) face area 0.40 +- 0.28 (0.00-->4.90) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123724 vertices processed 25000 of 123724 vertices processed 50000 of 123724 vertices processed 75000 of 123724 vertices processed 100000 of 123724 vertices processed 0 of 123724 vertices processed 25000 of 123724 vertices processed 50000 of 123724 vertices processed 75000 of 123724 vertices processed 100000 of 123724 vertices processed thickness calculation complete, 200:378 truncations. 43696 vertices at 0 distance 100593 vertices at 1 distance 65787 vertices at 2 distance 20625 vertices at 3 distance 5071 vertices at 4 distance 1380 vertices at 5 distance 398 vertices at 6 distance 124 vertices at 7 distance 46 vertices at 8 distance 21 vertices at 9 distance 16 vertices at 10 distance 9 vertices at 11 distance 8 vertices at 12 distance 4 vertices at 13 distance 4 vertices at 14 distance 5 vertices at 15 distance 7 vertices at 16 distance 6 vertices at 17 distance 2 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness positioning took 4.9 minutes #-------------------------------------------- #@# Make Pial Surf rh Mon Dec 21 03:25:26 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10209 bright wm thresholded. 1422 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... computing class statistics... border white: 231145 voxels (1.38%) border gray 251358 voxels (1.50%) WM (93.0): 94.5 +- 8.0 [70.0 --> 110.0] GM (81.0) : 78.8 +- 12.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.2 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.4 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=69+-11.3 mean inside = 93.5, mean outside = 74.7 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... 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 0 with 22 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=57.8, 77 (77) missing vertices, mean dist 1.8 [0.4 (%0.0)->2.0 (%100.0))] %35 local maxima, %49 large gradients and %12 min vals, 492 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25103038.0, rms=30.360 001: dt: 0.5000, sse=18804932.0, rms=25.473 (16.095%) 002: dt: 0.5000, sse=13973794.0, rms=21.123 (17.079%) 003: dt: 0.5000, sse=10449482.0, rms=17.578 (16.783%) 004: dt: 0.5000, sse=8398261.0, rms=15.137 (13.888%) 005: dt: 0.5000, sse=7628856.5, rms=13.113 (13.371%) 006: dt: 0.5000, sse=7042457.5, rms=11.329 (13.599%) 007: dt: 0.5000, sse=6655003.0, rms=9.609 (15.185%) 008: dt: 0.5000, sse=6378594.5, rms=8.176 (14.914%) 009: dt: 0.5000, sse=6298967.5, rms=6.944 (15.073%) 010: dt: 0.5000, sse=6311626.5, rms=6.184 (10.934%) 011: dt: 0.5000, sse=6371887.5, rms=5.580 (9.780%) 012: dt: 0.5000, sse=6403467.5, rms=5.325 (4.563%) 013: dt: 0.5000, sse=6458166.5, rms=5.034 (5.467%) rms = 4.99, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=6490707.5, rms=4.985 (0.961%) 015: dt: 0.2500, sse=4303849.0, rms=3.717 (25.434%) 016: dt: 0.2500, sse=4029786.2, rms=3.312 (10.893%) 017: dt: 0.2500, sse=3853031.2, rms=3.191 (3.677%) 018: dt: 0.2500, sse=3821592.8, rms=3.108 (2.601%) rms = 3.06, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3780075.8, rms=3.060 (1.521%) 020: dt: 0.1250, sse=3556760.8, rms=2.827 (7.627%) rms = 2.79, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3527470.8, rms=2.792 (1.232%) positioning took 1.5 minutes mean border=54.4, 366 (10) missing vertices, mean dist 0.2 [0.2 (%38.7)->0.4 (%61.3))] %56 local maxima, %31 large gradients and % 8 min vals, 131 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, 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=4246032.5, rms=5.850 022: dt: 0.5000, sse=4438664.5, rms=4.695 (19.735%) rms = 4.81, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4016145.8, rms=3.663 (21.983%) 024: dt: 0.2500, sse=4029810.0, rms=3.191 (12.883%) 025: dt: 0.2500, sse=4000602.5, rms=3.012 (5.608%) 026: dt: 0.2500, sse=4022911.2, rms=2.922 (3.004%) rms = 2.88, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=4001478.0, rms=2.878 (1.495%) 028: dt: 0.1250, sse=3815503.2, rms=2.611 (9.281%) 029: dt: 0.1250, sse=3794366.8, rms=2.560 (1.939%) rms = 2.55, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3773497.2, rms=2.551 (0.354%) positioning took 0.7 minutes mean border=51.8, 536 (5) missing vertices, mean dist 0.1 [0.1 (%35.1)->0.3 (%64.9))] %69 local maxima, %18 large gradients and % 8 min vals, 182 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, 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=4033488.5, rms=4.128 rms = 4.72, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3832611.2, rms=3.178 (23.017%) 032: dt: 0.2500, sse=3843435.8, rms=2.817 (11.347%) 033: dt: 0.2500, sse=3989419.5, rms=2.643 (6.192%) rms = 2.62, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4055573.8, rms=2.618 (0.940%) 035: dt: 0.1250, sse=3880033.5, rms=2.385 (8.914%) rms = 2.34, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=3868823.5, rms=2.341 (1.835%) positioning took 0.5 minutes mean border=50.5, 1141 (3) missing vertices, mean dist 0.1 [0.2 (%43.5)->0.2 (%56.5))] %73 local maxima, %14 large gradients and % 8 min vals, 144 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3920884.0, rms=2.788 rms = 4.14, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=3814355.8, rms=2.376 (14.789%) 038: dt: 0.2500, sse=3921571.5, rms=2.326 (2.114%) rms = 2.30, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3976204.2, rms=2.296 (1.276%) 040: dt: 0.1250, sse=3899454.0, rms=2.150 (6.368%) rms = 2.13, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3885617.2, rms=2.132 (0.817%) positioning took 0.4 minutes writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial vertex spacing 0.99 +- 0.39 (0.08-->5.80) (max @ vno 67751 --> 68671) face area 0.40 +- 0.28 (0.00-->5.29) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119710 vertices processed 25000 of 119710 vertices processed 50000 of 119710 vertices processed 75000 of 119710 vertices processed 100000 of 119710 vertices processed 0 of 119710 vertices processed 25000 of 119710 vertices processed 50000 of 119710 vertices processed 75000 of 119710 vertices processed 100000 of 119710 vertices processed thickness calculation complete, 93:401 truncations. 46960 vertices at 0 distance 98921 vertices at 1 distance 59888 vertices at 2 distance 17297 vertices at 3 distance 3958 vertices at 4 distance 1049 vertices at 5 distance 330 vertices at 6 distance 141 vertices at 7 distance 69 vertices at 8 distance 35 vertices at 9 distance 19 vertices at 10 distance 11 vertices at 11 distance 11 vertices at 12 distance 13 vertices at 13 distance 3 vertices at 14 distance 10 vertices at 15 distance 8 vertices at 16 distance 3 vertices at 17 distance 8 vertices at 18 distance 1 vertices at 19 distance 5 vertices at 20 distance writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness positioning took 4.7 minutes #-------------------------------------------- #@# Surf Volume lh Mon Dec 21 03:30:05 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Total face volume 189946 Total vertex volume 186305 (mask=0) #@# MRM_003_w_070655_171011_0000FD62 lh 186305 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Mon Dec 21 03:30:09 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Total face volume 176418 Total vertex volume 172579 (mask=0) #@# MRM_003_w_070655_171011_0000FD62 rh 172579 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Mon Dec 21 03:30:12 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 SUBJECTS_DIR is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 45 writing volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Mon Dec 21 03:38:31 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189946 Total vertex volume 186305 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1151 813 1559 2.013 0.414 0.091 0.017 5 0.8 bankssts 1058 729 1826 2.487 0.632 0.142 0.023 19 0.9 caudalanteriorcingulate 3555 2431 5727 2.159 0.479 0.128 0.029 37 4.1 caudalmiddlefrontal 2078 1317 2316 1.658 0.378 0.146 0.036 31 3.0 cuneus 468 353 1451 3.513 0.710 0.127 0.032 3 0.6 entorhinal 4045 2722 7065 2.300 0.627 0.135 0.032 58 5.1 fusiform 5530 3689 7787 1.957 0.471 0.133 0.030 68 6.8 inferiorparietal 4746 3212 9560 2.516 0.738 0.134 0.034 76 6.6 inferiortemporal 1458 949 1963 1.930 0.662 0.118 0.032 21 1.6 isthmuscingulate 6049 3827 7195 1.778 0.469 0.144 0.035 92 8.2 lateraloccipital 3453 2348 6083 2.407 0.597 0.144 0.037 50 5.1 lateralorbitofrontal 4895 3202 5764 1.729 0.468 0.148 0.044 72 8.3 lingual 3087 2035 4639 2.171 0.728 0.128 0.037 49 4.7 medialorbitofrontal 3666 2464 7474 2.612 0.620 0.132 0.030 52 4.6 middletemporal 826 563 2010 3.101 0.873 0.114 0.031 9 0.9 parahippocampal 2017 1249 3089 2.273 0.544 0.099 0.021 15 1.7 paracentral 1866 1264 2773 2.061 0.477 0.128 0.027 23 1.9 parsopercularis 860 602 2019 2.618 0.646 0.170 0.046 17 1.7 parsorbitalis 1619 1094 2463 2.061 0.508 0.142 0.033 22 2.0 parstriangularis 2386 1589 2062 1.445 0.419 0.134 0.031 28 3.2 pericalcarine 5890 3862 7867 1.890 0.564 0.109 0.023 56 5.4 postcentral 1688 1137 2646 2.123 0.632 0.124 0.025 23 1.5 posteriorcingulate 7185 4532 11926 2.396 0.577 0.106 0.024 58 7.0 precentral 4892 3247 6957 2.004 0.526 0.128 0.031 67 5.9 precuneus 1259 855 2454 2.491 0.696 0.141 0.037 22 2.1 rostralanteriorcingulate 8165 5625 13334 2.068 0.530 0.149 0.038 134 12.9 rostralmiddlefrontal 10113 6851 18720 2.386 0.557 0.125 0.029 111 11.4 superiorfrontal 8328 5493 11082 1.832 0.450 0.114 0.022 83 7.3 superiorparietal 4305 2984 8573 2.479 0.647 0.104 0.018 35 3.2 superiortemporal 5143 3424 7942 2.098 0.525 0.127 0.027 65 5.4 supramarginal 287 201 723 2.650 0.406 0.176 0.048 7 0.6 frontalpole 610 426 2099 3.430 0.862 0.134 0.034 8 0.8 temporalpole 688 395 1034 2.342 0.330 0.116 0.027 7 0.6 transversetemporal 3057 2030 6125 2.936 0.878 0.116 0.032 29 3.6 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 MRM_003_w_070655_171011_0000FD62 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189946 Total vertex volume 186305 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1151 741 1559 2.013 0.414 0.102 0.024 12 1.2 bankssts 1058 801 1826 2.487 0.632 0.173 0.045 45 1.9 caudalanteriorcingulate 3555 2830 5727 2.159 0.479 0.134 0.024 37 3.6 caudalmiddlefrontal 2078 1580 2316 1.658 0.378 0.139 0.030 22 2.7 cuneus 468 509 1451 3.513 0.710 0.165 0.038 6 0.9 entorhinal 4045 3313 7065 2.300 0.627 0.150 0.037 76 6.8 fusiform 5530 4273 7787 1.957 0.471 0.137 0.028 57 6.8 inferiorparietal 4746 4232 9560 2.516 0.738 0.153 0.035 69 7.2 inferiortemporal 1458 1130 1963 1.930 0.662 0.155 0.045 31 3.1 isthmuscingulate 6049 4507 7195 1.778 0.469 0.141 0.030 105 7.4 lateraloccipital 3453 2675 6083 2.407 0.597 0.149 0.040 150 5.6 lateralorbitofrontal 4895 3710 5764 1.729 0.468 0.141 0.036 91 7.6 lingual 3087 2366 4639 2.171 0.728 0.149 0.042 51 5.3 medialorbitofrontal 3666 3194 7474 2.612 0.620 0.141 0.028 44 4.5 middletemporal 826 769 2010 3.101 0.873 0.135 0.034 11 1.1 parahippocampal 2017 1478 3089 2.273 0.544 0.106 0.018 14 1.5 paracentral 1866 1455 2773 2.061 0.477 0.139 0.026 21 2.0 parsopercularis 860 899 2019 2.618 0.646 0.170 0.036 9 1.3 parsorbitalis 1619 1296 2463 2.061 0.508 0.159 0.035 24 2.4 parstriangularis 2386 1377 2062 1.445 0.419 0.125 0.033 53 3.2 pericalcarine 5890 4626 7867 1.890 0.564 0.114 0.020 47 5.0 postcentral 1688 1288 2646 2.123 0.632 0.139 0.029 33 2.2 posteriorcingulate 7185 5314 11926 2.396 0.577 0.108 0.018 61 5.7 precentral 4892 3656 6957 2.004 0.526 0.134 0.030 59 6.2 precuneus 1259 1127 2454 2.491 0.696 0.159 0.038 32 1.9 rostralanteriorcingulate 8165 7107 13334 2.068 0.530 0.161 0.033 105 11.8 rostralmiddlefrontal 10113 8413 18720 2.386 0.557 0.141 0.029 112 12.4 superiorfrontal 8328 6518 11082 1.832 0.450 0.126 0.021 78 7.1 superiorparietal 4305 3708 8573 2.479 0.647 0.126 0.022 36 4.1 superiortemporal 5143 4016 7942 2.098 0.525 0.133 0.027 59 5.7 supramarginal 287 335 723 2.650 0.406 0.202 0.039 3 0.5 frontalpole 610 754 2099 3.430 0.862 0.190 0.038 7 1.1 temporalpole 688 510 1034 2.342 0.330 0.106 0.022 5 0.6 transversetemporal 3057 1934 6125 2.936 0.878 0.124 0.031 53 3.8 insula #----------------------------------------- #@# Parcellation Stats rh Mon Dec 21 03:39:31 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176418 Total vertex volume 172579 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 911 638 1064 1.736 0.305 0.110 0.020 7 0.7 bankssts 1221 834 2199 2.217 0.799 0.135 0.026 20 1.2 caudalanteriorcingulate 3004 2070 4657 1.996 0.496 0.122 0.026 29 3.1 caudalmiddlefrontal 2581 1520 2779 1.644 0.440 0.140 0.039 40 4.1 cuneus 373 261 1165 3.231 0.730 0.121 0.035 4 0.4 entorhinal 3563 2315 5874 2.223 0.789 0.136 0.035 53 4.7 fusiform 5897 3915 7924 1.800 0.463 0.122 0.026 67 6.1 inferiorparietal 3935 2582 7083 2.301 0.678 0.130 0.031 56 4.8 inferiortemporal 1248 783 1836 2.197 0.740 0.127 0.039 20 1.8 isthmuscingulate 6066 3671 6600 1.640 0.431 0.137 0.035 88 8.2 lateraloccipital 3678 2469 5903 2.187 0.563 0.144 0.040 63 5.9 lateralorbitofrontal 4670 2939 5166 1.733 0.496 0.139 0.039 69 7.8 lingual 2710 1745 4171 2.136 0.625 0.132 0.029 50 3.3 medialorbitofrontal 4104 2752 7655 2.404 0.646 0.127 0.028 54 4.9 middletemporal 887 602 1837 2.736 0.782 0.112 0.026 9 0.8 parahippocampal 2259 1390 3455 2.233 0.568 0.104 0.022 15 2.0 paracentral 1942 1299 3061 2.156 0.494 0.117 0.042 84 4.4 parsopercularis 1014 688 1768 2.353 0.559 0.162 0.039 18 1.6 parsorbitalis 2135 1444 3363 2.098 0.448 0.129 0.028 27 2.5 parstriangularis 2464 1595 2134 1.434 0.394 0.126 0.035 28 3.6 pericalcarine 5813 3755 8103 1.907 0.617 0.103 0.021 51 5.1 postcentral 1541 1044 2469 2.149 0.710 0.145 0.031 24 1.9 posteriorcingulate 6443 4130 10702 2.374 0.602 0.106 0.021 48 5.6 precentral 4896 3197 6538 1.929 0.527 0.123 0.028 54 5.3 precuneus 978 654 1811 2.528 0.527 0.134 0.030 15 1.2 rostralanteriorcingulate 7649 5312 12055 1.981 0.524 0.150 0.036 126 11.3 rostralmiddlefrontal 9871 6685 17737 2.287 0.564 0.130 0.031 120 12.3 superiorfrontal 6595 4351 8432 1.743 0.464 0.120 0.024 72 6.3 superiorparietal 4562 3073 8496 2.432 0.583 0.102 0.018 38 3.3 superiortemporal 4202 2724 6351 2.141 0.470 0.125 0.028 50 4.6 supramarginal 364 258 924 2.528 0.591 0.199 0.053 10 0.8 frontalpole 506 340 2187 3.808 0.640 0.134 0.041 7 0.8 temporalpole 624 347 820 2.082 0.339 0.104 0.023 7 0.5 transversetemporal 3600 2320 6259 2.548 1.002 0.120 0.041 45 5.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab MRM_003_w_070655_171011_0000FD62 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176418 Total vertex volume 172579 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 911 580 1064 1.736 0.305 0.108 0.022 9 0.8 bankssts 1221 1058 2199 2.217 0.799 0.168 0.045 41 2.3 caudalanteriorcingulate 3004 2527 4657 1.996 0.496 0.135 0.024 30 2.9 caudalmiddlefrontal 2581 1919 2779 1.644 0.440 0.142 0.030 31 3.3 cuneus 373 418 1165 3.231 0.730 0.165 0.043 7 0.6 entorhinal 3563 2784 5874 2.223 0.789 0.142 0.033 55 5.2 fusiform 5897 4832 7924 1.800 0.463 0.137 0.023 59 6.3 inferiorparietal 3935 3368 7083 2.301 0.678 0.147 0.031 52 5.4 inferiortemporal 1248 915 1836 2.197 0.740 0.155 0.047 38 2.8 isthmuscingulate 6066 4514 6600 1.640 0.431 0.137 0.029 70 7.5 lateraloccipital 3678 2913 5903 2.187 0.563 0.153 0.038 58 5.9 lateralorbitofrontal 4670 3291 5166 1.733 0.496 0.128 0.031 60 6.4 lingual 2710 2212 4171 2.136 0.625 0.143 0.031 49 3.7 medialorbitofrontal 4104 3588 7655 2.404 0.646 0.141 0.026 44 4.5 middletemporal 887 732 1837 2.736 0.782 0.131 0.029 11 1.1 parahippocampal 2259 1653 3455 2.233 0.568 0.113 0.020 19 1.9 paracentral 1942 1506 3061 2.156 0.494 0.129 0.025 23 2.1 parsopercularis 1014 831 1768 2.353 0.559 0.151 0.036 13 1.5 parsorbitalis 2135 1816 3363 2.098 0.448 0.146 0.029 25 2.8 parstriangularis 2464 1502 2134 1.434 0.394 0.111 0.028 28 2.9 pericalcarine 5813 4685 8103 1.907 0.617 0.116 0.018 44 4.6 postcentral 1541 1196 2469 2.149 0.710 0.153 0.031 36 2.2 posteriorcingulate 6443 4787 10702 2.374 0.602 0.105 0.017 51 4.7 precentral 4896 3563 6538 1.929 0.527 0.131 0.027 54 5.3 precuneus 978 801 1811 2.528 0.527 0.172 0.048 82 2.1 rostralanteriorcingulate 7649 6735 12055 1.981 0.524 0.163 0.034 96 11.0 rostralmiddlefrontal 9871 8502 17737 2.287 0.564 0.147 0.031 114 12.6 superiorfrontal 6595 5235 8432 1.743 0.464 0.133 0.023 63 6.1 superiorparietal 4562 3792 8496 2.432 0.583 0.119 0.020 39 3.9 superiortemporal 4202 3086 6351 2.141 0.470 0.128 0.026 45 4.3 supramarginal 364 453 924 2.528 0.591 0.226 0.039 6 0.6 frontalpole 506 743 2187 3.808 0.640 0.195 0.036 4 0.8 temporalpole 624 436 820 2.082 0.339 0.096 0.015 3 0.3 transversetemporal 3600 2347 6259 2.548 1.002 0.139 0.112 117 26.0 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Dec 21 03:40:32 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 32 labels changed using aseg relabeling using gibbs priors... 000: 8490 changed, 123724 examined... 001: 2002 changed, 32076 examined... 002: 590 changed, 10417 examined... 003: 228 changed, 3371 examined... 004: 111 changed, 1351 examined... 005: 43 changed, 631 examined... 006: 30 changed, 246 examined... 007: 23 changed, 169 examined... 008: 12 changed, 129 examined... 009: 7 changed, 63 examined... 010: 1 changed, 40 examined... 011: 1 changed, 6 examined... 012: 2 changed, 5 examined... 013: 0 changed, 13 examined... 9 labels changed using aseg 000: 284 total segments, 203 labels (2182 vertices) changed 001: 94 total segments, 15 labels (127 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 121 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1063 vertices marked for relabeling... 1063 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 51 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Mon Dec 21 03:41:23 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 2 labels changed using aseg relabeling using gibbs priors... 000: 8276 changed, 119710 examined... 001: 1979 changed, 32094 examined... 002: 597 changed, 10177 examined... 003: 256 changed, 3211 examined... 004: 118 changed, 1435 examined... 005: 64 changed, 701 examined... 006: 45 changed, 369 examined... 007: 18 changed, 218 examined... 008: 10 changed, 98 examined... 009: 10 changed, 61 examined... 010: 7 changed, 55 examined... 011: 11 changed, 48 examined... 012: 5 changed, 49 examined... 013: 3 changed, 20 examined... 014: 4 changed, 21 examined... 015: 2 changed, 16 examined... 016: 0 changed, 12 examined... 2 labels changed using aseg 000: 207 total segments, 125 labels (1273 vertices) changed 001: 89 total segments, 7 labels (52 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 129 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1151 vertices marked for relabeling... 1151 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 49 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Dec 21 03:42:12 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189946 Total vertex volume 186305 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1230 838 1968 2.141 0.557 0.150 0.032 20 1.7 G_and_S_frontomargin 1474 956 1769 1.760 0.431 0.149 0.036 23 2.0 G_and_S_occipital_inf 1509 896 2308 2.155 0.597 0.112 0.030 16 1.8 G_and_S_paracentral 1400 910 2648 2.580 0.497 0.133 0.029 17 1.4 G_and_S_subcentral 545 395 1364 2.565 0.423 0.183 0.054 12 1.3 G_and_S_transv_frontopol 2376 1623 3878 2.248 0.577 0.123 0.029 29 3.0 G_and_S_cingul-Ant 1758 1199 2954 2.273 0.565 0.128 0.025 23 1.6 G_and_S_cingul-Mid-Ant 1225 852 2047 2.343 0.498 0.108 0.020 10 0.9 G_and_S_cingul-Mid-Post 512 335 1030 2.466 0.589 0.155 0.041 10 0.8 G_cingul-Post-dorsal 313 174 347 1.751 0.625 0.114 0.043 4 0.4 G_cingul-Post-ventral 1982 1244 2208 1.624 0.418 0.154 0.038 34 3.0 G_cuneus 1244 825 2298 2.252 0.507 0.133 0.030 19 1.5 G_front_inf-Opercular 313 207 883 2.944 0.412 0.154 0.032 4 0.5 G_front_inf-Orbital 984 649 1657 2.111 0.525 0.156 0.042 19 1.6 G_front_inf-Triangul 4750 3269 9065 2.224 0.500 0.156 0.042 85 8.1 G_front_middle 6582 4399 13946 2.564 0.520 0.134 0.033 89 8.7 G_front_sup 424 263 970 3.361 0.867 0.109 0.035 5 0.4 G_Ins_lg_and_S_cent_ins 631 420 2018 3.647 0.785 0.154 0.050 13 1.2 G_insular_short 1999 1263 3021 2.050 0.510 0.156 0.040 38 2.9 G_occipital_middle 1408 900 2035 1.925 0.416 0.135 0.031 18 1.7 G_occipital_sup 1223 794 2197 2.266 0.550 0.135 0.032 21 1.6 G_oc-temp_lat-fusifor 3560 2218 4247 1.725 0.490 0.154 0.049 58 7.1 G_oc-temp_med-Lingual 1046 732 3036 3.422 0.681 0.135 0.039 14 1.7 G_oc-temp_med-Parahip 2410 1622 4924 2.459 0.554 0.161 0.048 50 4.3 G_orbital 2289 1511 3771 2.038 0.445 0.142 0.035 38 3.0 G_pariet_inf-Angular 2683 1789 4996 2.298 0.499 0.141 0.030 43 3.3 G_pariet_inf-Supramar 3368 2231 5246 1.945 0.514 0.127 0.026 44 3.5 G_parietal_sup 2213 1414 3262 1.953 0.473 0.122 0.031 31 2.5 G_postcentral 2386 1441 4878 2.598 0.459 0.107 0.027 22 2.5 G_precentral 2225 1457 3859 2.132 0.575 0.146 0.040 44 3.1 G_precuneus 998 636 1843 2.233 0.576 0.137 0.041 19 1.6 G_rectus 652 448 1027 2.585 0.972 0.132 0.048 9 1.3 G_subcallosal 527 303 938 2.497 0.336 0.129 0.031 8 0.5 G_temp_sup-G_T_transv 1689 1146 4566 2.777 0.624 0.129 0.026 21 1.6 G_temp_sup-Lateral 420 287 1071 3.429 0.573 0.084 0.020 2 0.3 G_temp_sup-Plan_polar 673 503 950 1.846 0.399 0.077 0.013 3 0.3 G_temp_sup-Plan_tempo 2843 1890 6340 2.606 0.723 0.146 0.040 60 4.5 G_temporal_inf 2452 1615 5594 2.714 0.629 0.145 0.035 45 3.4 G_temporal_middle 381 258 473 1.865 0.427 0.128 0.022 4 0.3 Lat_Fis-ant-Horizont 198 142 223 1.728 0.567 0.141 0.022 2 0.1 Lat_Fis-ant-Vertical 1052 700 1175 2.011 0.422 0.113 0.022 7 1.0 Lat_Fis-post 2013 1181 2389 1.913 0.489 0.148 0.039 33 3.1 Pole_occipital 1597 1144 4913 3.253 0.759 0.142 0.042 23 2.5 Pole_temporal 3087 2146 3133 1.639 0.540 0.127 0.030 38 3.8 S_calcarine 3231 2127 3469 1.850 0.685 0.090 0.017 14 2.4 S_central 1108 772 1509 1.971 0.486 0.091 0.016 6 0.6 S_cingul-Marginalis 365 247 600 2.853 0.628 0.118 0.032 3 0.4 S_circular_insula_ant 1351 905 2137 2.582 0.727 0.079 0.012 5 0.7 S_circular_insula_inf 1666 1143 2285 2.351 0.439 0.108 0.020 8 1.5 S_circular_insula_sup 1265 888 2088 2.294 0.556 0.113 0.021 11 1.2 S_collat_transv_ant 374 250 419 1.609 0.367 0.153 0.036 5 0.5 S_collat_transv_post 1865 1286 2398 1.847 0.447 0.119 0.025 16 1.9 S_front_inf 1680 1139 2275 1.934 0.418 0.135 0.036 22 2.3 S_front_middle 3064 2100 4339 2.031 0.472 0.118 0.025 25 3.2 S_front_sup 605 388 472 1.444 0.324 0.097 0.012 4 0.4 S_interm_prim-Jensen 3163 2078 3347 1.679 0.359 0.104 0.018 25 2.3 S_intrapariet_and_P_trans 806 552 655 1.311 0.252 0.115 0.017 6 0.6 S_oc_middle_and_Lunatus 1141 756 1215 1.679 0.349 0.124 0.027 11 1.3 S_oc_sup_and_transversal 343 256 420 1.859 0.436 0.143 0.030 4 0.5 S_occipital_ant 982 652 1371 2.093 0.513 0.120 0.023 9 0.9 S_oc-temp_lat 1608 1119 2135 2.049 0.561 0.124 0.026 15 1.6 S_oc-temp_med_and_Lingual 483 327 538 1.797 0.405 0.126 0.026 5 0.5 S_orbital_lateral 675 496 865 1.939 0.585 0.112 0.021 5 0.5 S_orbital_med-olfact 1246 872 2193 2.493 0.721 0.150 0.040 17 2.1 S_orbital-H_Shaped 1765 1153 2097 1.918 0.480 0.107 0.022 11 1.7 S_parieto_occipital 1369 867 1206 1.878 0.836 0.129 0.026 24 1.2 S_pericallosal 2729 1828 3240 1.873 0.382 0.095 0.017 14 2.0 S_postcentral 1375 942 1785 2.041 0.391 0.109 0.021 9 1.2 S_precentral-inf-part 1079 716 1402 2.229 0.508 0.092 0.015 5 0.7 S_precentral-sup-part 534 347 762 2.183 0.698 0.136 0.030 9 0.6 S_suborbital 853 580 1026 1.822 0.384 0.122 0.023 8 0.7 S_subparietal 1085 740 1421 2.238 0.577 0.110 0.023 7 1.1 S_temporal_inf 3724 2569 4818 2.028 0.413 0.102 0.020 21 3.0 S_temporal_sup 245 191 356 2.203 0.340 0.114 0.012 2 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Mon Dec 21 03:42:44 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176418 Total vertex volume 172579 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1018 701 1616 1.946 0.626 0.155 0.039 19 1.6 G_and_S_frontomargin 1267 767 1489 1.765 0.457 0.144 0.038 19 1.7 G_and_S_occipital_inf 1386 801 1963 2.063 0.519 0.112 0.027 14 1.5 G_and_S_paracentral 1119 733 2159 2.650 0.461 0.121 0.027 12 1.1 G_and_S_subcentral 1109 772 2019 2.122 0.568 0.157 0.042 21 1.8 G_and_S_transv_frontopol 2541 1732 4276 2.367 0.496 0.135 0.029 36 3.0 G_and_S_cingul-Ant 1631 1105 3089 2.470 0.579 0.128 0.031 19 2.0 G_and_S_cingul-Mid-Ant 1397 955 2355 2.318 0.547 0.124 0.021 14 1.2 G_and_S_cingul-Mid-Post 497 319 1074 2.615 0.438 0.166 0.052 10 1.1 G_cingul-Post-dorsal 277 154 582 2.824 0.631 0.130 0.051 5 0.6 G_cingul-Post-ventral 2308 1341 2492 1.616 0.463 0.135 0.036 34 3.4 G_cuneus 1146 752 2292 2.423 0.466 0.128 0.029 17 1.4 G_front_inf-Opercular 391 259 758 2.287 0.451 0.170 0.043 8 0.7 G_front_inf-Orbital 1072 722 2050 2.235 0.417 0.142 0.034 18 1.6 G_front_inf-Triangul 3760 2660 7498 2.205 0.529 0.153 0.037 67 5.5 G_front_middle 6452 4247 13108 2.413 0.588 0.135 0.034 96 8.9 G_front_sup 448 310 1173 3.231 1.069 0.115 0.036 6 0.5 G_Ins_lg_and_S_cent_ins 696 427 1864 3.193 0.705 0.149 0.061 13 1.8 G_insular_short 2050 1247 2815 1.821 0.436 0.139 0.032 34 2.7 G_occipital_middle 1743 1079 2303 1.816 0.466 0.135 0.030 24 2.0 G_occipital_sup 1193 725 2004 2.138 0.603 0.132 0.035 21 1.5 G_oc-temp_lat-fusifor 3219 1923 3729 1.763 0.542 0.140 0.040 52 5.3 G_oc-temp_med-Lingual 1343 868 3261 3.004 0.770 0.135 0.051 20 2.6 G_oc-temp_med-Parahip 2487 1675 5101 2.447 0.538 0.158 0.047 54 4.3 G_orbital 2043 1300 3409 2.059 0.519 0.132 0.028 30 2.2 G_pariet_inf-Angular 2134 1332 3907 2.329 0.417 0.135 0.033 35 2.8 G_pariet_inf-Supramar 1733 1167 2821 1.947 0.500 0.124 0.027 23 1.9 G_parietal_sup 2107 1268 3462 2.123 0.526 0.109 0.025 25 2.1 G_postcentral 2368 1347 4819 2.663 0.495 0.103 0.024 21 2.3 G_precentral 1991 1280 3295 2.071 0.481 0.137 0.032 33 2.3 G_precuneus 859 512 1475 2.177 0.602 0.136 0.034 20 1.2 G_rectus 462 258 440 1.480 1.325 0.102 0.037 8 0.4 G_subcallosal 442 239 667 2.176 0.402 0.123 0.028 7 0.5 G_temp_sup-G_T_transv 1422 908 3192 2.601 0.615 0.130 0.028 21 1.5 G_temp_sup-Lateral 797 537 1793 2.897 0.532 0.082 0.017 3 0.5 G_temp_sup-Plan_polar 658 475 1060 1.991 0.458 0.075 0.013 2 0.3 G_temp_sup-Plan_tempo 2097 1365 4513 2.516 0.633 0.140 0.037 38 2.9 G_temporal_inf 2490 1625 5245 2.503 0.670 0.135 0.033 41 3.5 G_temporal_middle 380 249 425 2.038 0.442 0.091 0.016 2 0.2 Lat_Fis-ant-Horizont 255 177 336 2.076 0.545 0.146 0.022 3 0.3 Lat_Fis-ant-Vertical 1446 971 1797 2.078 0.438 0.108 0.023 9 1.4 Lat_Fis-post 2971 1731 3250 1.690 0.439 0.142 0.040 45 4.7 Pole_occipital 1369 953 4805 3.336 0.850 0.151 0.042 24 2.4 Pole_temporal 2927 1922 2881 1.660 0.523 0.124 0.035 33 4.4 S_calcarine 2931 2035 3403 1.842 0.647 0.096 0.017 14 2.2 S_central 1226 863 1415 1.726 0.440 0.107 0.019 7 1.0 S_cingul-Marginalis 571 383 716 2.310 0.409 0.103 0.022 3 0.5 S_circular_insula_ant 1048 690 1535 2.517 0.660 0.077 0.018 4 0.8 S_circular_insula_inf 1371 922 1898 2.332 0.397 0.105 0.045 70 3.8 S_circular_insula_sup 819 531 1164 2.261 0.610 0.110 0.024 9 0.7 S_collat_transv_ant 515 356 462 1.468 0.343 0.137 0.030 4 0.7 S_collat_transv_post 1665 1154 2005 1.759 0.425 0.122 0.025 14 1.6 S_front_inf 2107 1433 2621 1.804 0.402 0.143 0.033 28 2.8 S_front_middle 2434 1687 3316 1.919 0.425 0.116 0.029 23 3.0 S_front_sup 161 105 162 1.892 0.283 0.148 0.037 2 0.2 S_interm_prim-Jensen 2436 1658 2437 1.548 0.316 0.103 0.018 18 1.6 S_intrapariet_and_P_trans 931 627 744 1.336 0.299 0.132 0.031 9 1.2 S_oc_middle_and_Lunatus 1483 1004 1417 1.490 0.318 0.121 0.025 12 1.6 S_oc_sup_and_transversal 479 327 468 1.430 0.457 0.105 0.023 7 0.4 S_occipital_ant 818 558 863 1.676 0.396 0.130 0.022 9 0.8 S_oc-temp_lat 1443 1025 1837 2.084 0.571 0.124 0.026 13 1.5 S_oc-temp_med_and_Lingual 377 256 387 1.825 0.366 0.127 0.023 3 0.4 S_orbital_lateral 932 631 1040 1.791 0.582 0.116 0.029 9 1.0 S_orbital_med-olfact 1290 885 1821 2.007 0.544 0.141 0.033 19 1.9 S_orbital-H_Shaped 2092 1367 2290 1.781 0.470 0.118 0.025 19 2.1 S_parieto_occipital 1423 904 1219 1.794 0.728 0.130 0.027 26 1.2 S_pericallosal 2381 1618 2447 1.598 0.394 0.106 0.019 17 1.8 S_postcentral 1436 1005 1812 1.923 0.448 0.105 0.017 9 1.0 S_precentral-inf-part 1203 837 1388 1.877 0.485 0.113 0.019 9 1.1 S_precentral-sup-part 500 319 675 2.117 0.665 0.118 0.021 8 0.4 S_suborbital 873 584 1093 1.805 0.484 0.138 0.037 10 1.3 S_subparietal 1173 784 1427 2.001 0.465 0.131 0.025 13 1.3 S_temporal_inf 4432 3077 5545 1.891 0.433 0.101 0.017 28 3.3 S_temporal_sup 255 181 309 2.102 0.500 0.110 0.013 2 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Mon Dec 21 03:43:15 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 799 labels changed using aseg relabeling using gibbs priors... 000: 2580 changed, 123724 examined... 001: 602 changed, 10982 examined... 002: 165 changed, 3390 examined... 003: 53 changed, 948 examined... 004: 28 changed, 330 examined... 005: 16 changed, 156 examined... 006: 9 changed, 98 examined... 007: 6 changed, 53 examined... 008: 7 changed, 37 examined... 009: 5 changed, 43 examined... 010: 4 changed, 30 examined... 011: 2 changed, 21 examined... 012: 0 changed, 9 examined... 106 labels changed using aseg 000: 49 total segments, 16 labels (200 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 873 vertices marked for relabeling... 873 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Mon Dec 21 03:44:01 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 942 labels changed using aseg relabeling using gibbs priors... 000: 2320 changed, 119710 examined... 001: 526 changed, 10138 examined... 002: 124 changed, 2882 examined... 003: 43 changed, 692 examined... 004: 20 changed, 253 examined... 005: 13 changed, 120 examined... 006: 5 changed, 67 examined... 007: 2 changed, 36 examined... 008: 2 changed, 14 examined... 009: 3 changed, 14 examined... 010: 1 changed, 17 examined... 011: 1 changed, 7 examined... 012: 1 changed, 8 examined... 013: 0 changed, 7 examined... 115 labels changed using aseg 000: 57 total segments, 24 labels (276 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 22 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 783 vertices marked for relabeling... 783 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 45 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Dec 21 03:44:46 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189946 Total vertex volume 186305 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1663 1133 2758 2.445 0.563 0.133 0.025 27 1.5 caudalanteriorcingulate 3572 2431 5809 2.172 0.473 0.127 0.029 38 4.2 caudalmiddlefrontal 2825 1810 3201 1.679 0.378 0.138 0.033 39 3.7 cuneus 464 359 1401 3.394 0.686 0.124 0.028 3 0.6 entorhinal 3594 2402 5749 2.204 0.558 0.131 0.029 49 4.1 fusiform 5433 3612 7597 1.946 0.474 0.134 0.030 67 6.7 inferiorparietal 4801 3229 9932 2.558 0.767 0.137 0.037 80 7.0 inferiortemporal 1397 906 1883 1.935 0.642 0.121 0.033 21 1.6 isthmuscingulate 6323 3999 7593 1.792 0.473 0.145 0.035 96 8.7 lateraloccipital 4007 2717 7233 2.448 0.654 0.145 0.039 62 6.0 lateralorbitofrontal 4893 3190 5743 1.728 0.471 0.148 0.044 73 8.4 lingual 2366 1581 3734 2.099 0.641 0.133 0.036 40 3.5 medialorbitofrontal 4794 3267 9349 2.508 0.635 0.127 0.028 60 5.6 middletemporal 826 566 2011 3.110 0.879 0.115 0.031 9 0.9 parahippocampal 2327 1460 3579 2.300 0.525 0.098 0.020 16 2.0 paracentral 1649 1120 2394 2.085 0.483 0.124 0.026 18 1.6 parsopercularis 908 618 1896 2.431 0.630 0.136 0.032 11 1.1 parsorbitalis 1996 1362 2957 1.996 0.491 0.144 0.033 29 2.8 parstriangularis 2395 1600 2088 1.448 0.418 0.134 0.032 28 3.2 pericalcarine 6687 4414 9018 1.900 0.557 0.110 0.024 64 6.2 postcentral 1856 1255 2842 2.137 0.647 0.122 0.024 24 1.6 posteriorcingulate 7118 4502 11784 2.399 0.576 0.106 0.024 57 7.0 precentral 4713 3136 6952 2.034 0.531 0.131 0.033 70 5.8 precuneus 1735 1137 2936 2.367 0.733 0.136 0.036 28 2.8 rostralanteriorcingulate 5557 3835 9024 2.063 0.557 0.148 0.039 92 8.8 rostralmiddlefrontal 11555 7870 21620 2.342 0.565 0.134 0.033 148 15.0 superiorfrontal 6745 4446 8870 1.823 0.449 0.109 0.020 61 5.6 superiorparietal 5919 4100 12234 2.539 0.746 0.106 0.021 52 4.8 superiortemporal 4924 3279 7550 2.102 0.527 0.128 0.027 61 5.1 supramarginal 651 369 988 2.355 0.330 0.116 0.026 7 0.5 transversetemporal 2730 1808 5578 2.961 0.883 0.116 0.030 26 3.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Mon Dec 21 03:45:14 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176418 Total vertex volume 172579 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1266 863 2253 2.223 0.790 0.135 0.026 20 1.3 caudalanteriorcingulate 3005 2079 4670 2.002 0.496 0.121 0.026 28 3.1 caudalmiddlefrontal 3011 1808 3313 1.667 0.434 0.140 0.037 45 4.6 cuneus 390 271 1191 3.227 0.717 0.121 0.035 4 0.5 entorhinal 3017 1960 4653 2.143 0.680 0.134 0.034 44 3.8 fusiform 5527 3655 7472 1.811 0.467 0.125 0.026 64 6.0 inferiorparietal 4365 2870 8192 2.357 0.763 0.133 0.032 65 5.7 inferiortemporal 1254 785 1835 2.195 0.737 0.127 0.039 20 1.8 isthmuscingulate 6484 3934 7005 1.630 0.433 0.137 0.034 94 8.7 lateraloccipital 4327 2904 7128 2.188 0.614 0.149 0.043 79 7.4 lateralorbitofrontal 4639 2923 5130 1.733 0.497 0.140 0.039 69 7.8 lingual 2408 1496 3438 1.970 0.846 0.122 0.029 42 2.5 medialorbitofrontal 4895 3297 8571 2.293 0.657 0.123 0.027 60 5.6 middletemporal 868 593 1819 2.752 0.771 0.111 0.026 9 0.8 parahippocampal 2360 1449 3637 2.248 0.568 0.105 0.023 16 2.2 paracentral 2044 1364 3225 2.164 0.493 0.120 0.042 86 4.7 parsopercularis 1137 764 1840 2.245 0.498 0.146 0.034 17 1.6 parsorbitalis 2038 1394 3169 2.052 0.459 0.126 0.027 25 2.3 parstriangularis 2493 1609 2152 1.433 0.391 0.126 0.035 28 3.6 pericalcarine 6287 4064 8733 1.908 0.620 0.106 0.022 57 5.7 postcentral 1683 1138 2759 2.176 0.694 0.143 0.030 26 2.0 posteriorcingulate 6195 3952 10394 2.389 0.600 0.107 0.021 47 5.4 precentral 4904 3197 6670 1.933 0.531 0.122 0.027 53 5.3 precuneus 1106 732 1992 2.506 0.505 0.139 0.031 19 1.5 rostralanteriorcingulate 4669 3261 7334 1.976 0.523 0.149 0.035 74 6.6 rostralmiddlefrontal 13073 8899 22831 2.220 0.564 0.136 0.033 182 17.6 superiorfrontal 5556 3671 7154 1.752 0.462 0.116 0.024 60 5.1 superiorparietal 5816 3917 11622 2.506 0.728 0.106 0.022 52 4.9 superiortemporal 4007 2608 6016 2.133 0.452 0.122 0.028 46 4.2 supramarginal 597 327 787 2.077 0.344 0.103 0.023 7 0.5 transversetemporal 2885 1916 5595 2.761 0.807 0.118 0.036 30 4.2 insula #----------------------------------------- #@# WM/GM Contrast lh Mon Dec 21 03:45:44 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts pctsurfcon --s MRM_003_w_070655_171011_0000FD62 --lh-only Log file is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/pctsurfcon.log Mon Dec 21 03:45:45 GMT 2015 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.wm.mgh --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 68451 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.wm.mgh Dim: 123724 1 1 mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.gm.mgh --projfrac 0.3 --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Done reading source surface Reading thickness /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 81171 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.gm.mgh Dim: 123724 1 1 mri_concat /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.wm.mgh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30217/lh.gm.mgh --paired-diff-norm --mul 100 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 lh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 lh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/lh.w-g.pct.stats --snr sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 Constructing seg from annotation Reading annotation /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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) Seg base 1000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh Vertex Area is 0.66517 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 Mon Dec 21 03:45:51 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts pctsurfcon --s MRM_003_w_070655_171011_0000FD62 --rh-only Log file is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/pctsurfcon.log Mon Dec 21 03:45:51 GMT 2015 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.wm.mgh --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 64966 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.wm.mgh Dim: 119710 1 1 mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.gm.mgh --projfrac 0.3 --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Done reading source surface Reading thickness /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 78821 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.gm.mgh Dim: 119710 1 1 mri_concat /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.wm.mgh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.30268/rh.gm.mgh --paired-diff-norm --mul 100 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 rh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 rh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/rh.w-g.pct.stats --snr sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 Constructing seg from annotation Reading annotation /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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) Seg base 2000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh Vertex Area is 0.655866 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 Mon Dec 21 03:45:57 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 428 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 262 voxels changed to hypointensity... 634 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg Mon Dec 21 03:46:16 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_aparc2aseg --s MRM_003_w_070655_171011_0000FD62 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer subject MRM_003_w_070655_171011_0000FD62 outvol /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 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/exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 357658 Used brute-force search on 0 voxels Writing output aseg to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Mon Dec 21 03:48:44 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Mon Dec 21 03:48:44 GMT 2015 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 $Id: apas2aseg,v 1.1 2014/08/14 22:25:53 greve Exp $ Linux eddie423 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 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 1.41 2014/08/17 17:47:29 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri cmdline 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 sysname Linux hostname eddie423 machine x86_64 user s1158296 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 Mon Dec 21 03:48:44 GMT 2015 Ended at Mon Dec 21 03:48:51 GMT 2015 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Mon Dec 21 03:48:51 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/ASegStatsLUT.txt --subject MRM_003_w_070655_171011_0000FD62 $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/ASegStatsLUT.txt --subject MRM_003_w_070655_171011_0000FD62 sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) Computing euler number orig.nofix lheno = -30, rheno = -28 orig.nofix lhholes = 16, rhholes = 15 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 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 Mon Dec 21 03:51:17 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_aparc2aseg --s MRM_003_w_070655_171011_0000FD62 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer subject MRM_003_w_070655_171011_0000FD62 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc+aseg.mgz Reading lh white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz Loading filled from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7301 vertices from left hemi Ripped 7404 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aseg.mgz Loading Ctx Seg File /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 764243 Used brute-force search on 33 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 19.000000 7 k 1224.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 3.000000 2 k 1.000000 3 k 1.000000 4 k 1283.000000 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 MRM_003_w_070655_171011_0000FD62 --surf-wm-vol --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 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 MRM_003_w_070655_171011_0000FD62 --surf-wm-vol --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname eddie423 machine x86_64 user s1158296 UseRobust 0 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Dec 21 03:59:45 GMT 2015 mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4345 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 470 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8379 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4265 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 257 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4327 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 961 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14550 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 308 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3865 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 1889 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6530 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 2770 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10884 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2201 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1270 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1043 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2222 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2112 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1665 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7282 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2022 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1366 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 1498 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4903 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 1269 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4603 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 549 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 484 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123724 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 464 mri_label2label: Done mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie423 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi lh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 84705 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.BA_exvivo.annot mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie423 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi lh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 100422 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189946 Total vertex volume 186305 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 942 586 1525 2.075 0.443 0.149 0.041 20 1.5 BA1_exvivo 3872 2554 5124 1.943 0.423 0.100 0.020 28 3.0 BA2_exvivo 1018 691 850 1.506 0.309 0.122 0.024 7 1.0 BA3a_exvivo 2298 1544 2839 1.686 0.567 0.107 0.023 21 2.2 BA3b_exvivo 1676 905 2873 2.671 0.496 0.096 0.027 13 1.8 BA4a_exvivo 1402 848 2061 2.482 0.513 0.085 0.021 6 1.3 BA4p_exvivo 8306 5508 15799 2.424 0.551 0.117 0.027 81 8.7 BA6_exvivo 2271 1539 3602 2.127 0.477 0.125 0.027 27 2.4 BA44_exvivo 2509 1731 3787 1.948 0.538 0.142 0.033 36 3.3 BA45_exvivo 4156 2623 4129 1.575 0.477 0.134 0.038 56 6.3 V1_exvivo 8030 5127 9251 1.754 0.463 0.155 0.041 133 13.3 V2_exvivo 1448 984 1788 1.800 0.459 0.137 0.029 19 1.6 MT_exvivo 499 313 1165 3.342 0.724 0.119 0.026 7 0.5 perirhinal_exvivo 592 450 1821 3.635 0.763 0.147 0.042 7 1.1 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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189946 Total vertex volume 186305 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 556 311 881 2.143 0.398 0.158 0.049 13 0.9 BA1_exvivo 1473 975 2078 1.989 0.424 0.092 0.017 10 1.0 BA2_exvivo 852 583 692 1.499 0.315 0.126 0.025 6 0.9 BA3a_exvivo 1414 985 1389 1.380 0.295 0.078 0.014 6 0.8 BA3b_exvivo 1730 929 2820 2.644 0.488 0.086 0.024 10 1.7 BA4a_exvivo 1138 690 1601 2.437 0.521 0.089 0.022 5 1.1 BA4p_exvivo 4259 2801 8456 2.537 0.525 0.113 0.027 41 4.0 BA6_exvivo 1331 909 2069 2.074 0.456 0.132 0.028 18 1.4 BA44_exvivo 1055 724 1800 2.066 0.526 0.153 0.043 19 1.7 BA45_exvivo 4485 2803 4564 1.601 0.479 0.137 0.041 65 7.2 V1_exvivo 4118 2665 4500 1.675 0.453 0.162 0.043 71 7.4 V2_exvivo 376 276 470 1.692 0.406 0.154 0.031 7 0.5 MT_exvivo 236 153 761 3.596 0.505 0.098 0.015 1 0.2 perirhinal_exvivo 279 230 863 3.505 0.707 0.115 0.027 2 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Mon Dec 21 04:04:14 GMT 2015 mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4167 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4092 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6002 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4612 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 677 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12933 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 537 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7449 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 724 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6079 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 1861 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6588 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 2946 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2205 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1150 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 820 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 922 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2839 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1728 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2321 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1459 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1549 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1398 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 1371 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4603 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 1342 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4779 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 744 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119710 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 328 mri_label2label: Done mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie423 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi rh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 80718 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.BA_exvivo.annot mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie423 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi rh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 97020 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 176418 Total vertex volume 172579 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 798 430 1392 2.320 0.450 0.125 0.034 14 1.0 BA1_exvivo 3059 2078 3808 1.742 0.487 0.101 0.017 21 2.2 BA2_exvivo 1014 724 896 1.532 0.407 0.127 0.024 7 1.1 BA3a_exvivo 1985 1280 2404 1.671 0.514 0.096 0.020 17 1.8 BA3b_exvivo 1483 796 2475 2.570 0.469 0.093 0.021 8 1.4 BA4a_exvivo 1115 732 1836 2.523 0.521 0.088 0.017 5 0.7 BA4p_exvivo 7284 4752 13281 2.347 0.593 0.115 0.025 67 7.2 BA6_exvivo 3170 2147 5129 2.216 0.517 0.117 0.033 94 5.5 BA44_exvivo 3878 2619 5962 2.037 0.489 0.133 0.031 51 4.8 BA45_exvivo 4395 2684 4343 1.572 0.440 0.133 0.040 61 7.2 V1_exvivo 8257 5043 8892 1.696 0.475 0.140 0.037 118 12.5 V2_exvivo 1757 1169 1783 1.502 0.447 0.120 0.025 23 1.7 MT_exvivo 449 293 1186 3.294 0.622 0.144 0.051 8 0.9 perirhinal_exvivo 348 241 826 3.056 0.777 0.127 0.028 4 0.4 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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 176418 Total vertex volume 172579 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186609.144 186486.000 diff= 123.1 pctdiff= 0.066 rhCtxGM: 172679.428 172362.000 diff= 317.4 pctdiff= 0.184 lhCtxWM: 209585.497 209888.000 diff= -302.5 pctdiff=-0.144 rhCtxWM: 197385.436 197668.000 diff= -282.6 pctdiff=-0.143 SubCortGMVol 48444.000 SupraTentVol 835564.505 (834699.000) diff=865.505 pctdiff=0.104 SupraTentVolNotVent 815816.505 (814951.000) diff=865.505 pctdiff=0.106 BrainSegVol 964504.000 (960735.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939732.000 (939392.505) diff=339.495 pctdiff=0.036 BrainSegVolNotVent 939732.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 589 303 1017 2.335 0.385 0.124 0.030 9 0.8 BA1_exvivo 1903 1265 2464 1.783 0.535 0.092 0.016 13 1.2 BA2_exvivo 876 644 723 1.478 0.349 0.136 0.026 6 1.0 BA3a_exvivo 1608 1080 1712 1.524 0.411 0.084 0.015 8 1.1 BA3b_exvivo 897 460 1504 2.629 0.518 0.091 0.024 6 0.9 BA4a_exvivo 978 651 1643 2.569 0.518 0.085 0.015 4 0.6 BA4p_exvivo 4540 2945 8327 2.383 0.603 0.116 0.025 42 4.6 BA6_exvivo 859 579 1607 2.282 0.472 0.126 0.028 12 0.9 BA44_exvivo 1133 776 2127 2.214 0.445 0.143 0.034 18 1.6 BA45_exvivo 4234 2609 4096 1.555 0.434 0.132 0.039 58 6.8 V1_exvivo 4337 2640 4663 1.676 0.481 0.145 0.039 67 7.0 V2_exvivo 269 189 226 1.280 0.280 0.113 0.018 2 0.2 MT_exvivo 228 154 804 3.415 0.598 0.128 0.034 3 0.2 perirhinal_exvivo 239 157 506 2.941 0.611 0.098 0.032 2 0.2 entorhinal_exvivo #-------------------------------------------- #@# Segmentation of brainstem substructures Mon Dec 21 04:08:38 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/segmentBS.sh /exports/work/mcm_cric_nas/Kaiming/freesurfer/MCRv80 /exports/work/mcm_cric_nas/Kaiming/freesurfer MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer See log file: /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/brainstem-structures.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Mon Dec 21 04:29:17 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/segmentSF_T1.sh /exports/work/mcm_cric_nas/Kaiming/freesurfer/MCRv80 /exports/work/mcm_cric_nas/Kaiming/freesurfer MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer left See log file: /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/hippocampal-subfields-T1.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Mon Dec 21 04:52:03 GMT 2015 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/segmentSF_T1.sh /exports/work/mcm_cric_nas/Kaiming/freesurfer/MCRv80 /exports/work/mcm_cric_nas/Kaiming/freesurfer MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer right See log file: /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/hippocampal-subfields-T1.log #------------------------------------------ Started at Sun Dec 20 20:04:09 GMT 2015 Ended at Mon Dec 21 05:14:44 GMT 2015 #@#%# recon-all-run-time-hours 9.176 recon-all -s MRM_003_w_070655_171011_0000FD62 finished without error at Mon Dec 21 05:14:45 GMT 2015 New invocation of recon-all Tue Jan 12 16:30:08 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/recon-all -s MRM_003_w_070655_171011_0000FD62 -autorecon2-wm -autorecon3 subjid MRM_003_w_070655_171011_0000FD62 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Actual FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Linux eddie412 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 122880 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 27033600 kbytes descriptors 1024 memorylocked 301989888 kbytes maxproc 191984 total used free shared buffers cached Mem: 24594348 2840940 21753408 0 80408 141104 -/+ buffers/cache: 2619428 21974920 Swap: 50331640 37192 50294448 ######################################## program versions used $Id: recon-all,v 1.515.2.24 2015/10/01 21:23:52 greve 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: $ TimeStamp: 2016/01/12-16:30:08-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:09-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.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: 2016/01/12-16:30:09-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/12-16:30:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize.c,v 1.84.2.1 2015/08/13 17:12:10 zkaufman Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:10-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_watershed.cpp,v 1.100.2.1 2015/07/10 18:57:54 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:11-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:11-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:12-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:12-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_em_register.c,v 1.101.2.1 2015/06/24 20:18:26 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:13-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_normalize.c,v 1.62.2.1 2015/06/24 20:18:24 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:13-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_register.c,v 1.92.2.1 2015/06/24 20:18:25 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:14-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_label.c,v 1.108 2014/11/24 20:09:20 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:14-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:15-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:15-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:15-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_concatenate_lta.c,v 1.13.2.2 2015/08/19 16:36:35 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:16-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:17-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:17-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:18-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:18-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:19-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:19-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/12-16:30:20-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_make_surfaces.c,v 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:20-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:20-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:21-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_anatomical_stats.c,v 1.76.2.2 2015/07/06 21:59:22 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature_stats.c,v 1.64.4.1 2015/06/04 21:12:38 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_calc.c,v 1.51.2.2 2015/06/04 21:12:37 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/01/12-16:30:25-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_relabel_hypointensities.c,v 1.11.2.1 2015/05/15 18:45:54 nicks Exp $ User: s1158296 Machine: eddie412 Platform: Linux PlatformVersion: 2.6.32-431.20.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Tue Jan 12 16:30:25 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1825 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 71 (71), valley at 46 (46) csf peak at 17, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 72 (72), valley at 46 (46) csf peak at 17, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 37 seconds. #-------------------------------------------- #@# Mask BFS Tue Jan 12 16:34:04 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1434350 voxels in mask (pct= 8.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Jan 12 16:34:06 GMT 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname eddie412 machine x86_64 user s1158296 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 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 mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname eddie412 machine x86_64 user s1158296 input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 2595 values in range Counting number of voxels in first frame Found 2595 voxels in final mask Count: 2595 2595.000000 16777216 0.015467 mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 2595 deletes, 0 fills cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.2 +- 5.4 [80.0 --> 125.0] GM (72.0) : 70.1 +- 10.7 [30.0 --> 96.0] setting bottom of white matter range to 80.7 setting top of gray matter range to 91.4 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... 4647 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4112 filled 949 bright non-wm voxels segmented. 2704 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... 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 0.55 minutes reading wm segmentation from wm.seg.mgz... 86 voxels added to wm to prevent paths from MTL structures to cortex 2362 additional wm voxels added 0 additional wm voxels added SEG EDIT: 46720 voxels turned on, 39416 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 13 found - 13 modified | TOTAL: 23 pass 2 (xy-): 0 found - 13 modified | TOTAL: 23 pass 1 (yz+): 19 found - 19 modified | TOTAL: 42 pass 2 (yz+): 0 found - 19 modified | TOTAL: 42 pass 1 (yz-): 11 found - 11 modified | TOTAL: 53 pass 2 (yz-): 0 found - 11 modified | TOTAL: 53 pass 1 (xz+): 13 found - 13 modified | TOTAL: 66 pass 2 (xz+): 0 found - 13 modified | TOTAL: 66 pass 1 (xz-): 9 found - 9 modified | TOTAL: 75 pass 2 (xz-): 0 found - 9 modified | TOTAL: 75 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 11 found - 11 modified | TOTAL: 21 pass 2 (+++): 0 found - 11 modified | TOTAL: 21 pass 1 (+++): 6 found - 6 modified | TOTAL: 27 pass 2 (+++): 0 found - 6 modified | TOTAL: 27 Iteration Number : 1 pass 1 (++): 87 found - 87 modified | TOTAL: 87 pass 2 (++): 0 found - 87 modified | TOTAL: 87 pass 1 (+-): 60 found - 60 modified | TOTAL: 147 pass 2 (+-): 0 found - 60 modified | TOTAL: 147 pass 1 (--): 69 found - 69 modified | TOTAL: 216 pass 2 (--): 0 found - 69 modified | TOTAL: 216 pass 1 (-+): 46 found - 46 modified | TOTAL: 262 pass 2 (-+): 0 found - 46 modified | TOTAL: 262 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 5 found - 5 modified | TOTAL: 8 pass 2 (xy-): 0 found - 5 modified | TOTAL: 8 pass 1 (yz+): 0 found - 0 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 376 (out of 495933: 0.075817) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 2595 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue Jan 12 16:36:33 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10394; 0.11181 -0.17378 1.07020 -11.22430; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.97571 -0.07948 -0.10919 24.78552; 0.09932 1.23889 0.22222 -41.10394; 0.11181 -0.17378 1.07020 -11.22430; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1157 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (125, 119, 152), TAL = (3.0, 24.0, 9.0) talairach voxel to voxel transform 1.00713 0.07679 0.08681 -20.83151; -0.06011 0.77975 -0.16805 31.65449; -0.11498 0.11859 0.89805 17.80442; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 119, 152) --> (3.0, 24.0, 9.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, 24.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 24.00, 9.00) SRC: (109.27, 92.47, 156.12) search lh wm seed point around talairach space (-15.00, 24.00, 9.00), SRC: (145.52, 90.31, 151.98) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Jan 12 16:37:20 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 4 found - 4 modified | TOTAL: 8 pass 2 (yz-): 0 found - 4 modified | TOTAL: 8 pass 1 (xz+): 2 found - 2 modified | TOTAL: 10 pass 2 (xz+): 0 found - 2 modified | TOTAL: 10 pass 1 (xz-): 0 found - 0 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 = 13 (out of 242346: 0.005364) 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ slice 50: 2429 vertices, 2575 faces slice 60: 9033 vertices, 9285 faces slice 70: 17784 vertices, 18140 faces slice 80: 28335 vertices, 28668 faces slice 90: 38933 vertices, 39245 faces slice 100: 49796 vertices, 50198 faces slice 110: 60922 vertices, 61290 faces slice 120: 71359 vertices, 71761 faces slice 130: 81843 vertices, 82241 faces slice 140: 91976 vertices, 92335 faces slice 150: 100801 vertices, 101105 faces slice 160: 108636 vertices, 108919 faces slice 170: 115172 vertices, 115400 faces slice 180: 120583 vertices, 120772 faces slice 190: 123922 vertices, 124014 faces slice 200: 124310 vertices, 124338 faces slice 210: 124310 vertices, 124338 faces slice 220: 124310 vertices, 124338 faces slice 230: 124310 vertices, 124338 faces slice 240: 124310 vertices, 124338 faces slice 250: 124310 vertices, 124338 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... 124310 voxel in cpt #1: X=-28 [v=124310,e=373014,f=248676] located at (-24.532957, -16.210184, 36.181118) For the whole surface: X=-28 [v=124310,e=373014,f=248676] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Jan 12 16:37:27 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 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 : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 235961: 0.003390) 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ slice 50: 1166 vertices, 1254 faces slice 60: 6349 vertices, 6538 faces slice 70: 14370 vertices, 14685 faces slice 80: 24292 vertices, 24626 faces slice 90: 33735 vertices, 34035 faces slice 100: 43759 vertices, 44119 faces slice 110: 54871 vertices, 55247 faces slice 120: 65369 vertices, 65726 faces slice 130: 75492 vertices, 75866 faces slice 140: 85506 vertices, 85861 faces slice 150: 94416 vertices, 94733 faces slice 160: 102287 vertices, 102563 faces slice 170: 109201 vertices, 109441 faces slice 180: 115008 vertices, 115233 faces slice 190: 119263 vertices, 119381 faces slice 200: 120156 vertices, 120184 faces slice 210: 120156 vertices, 120184 faces slice 220: 120156 vertices, 120184 faces slice 230: 120156 vertices, 120184 faces slice 240: 120156 vertices, 120184 faces slice 250: 120156 vertices, 120184 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... 120156 voxel in cpt #1: X=-28 [v=120156,e=360552,f=240368] located at (31.832510, -12.610032, 33.926437) For the whole surface: X=-28 [v=120156,e=360552,f=240368] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Jan 12 16:37:34 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Tue Jan 12 16:37:39 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Jan 12 16:37:44 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.6 mm, total surface area = 65400 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Inflation1 rh Tue Jan 12 16:38:17 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.0 mm, total surface area = 63198 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.153 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Jan 12 16:38:49 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.57 (0.00-->6.98) (max @ vno 90780 --> 91720) face area 0.03 +- 0.03 (-0.15-->0.76) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.336... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.208, avgs=0 005/300: dt: 0.9000, rms radial error=175.953, avgs=0 010/300: dt: 0.9000, rms radial error=175.405, avgs=0 015/300: dt: 0.9000, rms radial error=174.684, avgs=0 020/300: dt: 0.9000, rms radial error=173.862, avgs=0 025/300: dt: 0.9000, rms radial error=172.980, avgs=0 030/300: dt: 0.9000, rms radial error=172.061, avgs=0 035/300: dt: 0.9000, rms radial error=171.126, avgs=0 040/300: dt: 0.9000, rms radial error=170.182, avgs=0 045/300: dt: 0.9000, rms radial error=169.235, avgs=0 050/300: dt: 0.9000, rms radial error=168.289, avgs=0 055/300: dt: 0.9000, rms radial error=167.346, avgs=0 060/300: dt: 0.9000, rms radial error=166.408, avgs=0 065/300: dt: 0.9000, rms radial error=165.475, avgs=0 070/300: dt: 0.9000, rms radial error=164.545, avgs=0 075/300: dt: 0.9000, rms radial error=163.621, avgs=0 080/300: dt: 0.9000, rms radial error=162.701, avgs=0 085/300: dt: 0.9000, rms radial error=161.786, avgs=0 090/300: dt: 0.9000, rms radial error=160.876, avgs=0 095/300: dt: 0.9000, rms radial error=159.971, avgs=0 100/300: dt: 0.9000, rms radial error=159.070, avgs=0 105/300: dt: 0.9000, rms radial error=158.175, avgs=0 110/300: dt: 0.9000, rms radial error=157.284, avgs=0 115/300: dt: 0.9000, rms radial error=156.399, avgs=0 120/300: dt: 0.9000, rms radial error=155.518, avgs=0 125/300: dt: 0.9000, rms radial error=154.642, avgs=0 130/300: dt: 0.9000, rms radial error=153.771, avgs=0 135/300: dt: 0.9000, rms radial error=152.905, avgs=0 140/300: dt: 0.9000, rms radial error=152.043, avgs=0 145/300: dt: 0.9000, rms radial error=151.186, avgs=0 150/300: dt: 0.9000, rms radial error=150.334, avgs=0 155/300: dt: 0.9000, rms radial error=149.487, avgs=0 160/300: dt: 0.9000, rms radial error=148.644, avgs=0 165/300: dt: 0.9000, rms radial error=147.806, avgs=0 170/300: dt: 0.9000, rms radial error=146.972, avgs=0 175/300: dt: 0.9000, rms radial error=146.143, avgs=0 180/300: dt: 0.9000, rms radial error=145.319, avgs=0 185/300: dt: 0.9000, rms radial error=144.499, avgs=0 190/300: dt: 0.9000, rms radial error=143.683, avgs=0 195/300: dt: 0.9000, rms radial error=142.873, avgs=0 200/300: dt: 0.9000, rms radial error=142.066, avgs=0 205/300: dt: 0.9000, rms radial error=141.264, avgs=0 210/300: dt: 0.9000, rms radial error=140.467, avgs=0 215/300: dt: 0.9000, rms radial error=139.674, avgs=0 220/300: dt: 0.9000, rms radial error=138.885, avgs=0 225/300: dt: 0.9000, rms radial error=138.101, avgs=0 230/300: dt: 0.9000, rms radial error=137.321, avgs=0 235/300: dt: 0.9000, rms radial error=136.546, avgs=0 240/300: dt: 0.9000, rms radial error=135.774, avgs=0 245/300: dt: 0.9000, rms radial error=135.008, avgs=0 250/300: dt: 0.9000, rms radial error=134.245, avgs=0 255/300: dt: 0.9000, rms radial error=133.487, avgs=0 260/300: dt: 0.9000, rms radial error=132.733, avgs=0 265/300: dt: 0.9000, rms radial error=131.983, avgs=0 270/300: dt: 0.9000, rms radial error=131.237, avgs=0 275/300: dt: 0.9000, rms radial error=130.495, avgs=0 280/300: dt: 0.9000, rms radial error=129.758, avgs=0 285/300: dt: 0.9000, rms radial error=129.025, avgs=0 290/300: dt: 0.9000, rms radial error=128.296, avgs=0 295/300: dt: 0.9000, rms radial error=127.570, avgs=0 300/300: dt: 0.9000, rms radial error=126.849, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14116.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2197.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 3 (K=160.0), pass 1, starting sse = 196.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01016 epoch 4 (K=640.0), pass 1, starting sse = 10.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.21/20 = 0.01052 final distance error %24.91 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours #-------------------------------------------- #@# QSphere rh Tue Jan 12 16:42:47 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.57 (0.00-->9.53) (max @ vno 49210 --> 50262) face area 0.03 +- 0.03 (-0.08-->0.80) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.339... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.308, avgs=0 005/300: dt: 0.9000, rms radial error=176.051, avgs=0 010/300: dt: 0.9000, rms radial error=175.499, avgs=0 015/300: dt: 0.9000, rms radial error=174.773, avgs=0 020/300: dt: 0.9000, rms radial error=173.945, avgs=0 025/300: dt: 0.9000, rms radial error=173.060, avgs=0 030/300: dt: 0.9000, rms radial error=172.142, avgs=0 035/300: dt: 0.9000, rms radial error=171.207, avgs=0 040/300: dt: 0.9000, rms radial error=170.265, avgs=0 045/300: dt: 0.9000, rms radial error=169.320, avgs=0 050/300: dt: 0.9000, rms radial error=168.376, avgs=0 055/300: dt: 0.9000, rms radial error=167.434, avgs=0 060/300: dt: 0.9000, rms radial error=166.496, avgs=0 065/300: dt: 0.9000, rms radial error=165.562, avgs=0 070/300: dt: 0.9000, rms radial error=164.633, avgs=0 075/300: dt: 0.9000, rms radial error=163.708, avgs=0 080/300: dt: 0.9000, rms radial error=162.789, avgs=0 085/300: dt: 0.9000, rms radial error=161.874, avgs=0 090/300: dt: 0.9000, rms radial error=160.965, avgs=0 095/300: dt: 0.9000, rms radial error=160.062, avgs=0 100/300: dt: 0.9000, rms radial error=159.164, avgs=0 105/300: dt: 0.9000, rms radial error=158.271, avgs=0 110/300: dt: 0.9000, rms radial error=157.383, avgs=0 115/300: dt: 0.9000, rms radial error=156.500, avgs=0 120/300: dt: 0.9000, rms radial error=155.621, avgs=0 125/300: dt: 0.9000, rms radial error=154.747, avgs=0 130/300: dt: 0.9000, rms radial error=153.878, avgs=0 135/300: dt: 0.9000, rms radial error=153.013, avgs=0 140/300: dt: 0.9000, rms radial error=152.154, avgs=0 145/300: dt: 0.9000, rms radial error=151.299, avgs=0 150/300: dt: 0.9000, rms radial error=150.448, avgs=0 155/300: dt: 0.9000, rms radial error=149.603, avgs=0 160/300: dt: 0.9000, rms radial error=148.762, avgs=0 165/300: dt: 0.9000, rms radial error=147.925, avgs=0 170/300: dt: 0.9000, rms radial error=147.093, avgs=0 175/300: dt: 0.9000, rms radial error=146.266, avgs=0 180/300: dt: 0.9000, rms radial error=145.443, avgs=0 185/300: dt: 0.9000, rms radial error=144.625, avgs=0 190/300: dt: 0.9000, rms radial error=143.812, avgs=0 195/300: dt: 0.9000, rms radial error=143.003, avgs=0 200/300: dt: 0.9000, rms radial error=142.198, avgs=0 205/300: dt: 0.9000, rms radial error=141.398, avgs=0 210/300: dt: 0.9000, rms radial error=140.602, avgs=0 215/300: dt: 0.9000, rms radial error=139.810, avgs=0 220/300: dt: 0.9000, rms radial error=139.023, avgs=0 225/300: dt: 0.9000, rms radial error=138.240, avgs=0 230/300: dt: 0.9000, rms radial error=137.462, avgs=0 235/300: dt: 0.9000, rms radial error=136.687, avgs=0 240/300: dt: 0.9000, rms radial error=135.918, avgs=0 245/300: dt: 0.9000, rms radial error=135.152, avgs=0 250/300: dt: 0.9000, rms radial error=134.391, avgs=0 255/300: dt: 0.9000, rms radial error=133.634, avgs=0 260/300: dt: 0.9000, rms radial error=132.881, avgs=0 265/300: dt: 0.9000, rms radial error=132.132, avgs=0 270/300: dt: 0.9000, rms radial error=131.388, avgs=0 275/300: dt: 0.9000, rms radial error=130.648, avgs=0 280/300: dt: 0.9000, rms radial error=129.911, avgs=0 285/300: dt: 0.9000, rms radial error=129.179, avgs=0 290/300: dt: 0.9000, rms radial error=128.452, avgs=0 295/300: dt: 0.9000, rms radial error=127.728, avgs=0 300/300: dt: 0.9000, rms radial error=127.008, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13607.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00020 epoch 2 (K=40.0), pass 1, starting sse = 2105.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 187.22 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01043 epoch 4 (K=640.0), pass 1, starting sse = 8.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/16 = 0.00645 final distance error %24.73 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours #-------------------------------------------- #@# Fix Topology lh Tue Jan 12 16:46:24 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology rh Tue Jan 12 16:46:25 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MRM_003_w_070655_171011_0000FD62 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-28 (nv=124310, nf=248676, ne=373014, g=15) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 1703 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 22 defects to be corrected 0 vertices coincident reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5427 (-4.7713) -vertex loglikelihood: -6.4049 (-3.2024) -normal dot loglikelihood: -3.6015 (-3.6015) -quad curv loglikelihood: -6.5615 (-3.2807) Total Loglikelihood : -26.1105 CORRECTING DEFECT 0 (vertices=44, convex hull=82) After retessellation of defect 0, euler #=-18 (123235,369210,245957) : difference with theory (-19) = -1 CORRECTING DEFECT 1 (vertices=61, convex hull=85) After retessellation of defect 1, euler #=-17 (123267,369343,246059) : difference with theory (-18) = -1 CORRECTING DEFECT 2 (vertices=32, convex hull=50) After retessellation of defect 2, euler #=-16 (123276,369390,246098) : difference with theory (-17) = -1 CORRECTING DEFECT 3 (vertices=50, convex hull=83) After retessellation of defect 3, euler #=-15 (123294,369479,246170) : difference with theory (-16) = -1 CORRECTING DEFECT 4 (vertices=41, convex hull=82) After retessellation of defect 4, euler #=-14 (123323,369601,246264) : difference with theory (-15) = -1 CORRECTING DEFECT 5 (vertices=19, convex hull=55) After retessellation of defect 5, euler #=-13 (123333,369649,246303) : difference with theory (-14) = -1 CORRECTING DEFECT 6 (vertices=145, convex hull=118) After retessellation of defect 6, euler #=-12 (123407,369923,246504) : difference with theory (-13) = -1 CORRECTING DEFECT 7 (vertices=35, convex hull=51) After retessellation of defect 7, euler #=-11 (123430,370012,246571) : difference with theory (-12) = -1 CORRECTING DEFECT 8 (vertices=21, convex hull=51) After retessellation of defect 8, euler #=-10 (123439,370060,246611) : difference with theory (-11) = -1 CORRECTING DEFECT 9 (vertices=36, convex hull=62) After retessellation of defect 9, euler #=-9 (123456,370136,246671) : difference with theory (-10) = -1 CORRECTING DEFECT 10 (vertices=11, convex hull=29) After retessellation of defect 10, euler #=-8 (123459,370156,246689) : difference with theory (-9) = -1 CORRECTING DEFECT 11 (vertices=70, convex hull=36) After retessellation of defect 11, euler #=-7 (123470,370201,246724) : difference with theory (-8) = -1 CORRECTING DEFECT 12 (vertices=194, convex hull=79) After retessellation of defect 12, euler #=-7 (123500,370332,246825) : difference with theory (-7) = 0 CORRECTING DEFECT 13 (vertices=85, convex hull=55) After retessellation of defect 13, euler #=-6 (123516,370402,246880) : difference with theory (-6) = 0 CORRECTING DEFECT 14 (vertices=57, convex hull=31) After retessellation of defect 14, euler #=-5 (123524,370435,246906) : difference with theory (-5) = 0 CORRECTING DEFECT 15 (vertices=12, convex hull=18) After retessellation of defect 15, euler #=-4 (123524,370440,246912) : difference with theory (-4) = 0 CORRECTING DEFECT 16 (vertices=21, convex hull=28) After retessellation of defect 16, euler #=-3 (123527,370456,246926) : difference with theory (-3) = 0 CORRECTING DEFECT 17 (vertices=13, convex hull=28) After retessellation of defect 17, euler #=-2 (123530,370473,246941) : difference with theory (-2) = 0 CORRECTING DEFECT 18 (vertices=67, convex hull=106) After retessellation of defect 18, euler #=-1 (123558,370607,247048) : difference with theory (-1) = 0 CORRECTING DEFECT 19 (vertices=21, convex hull=61) After retessellation of defect 19, euler #=0 (123567,370660,247093) : difference with theory (0) = 0 CORRECTING DEFECT 20 (vertices=25, convex hull=23) After retessellation of defect 20, euler #=1 (123568,370669,247102) : difference with theory (1) = 0 CORRECTING DEFECT 21 (vertices=25, convex hull=75) After retessellation of defect 21, euler #=2 (123586,370752,247168) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.10-->6.17) (max @ vno 49102 --> 123609) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.10-->6.17) (max @ vno 49102 --> 123609) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (34.2%), 133 crossovers (65.8%), 41 vertices were eliminated building final representation... 724 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=123586, nf=247168, ne=370752, g=0) writing corrected surface to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 10.1 minutes 0 defective edges removing intersecting faces 000: 115 intersecting mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MRM_003_w_070655_171011_0000FD62 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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-28 (nv=120156, nf=240368, ne=360552, g=15) 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... 1406 ambiguous faces found in tessellation segmenting defects... 20 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 20 defects to be corrected 0 vertices coincident reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4833 (-4.7416) -vertex loglikelihood: -6.4677 (-3.2338) -normal dot loglikelihood: -3.6612 (-3.6612) -quad curv loglikelihood: -6.1649 (-3.0824) Total Loglikelihood : -25.7771 CORRECTING DEFECT 0 (vertices=30, convex hull=58) After retessellation of defect 0, euler #=-17 (119267,357371,238087) : difference with theory (-17) = 0 CORRECTING DEFECT 1 (vertices=172, convex hull=109) After retessellation of defect 1, euler #=-16 (119330,357609,238263) : difference with theory (-16) = 0 CORRECTING DEFECT 2 (vertices=68, convex hull=104) After retessellation of defect 2, euler #=-15 (119364,357759,238380) : difference with theory (-15) = 0 CORRECTING DEFECT 3 (vertices=11, convex hull=17) After retessellation of defect 3, euler #=-14 (119367,357771,238390) : difference with theory (-14) = 0 CORRECTING DEFECT 4 (vertices=13, convex hull=31) After retessellation of defect 4, euler #=-13 (119370,357790,238407) : difference with theory (-13) = 0 CORRECTING DEFECT 5 (vertices=18, convex hull=19) After retessellation of defect 5, euler #=-12 (119372,357800,238416) : difference with theory (-12) = 0 CORRECTING DEFECT 6 (vertices=34, convex hull=76) After retessellation of defect 6, euler #=-11 (119389,357882,238482) : difference with theory (-11) = 0 CORRECTING DEFECT 7 (vertices=20, convex hull=20) After retessellation of defect 7, euler #=-10 (119393,357897,238494) : difference with theory (-10) = 0 CORRECTING DEFECT 8 (vertices=62, convex hull=96) After retessellation of defect 8, euler #=-9 (119419,358021,238593) : difference with theory (-9) = 0 CORRECTING DEFECT 9 (vertices=23, convex hull=52) After retessellation of defect 9, euler #=-8 (119435,358091,238648) : difference with theory (-8) = 0 CORRECTING DEFECT 10 (vertices=33, convex hull=25) After retessellation of defect 10, euler #=-7 (119442,358120,238671) : difference with theory (-7) = 0 CORRECTING DEFECT 11 (vertices=23, convex hull=36) After retessellation of defect 11, euler #=-6 (119448,358149,238695) : difference with theory (-6) = 0 CORRECTING DEFECT 12 (vertices=57, convex hull=35) After retessellation of defect 12, euler #=-5 (119456,358184,238723) : difference with theory (-5) = 0 CORRECTING DEFECT 13 (vertices=37, convex hull=66) After retessellation of defect 13, euler #=-4 (119471,358256,238781) : difference with theory (-4) = 0 CORRECTING DEFECT 14 (vertices=54, convex hull=37) After retessellation of defect 14, euler #=-3 (119480,358296,238813) : difference with theory (-3) = 0 CORRECTING DEFECT 15 (vertices=68, convex hull=100) After retessellation of defect 15, euler #=-2 (119511,358436,238923) : difference with theory (-2) = 0 CORRECTING DEFECT 16 (vertices=37, convex hull=63) After retessellation of defect 16, euler #=-1 (119524,358502,238977) : difference with theory (-1) = 0 CORRECTING DEFECT 17 (vertices=63, convex hull=77) After retessellation of defect 17, euler #=0 (119554,358622,239068) : difference with theory (0) = 0 CORRECTING DEFECT 18 (vertices=32, convex hull=55) After retessellation of defect 18, euler #=1 (119566,358679,239114) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=47, convex hull=28) After retessellation of defect 19, euler #=2 (119567,358695,239130) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.11-->4.61) (max @ vno 114392 --> 116766) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.11-->4.61) (max @ vno 114392 --> 116766) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 77 mutations (37.6%), 128 crossovers (62.4%), 34 vertices were eliminated building final representation... 589 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119567, nf=239130, ne=358695, g=0) writing corrected surface to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 8.2 minutes 0 defective edges removing intersecting faces 000: 54 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 123586 - 370752 + 247168 = 2 --> 0 holes F =2V-4: 247168 = 247172-4 (0) 2E=3F: 741504 = 741504 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 119567 - 358695 + 239130 = 2 --> 0 holes F =2V-4: 239130 = 239134-4 (0) 2E=3F: 717390 = 717390 (0) total defect index = 0 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 14 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 8 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Jan 12 17:04:51 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10714 bright wm thresholded. 1432 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... computing class statistics... border white: 230601 voxels (1.37%) border gray 248839 voxels (1.48%) WM (94.0): 94.7 +- 8.3 [70.0 --> 110.0] GM (81.0) : 78.7 +- 12.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.0 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 43.0 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.47) (max @ vno 49102 --> 123399) face area 0.28 +- 0.12 (0.00-->1.58) mean absolute distance = 0.86 +- 1.13 3340 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=67+-10.4 mean inside = 94.0, mean outside = 75.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=79.5, 87 (87) missing vertices, mean dist 0.3 [0.9 (%34.2)->0.8 (%65.8))] %46 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 0.92 +- 0.27 (0.07-->4.11) (max @ vno 87113 --> 87143) face area 0.28 +- 0.13 (0.00-->1.61) mean absolute distance = 0.45 +- 0.86 3618 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5172032.0, rms=11.133 001: dt: 0.5000, sse=5795954.0, rms=8.077 (27.453%) 002: dt: 0.5000, sse=6070435.5, rms=6.169 (23.620%) 003: dt: 0.5000, sse=6372646.5, rms=4.909 (20.430%) 004: dt: 0.5000, sse=6545460.5, rms=4.137 (15.726%) 005: dt: 0.5000, sse=6763987.0, rms=3.720 (10.072%) 006: dt: 0.5000, sse=6841160.5, rms=3.502 (5.858%) 007: dt: 0.5000, sse=6930354.0, rms=3.397 (3.010%) 008: dt: 0.5000, sse=6932680.5, rms=3.332 (1.901%) rms = 3.30, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6953360.5, rms=3.304 (0.832%) 010: dt: 0.2500, sse=4318753.5, rms=2.244 (32.101%) 011: dt: 0.2500, sse=3950796.5, rms=1.956 (12.832%) 012: dt: 0.2500, sse=3782627.2, rms=1.894 (3.154%) rms = 1.87, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3735142.5, rms=1.865 (1.520%) 014: dt: 0.1250, sse=3663795.2, rms=1.813 (2.814%) rms = 1.81, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3638495.5, rms=1.808 (0.264%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.1, 75 (24) missing vertices, mean dist -0.3 [0.6 (%63.1)->0.3 (%36.9))] %54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.08-->4.38) (max @ vno 31208 --> 32313) face area 0.35 +- 0.17 (0.00-->2.24) mean absolute distance = 0.34 +- 0.53 2664 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4177416.2, rms=4.546 016: dt: 0.5000, sse=4575384.0, rms=3.034 (33.264%) rms = 3.02, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=5185649.5, rms=3.016 (0.590%) 018: dt: 0.2500, sse=4180423.2, rms=1.905 (36.821%) 019: dt: 0.2500, sse=4013087.2, rms=1.658 (12.971%) 020: dt: 0.2500, sse=3894654.8, rms=1.598 (3.627%) rms = 1.56, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3875570.2, rms=1.561 (2.289%) rms = 1.52, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3811058.2, rms=1.519 (2.736%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.9, 70 (16) missing vertices, mean dist -0.2 [0.4 (%69.1)->0.2 (%30.9))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.04-->4.70) (max @ vno 31208 --> 32313) face area 0.34 +- 0.16 (0.00-->2.75) mean absolute distance = 0.26 +- 0.39 2782 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4110338.8, rms=3.968 023: dt: 0.5000, sse=4390028.0, rms=2.616 (34.074%) rms = 2.89, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4100226.2, rms=1.901 (27.353%) 025: dt: 0.2500, sse=4013195.0, rms=1.517 (20.178%) 026: dt: 0.2500, sse=3965424.0, rms=1.406 (7.321%) rms = 1.41, time step reduction 2 of 3 to 0.125... rms = 1.38, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3939395.0, rms=1.382 (1.702%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.1, 64 (12) missing vertices, mean dist -0.1 [0.3 (%59.1)->0.2 (%40.9))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3989842.2, rms=2.128 028: dt: 0.5000, sse=5074184.0, rms=2.054 (3.483%) rms = 2.58, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4492306.0, rms=1.369 (33.337%) 030: dt: 0.2500, sse=4271453.5, rms=1.213 (11.364%) 031: dt: 0.2500, sse=4378409.0, rms=1.127 (7.124%) rms = 1.17, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4359207.5, rms=1.097 (2.672%) positioning took 0.5 minutes generating cortex label... 18 non-cortical segments detected only using segment with 6372 vertices erasing segment 0 (vno[0] = 27963) erasing segment 1 (vno[0] = 33321) erasing segment 2 (vno[0] = 33323) erasing segment 3 (vno[0] = 37589) erasing segment 5 (vno[0] = 73865) erasing segment 6 (vno[0] = 78078) erasing segment 7 (vno[0] = 78955) erasing segment 8 (vno[0] = 81018) erasing segment 9 (vno[0] = 82056) erasing segment 10 (vno[0] = 86074) erasing segment 11 (vno[0] = 87099) erasing segment 12 (vno[0] = 87170) erasing segment 13 (vno[0] = 88094) erasing segment 14 (vno[0] = 89043) erasing segment 15 (vno[0] = 89913) erasing segment 16 (vno[0] = 91766) erasing segment 17 (vno[0] = 94679) writing cortex label to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label... writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv writing smoothed area to lh.area writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->4.65) (max @ vno 31208 --> 32313) face area 0.34 +- 0.16 (0.00-->2.87) refinement took 4.2 minutes #-------------------------------------------- #@# Make White Surf rh Tue Jan 12 17:09:04 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10185 bright wm thresholded. 1430 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... computing class statistics... border white: 230601 voxels (1.37%) border gray 248839 voxels (1.48%) WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0] GM (82.0) : 79.0 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.3 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.6 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->2.88) (max @ vno 59867 --> 119351) face area 0.28 +- 0.12 (0.00-->1.69) mean absolute distance = 0.88 +- 1.18 3521 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=69+-11.3 mean inside = 93.5, mean outside = 74.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.0, 51 (51) missing vertices, mean dist 0.1 [1.0 (%38.4)->0.8 (%61.6))] %35 local maxima, %60 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.10-->3.29) (max @ vno 86392 --> 87217) face area 0.28 +- 0.13 (0.00-->2.09) mean absolute distance = 0.48 +- 0.93 4049 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4884345.0, rms=10.886 001: dt: 0.5000, sse=5413196.0, rms=7.470 (31.382%) 002: dt: 0.5000, sse=5736869.0, rms=5.452 (27.008%) 003: dt: 0.5000, sse=6055476.0, rms=4.373 (19.790%) 004: dt: 0.5000, sse=6296074.5, rms=3.766 (13.881%) 005: dt: 0.5000, sse=6486508.0, rms=3.473 (7.792%) 006: dt: 0.5000, sse=6528822.5, rms=3.328 (4.158%) 007: dt: 0.5000, sse=6613305.5, rms=3.266 (1.880%) rms = 3.22, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=6562171.5, rms=3.224 (1.283%) 009: dt: 0.2500, sse=4105368.8, rms=2.176 (32.497%) 010: dt: 0.2500, sse=3754685.2, rms=1.889 (13.205%) 011: dt: 0.2500, sse=3607091.8, rms=1.829 (3.181%) rms = 1.80, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3555875.0, rms=1.798 (1.686%) rms = 1.75, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3488492.0, rms=1.753 (2.508%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=83.5, 83 (24) missing vertices, mean dist -0.3 [0.6 (%61.9)->0.3 (%38.1))] %44 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.04-->3.21) (max @ vno 44387 --> 44355) face area 0.35 +- 0.16 (0.00-->2.71) mean absolute distance = 0.37 +- 0.58 3028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3948299.5, rms=4.289 014: dt: 0.5000, sse=4295922.5, rms=2.841 (33.765%) rms = 2.88, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3972391.2, rms=2.318 (18.399%) 016: dt: 0.2500, sse=3807648.5, rms=1.850 (20.176%) 017: dt: 0.2500, sse=3703626.5, rms=1.633 (11.720%) 018: dt: 0.2500, sse=3655929.5, rms=1.546 (5.365%) rms = 1.51, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3635199.2, rms=1.510 (2.319%) rms = 1.47, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3588971.0, rms=1.471 (2.600%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.2, 57 (12) missing vertices, mean dist -0.2 [0.4 (%66.8)->0.2 (%33.2))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.11-->3.49) (max @ vno 84609 --> 119394) face area 0.34 +- 0.16 (0.00-->2.86) mean absolute distance = 0.28 +- 0.42 2737 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3877176.2, rms=3.927 021: dt: 0.5000, sse=4105142.5, rms=2.509 (36.104%) rms = 2.73, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3847131.5, rms=1.874 (25.333%) 023: dt: 0.2500, sse=3772878.5, rms=1.484 (20.768%) 024: dt: 0.2500, sse=3733729.2, rms=1.369 (7.799%) rms = 1.36, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3706438.2, rms=1.355 (0.987%) rms = 1.32, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3668252.5, rms=1.320 (2.571%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.5, 53 (10) missing vertices, mean dist -0.1 [0.3 (%58.7)->0.2 (%41.3))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3718941.5, rms=2.132 027: dt: 0.5000, sse=4660799.0, rms=1.902 (10.760%) rms = 2.41, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4193608.5, rms=1.284 (32.517%) 029: dt: 0.2500, sse=3990824.5, rms=1.130 (11.935%) 030: dt: 0.2500, sse=4079460.0, rms=1.049 (7.196%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4069994.2, rms=1.039 (0.948%) positioning took 0.5 minutes generating cortex label... 24 non-cortical segments detected only using segment with 6421 vertices erasing segment 0 (vno[0] = 27843) erasing segment 2 (vno[0] = 39186) erasing segment 3 (vno[0] = 49739) erasing segment 4 (vno[0] = 49741) erasing segment 5 (vno[0] = 50839) erasing segment 6 (vno[0] = 52912) erasing segment 7 (vno[0] = 54188) erasing segment 8 (vno[0] = 59539) erasing segment 9 (vno[0] = 61507) erasing segment 10 (vno[0] = 65825) erasing segment 11 (vno[0] = 67368) erasing segment 12 (vno[0] = 67734) erasing segment 13 (vno[0] = 67756) erasing segment 14 (vno[0] = 69840) erasing segment 15 (vno[0] = 71500) erasing segment 16 (vno[0] = 78583) erasing segment 17 (vno[0] = 79636) erasing segment 18 (vno[0] = 81801) erasing segment 19 (vno[0] = 81823) erasing segment 20 (vno[0] = 83780) erasing segment 21 (vno[0] = 85589) erasing segment 22 (vno[0] = 85634) erasing segment 23 (vno[0] = 96504) writing cortex label to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label... writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv writing smoothed area to rh.area writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area vertex spacing 0.89 +- 0.25 (0.05-->3.72) (max @ vno 84609 --> 119394) face area 0.33 +- 0.16 (0.00-->3.00) refinement took 4.0 minutes #-------------------------------------------- #@# Smooth2 lh Tue Jan 12 17:13:02 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Tue Jan 12 17:13:07 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Tue Jan 12 17:13:12 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.8 mm, total surface area = 74932 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (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=0.021 (target=0.015) inflation complete. inflation took 0.5 minutes #-------------------------------------------- #@# Inflation2 rh Tue Jan 12 17:13:45 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.1 mm, total surface area = 71616 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.5 minutes #-------------------------------------------- #@# Curv .H and .K lh Tue Jan 12 17:14:17 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature -w lh.white total integrated curvature = -7.174*4pi (-90.145) --> 8 handles ICI = 145.9, FI = 1520.7, variation=24138.319 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 179 vertices thresholded to be in k1 ~ [-0.17 2.43], k2 ~ [-0.08 0.07] total integrated curvature = 0.638*4pi (8.021) --> 0 handles ICI = 1.6, FI = 8.4, variation=150.777 89 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 85 vertices thresholded to be in [-0.11 0.51] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #-------------------------------------------- #@# Curv .H and .K rh Tue Jan 12 17:15:38 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature -w rh.white total integrated curvature = 0.287*4pi (3.606) --> 1 handles ICI = 140.6, FI = 1472.8, variation=23218.347 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 146 vertices thresholded to be in k1 ~ [-0.18 0.59], k2 ~ [-0.09 0.10] total integrated curvature = 0.628*4pi (7.895) --> 0 handles ICI = 1.4, FI = 7.6, variation=135.848 91 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 123 vertices thresholded to be in [-0.12 0.29] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Tue Jan 12 17:16:57 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MRM_003_w_070655_171011_0000FD62 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 [ MRM_003_w_070655_171011_0000FD62/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 [ 199 ] Gb_filter = 0 WARN: S lookup min: -0.275577 WARN: S explicit min: 0.000000 vertex = 12 #----------------------------------------- #@# Curvature Stats rh Tue Jan 12 17:17:01 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MRM_003_w_070655_171011_0000FD62 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 [ MRM_003_w_070655_171011_0000FD62/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 [ 194 ] Gb_filter = 0 WARN: S lookup min: -0.016209 WARN: S explicit min: 0.000000 vertex = 937 #-------------------------------------------- #@# Sphere lh Tue Jan 12 17:17:05 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.312... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=eddie, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.10 pass 1: epoch 2 of 3 starting distance error %19.09 unfolding complete - removing small folds... starting distance error %19.06 removing remaining folds... final distance error %19.06 MRISunfold() return, current seed 1234 -01: dt=0.0000, 355 negative triangles 096: dt=0.9900, 355 negative triangles 097: dt=0.9900, 107 negative triangles 098: dt=0.9900, 77 negative triangles 099: dt=0.9900, 56 negative triangles 100: dt=0.9900, 50 negative triangles 101: dt=0.9900, 42 negative triangles 102: dt=0.9900, 36 negative triangles 103: dt=0.9900, 32 negative triangles 104: dt=0.9900, 32 negative triangles 105: dt=0.9900, 32 negative triangles 106: dt=0.9900, 32 negative triangles 107: dt=0.9900, 31 negative triangles 108: dt=0.9900, 28 negative triangles 109: dt=0.9900, 25 negative triangles 110: dt=0.9900, 29 negative triangles 111: dt=0.9900, 27 negative triangles 112: dt=0.9900, 29 negative triangles 113: dt=0.9900, 30 negative triangles 114: dt=0.9900, 24 negative triangles 115: dt=0.9900, 26 negative triangles 116: dt=0.9900, 24 negative triangles 117: dt=0.9900, 24 negative triangles 118: dt=0.9900, 20 negative triangles 119: dt=0.9900, 28 negative triangles 120: dt=0.9900, 22 negative triangles 121: dt=0.9900, 26 negative triangles 122: dt=0.9900, 22 negative triangles 123: dt=0.9900, 22 negative triangles 124: dt=0.9900, 24 negative triangles 125: dt=0.9900, 25 negative triangles 126: dt=0.9900, 24 negative triangles 127: dt=0.9900, 21 negative triangles 128: dt=0.9405, 25 negative triangles 129: dt=0.9405, 22 negative triangles 130: dt=0.9405, 25 negative triangles 131: dt=0.9405, 24 negative triangles 132: dt=0.9405, 24 negative triangles 133: dt=0.9405, 22 negative triangles 134: dt=0.9405, 27 negative triangles 135: dt=0.9405, 24 negative triangles 136: dt=0.9405, 24 negative triangles 137: dt=0.9405, 23 negative triangles 138: dt=0.8935, 25 negative triangles 139: dt=0.8935, 20 negative triangles 140: dt=0.8935, 18 negative triangles 141: dt=0.8935, 23 negative triangles 142: dt=0.8935, 19 negative triangles 143: dt=0.8935, 24 negative triangles 144: dt=0.8935, 20 negative triangles 145: dt=0.8935, 20 negative triangles 146: dt=0.8935, 19 negative triangles 147: dt=0.8935, 22 negative triangles 148: dt=0.8935, 24 negative triangles 149: dt=0.8935, 19 negative triangles 150: dt=0.8488, 19 negative triangles 151: dt=0.8488, 16 negative triangles 152: dt=0.8488, 20 negative triangles 153: dt=0.8488, 19 negative triangles 154: dt=0.8488, 18 negative triangles 155: dt=0.8488, 19 negative triangles 156: dt=0.8488, 19 negative triangles 157: dt=0.8488, 16 negative triangles 158: dt=0.8488, 17 negative triangles 159: dt=0.8488, 17 negative triangles 160: dt=0.8488, 18 negative triangles 161: dt=0.8488, 13 negative triangles 162: dt=0.8488, 15 negative triangles 163: dt=0.8488, 16 negative triangles 164: dt=0.8488, 15 negative triangles 165: dt=0.8488, 15 negative triangles 166: dt=0.8488, 15 negative triangles 167: dt=0.8488, 12 negative triangles 168: dt=0.8488, 9 negative triangles 169: dt=0.8488, 13 negative triangles 170: dt=0.8488, 9 negative triangles 171: dt=0.8488, 12 negative triangles 172: dt=0.8488, 12 negative triangles 173: dt=0.8488, 8 negative triangles 174: dt=0.8488, 8 negative triangles 175: dt=0.8488, 7 negative triangles 176: dt=0.8488, 7 negative triangles 177: dt=0.8488, 11 negative triangles 178: dt=0.8488, 8 negative triangles 179: dt=0.8488, 8 negative triangles 180: dt=0.8488, 7 negative triangles 181: dt=0.8488, 6 negative triangles 182: dt=0.8488, 5 negative triangles 183: dt=0.8488, 5 negative triangles 184: dt=0.8488, 7 negative triangles 185: dt=0.8488, 4 negative triangles 186: dt=0.8488, 6 negative triangles 187: dt=0.8488, 5 negative triangles 188: dt=0.8488, 9 negative triangles 189: dt=0.8488, 7 negative triangles 190: dt=0.8488, 4 negative triangles 191: dt=0.8488, 7 negative triangles 192: dt=0.8488, 4 negative triangles 193: dt=0.8488, 6 negative triangles 194: dt=0.8488, 5 negative triangles 195: dt=0.8064, 4 negative triangles 196: dt=0.8064, 5 negative triangles 197: dt=0.8064, 2 negative triangles 198: dt=0.8064, 4 negative triangles 199: dt=0.8064, 2 negative triangles 200: dt=0.8064, 4 negative triangles 201: dt=0.8064, 2 negative triangles 202: dt=0.8064, 4 negative triangles 203: dt=0.8064, 5 negative triangles 204: dt=0.8064, 5 negative triangles 205: dt=0.8064, 2 negative triangles 206: dt=0.8064, 3 negative triangles 207: dt=0.8064, 1 negative triangles 208: dt=0.8064, 2 negative triangles 209: dt=0.8064, 1 negative triangles 210: dt=0.8064, 1 negative triangles 211: dt=0.8064, 2 negative triangles 212: dt=0.8064, 1 negative triangles 213: dt=0.8064, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.63 hours #-------------------------------------------- #@# Sphere rh Tue Jan 12 17:55:10 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.316... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=eddie, 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 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.22 pass 1: epoch 2 of 3 starting distance error %19.20 unfolding complete - removing small folds... starting distance error %19.16 removing remaining folds... final distance error %19.17 MRISunfold() return, current seed 1234 -01: dt=0.0000, 47 negative triangles 156: dt=0.9900, 47 negative triangles 157: dt=0.9900, 6 negative triangles 158: dt=0.9900, 7 negative triangles 159: dt=0.9900, 5 negative triangles 160: dt=0.9900, 1 negative triangles 161: dt=0.9900, 2 negative triangles 162: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.60 hours #-------------------------------------------- #@# Surf Reg lh Tue Jan 12 18:31:03 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_register -curv ../surf/lh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cmdline mris_register -curv ../surf/lh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=eddie, 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=eddie, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.592 curvature mean = 0.038, std = 0.942 curvature mean = 0.023, std = 0.869 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 278719.4, tmin=1.0325 d=32.00 min @ (8.00, 8.00, 0.00) sse = 203944.1, tmin=2.0880 d=16.00 min @ (0.00, 0.00, 4.00) sse = 182301.4, tmin=3.1590 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 180116.5, tmin=5.3189 d=2.00 min @ (0.00, 0.00, -0.50) sse = 180008.0, tmin=6.4078 d=1.00 min @ (0.25, 0.00, 0.25) sse = 179812.7, tmin=7.4954 tol=1.0e+00, sigma=0.5, host=eddie, 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 8.59 min curvature mean = 0.014, std = 0.966 curvature mean = 0.011, std = 0.944 curvature mean = 0.012, std = 0.978 curvature mean = 0.005, std = 0.975 curvature mean = 0.010, std = 0.979 curvature mean = 0.002, std = 0.990 2 Reading smoothwm curvature mean = -0.025, std = 0.277 curvature mean = 0.004, std = 0.068 curvature mean = 0.071, std = 0.360 curvature mean = 0.003, std = 0.081 curvature mean = 0.031, std = 0.565 curvature mean = 0.004, std = 0.087 curvature mean = 0.015, std = 0.711 curvature mean = 0.004, std = 0.090 curvature mean = 0.006, std = 0.818 MRISregister() return, current seed 0 -01: dt=0.0000, 34 negative triangles 104: dt=0.9900, 34 negative triangles 105: dt=0.9900, 33 negative triangles 106: dt=0.9900, 23 negative triangles 107: dt=0.9900, 21 negative triangles 108: dt=0.9900, 15 negative triangles 109: dt=0.9900, 17 negative triangles 110: dt=0.9900, 13 negative triangles 111: dt=0.9900, 17 negative triangles 112: dt=0.9900, 16 negative triangles 113: dt=0.9900, 12 negative triangles 114: dt=0.9900, 13 negative triangles 115: dt=0.9900, 9 negative triangles 116: dt=0.9900, 12 negative triangles 117: dt=0.9900, 9 negative triangles 118: dt=0.9900, 11 negative triangles 119: dt=0.9900, 9 negative triangles 120: dt=0.9900, 13 negative triangles 121: dt=0.9900, 10 negative triangles 122: dt=0.9900, 11 negative triangles 123: dt=0.9900, 5 negative triangles 124: dt=0.9900, 8 negative triangles 125: dt=0.9900, 5 negative triangles 126: dt=0.9900, 10 negative triangles 127: dt=0.9900, 5 negative triangles 128: dt=0.9900, 11 negative triangles 129: dt=0.9900, 8 negative triangles 130: dt=0.9900, 3 negative triangles 131: dt=0.9900, 7 negative triangles 132: dt=0.9900, 4 negative triangles 133: dt=0.9900, 5 negative triangles 134: dt=0.9900, 4 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 2 negative triangles 137: dt=0.9900, 6 negative triangles 138: dt=0.9900, 2 negative triangles 139: dt=0.9900, 3 negative triangles 140: dt=0.9900, 3 negative triangles 141: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.65 hours #-------------------------------------------- #@# Surf Reg rh Tue Jan 12 19:09:53 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_register -curv ../surf/rh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts cmdline mris_register -curv ../surf/rh.sphere /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=eddie, 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=eddie, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.597 curvature mean = 0.023, std = 0.928 curvature mean = 0.024, std = 0.876 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 266866.9, tmin=0.9960 d=32.00 min @ (0.00, 0.00, 8.00) sse = 201523.5, tmin=2.0156 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 195657.7, tmin=3.0447 d=8.00 min @ (2.00, 2.00, 0.00) sse = 184822.1, tmin=4.1077 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 182379.5, tmin=5.1841 d=1.00 min @ (0.00, 0.00, 0.25) sse = 182291.7, tmin=7.3494 tol=1.0e+00, sigma=0.5, host=eddie, 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 8.41 min curvature mean = 0.013, std = 0.957 curvature mean = 0.010, std = 0.950 curvature mean = 0.012, std = 0.970 curvature mean = 0.004, std = 0.978 curvature mean = 0.011, std = 0.972 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.029, std = 0.279 curvature mean = 0.006, std = 0.071 curvature mean = 0.067, std = 0.380 curvature mean = 0.005, std = 0.086 curvature mean = 0.026, std = 0.587 curvature mean = 0.006, std = 0.092 curvature mean = 0.013, std = 0.732 curvature mean = 0.006, std = 0.094 curvature mean = 0.005, std = 0.834 MRISregister() return, current seed 0 -01: dt=0.0000, 11 negative triangles 104: dt=0.9900, 11 negative triangles 105: dt=0.9900, 10 negative triangles 106: dt=0.9900, 3 negative triangles 107: dt=0.9900, 1 negative triangles 108: dt=0.9900, 3 negative triangles 109: dt=0.9900, 4 negative triangles 110: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.72 hours #-------------------------------------------- #@# Jacobian white lh Tue Jan 12 19:52:55 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Tue Jan 12 19:52:57 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 Tue Jan 12 19:52:59 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mrisp_paint -a 5 /exports/work/mcm_cric_nas/Kaiming/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Tue Jan 12 19:53:01 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mrisp_paint -a 5 /exports/work/mcm_cric_nas/Kaiming/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jan 12 19:53:03 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 1045 labels changed using aseg relabeling using gibbs priors... 000: 2803 changed, 123586 examined... 001: 650 changed, 12120 examined... 002: 154 changed, 3601 examined... 003: 46 changed, 930 examined... 004: 23 changed, 292 examined... 005: 12 changed, 130 examined... 006: 7 changed, 74 examined... 007: 2 changed, 42 examined... 008: 0 changed, 14 examined... 233 labels changed using aseg 000: 110 total segments, 71 labels (229 vertices) changed 001: 41 total segments, 2 labels (2 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1531 vertices marked for relabeling... 1531 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Cortical Parc rh Tue Jan 12 19:53:50 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 953 labels changed using aseg relabeling using gibbs priors... 000: 2663 changed, 119567 examined... 001: 618 changed, 11447 examined... 002: 121 changed, 3445 examined... 003: 41 changed, 733 examined... 004: 20 changed, 262 examined... 005: 9 changed, 116 examined... 006: 7 changed, 55 examined... 007: 3 changed, 39 examined... 008: 1 changed, 19 examined... 009: 2 changed, 7 examined... 010: 0 changed, 10 examined... 159 labels changed using aseg 000: 96 total segments, 57 labels (321 vertices) changed 001: 41 total segments, 2 labels (2 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1408 vertices marked for relabeling... 1408 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 45 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jan 12 19:54:35 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10714 bright wm thresholded. 1432 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.orig... computing class statistics... border white: 230601 voxels (1.37%) border gray 248839 voxels (1.48%) WM (94.0): 94.7 +- 8.3 [70.0 --> 110.0] GM (81.0) : 78.7 +- 12.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.0 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 43.0 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=67+-10.4 mean inside = 94.0, mean outside = 75.2 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... 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 0 with 81 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=56.6, 118 (118) missing vertices, mean dist 1.7 [1.9 (%0.1)->2.1 (%99.9))] %30 local maxima, %50 large gradients and %17 min vals, 552 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=26068760.0, rms=30.234 001: dt: 0.5000, sse=19343946.0, rms=25.197 (16.660%) 002: dt: 0.5000, sse=14301430.0, rms=20.788 (17.496%) 003: dt: 0.5000, sse=10666858.0, rms=17.252 (17.009%) 004: dt: 0.5000, sse=8481742.0, rms=14.776 (14.353%) 005: dt: 0.5000, sse=7622060.5, rms=12.797 (13.393%) 006: dt: 0.5000, sse=7025117.5, rms=11.078 (13.432%) 007: dt: 0.5000, sse=6723471.5, rms=9.492 (14.317%) 008: dt: 0.5000, sse=6454438.5, rms=8.120 (14.456%) 009: dt: 0.5000, sse=6412858.5, rms=6.928 (14.677%) 010: dt: 0.5000, sse=6377874.5, rms=6.066 (12.451%) 011: dt: 0.5000, sse=6487402.5, rms=5.433 (10.431%) 012: dt: 0.5000, sse=6516758.0, rms=5.091 (6.291%) 013: dt: 0.5000, sse=6629871.5, rms=4.818 (5.355%) 014: dt: 0.5000, sse=6630895.5, rms=4.702 (2.421%) 015: dt: 0.5000, sse=6684767.5, rms=4.565 (2.916%) rms = 4.53, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=6666483.5, rms=4.529 (0.786%) 017: dt: 0.2500, sse=4479467.5, rms=3.467 (23.438%) 018: dt: 0.2500, sse=4216124.0, rms=3.155 (8.996%) 019: dt: 0.2500, sse=4056489.2, rms=3.084 (2.259%) rms = 3.04, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4018074.0, rms=3.039 (1.460%) 021: dt: 0.1250, sse=3814953.5, rms=2.882 (5.183%) rms = 2.86, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3778239.8, rms=2.864 (0.621%) positioning took 1.7 minutes mean border=53.7, 754 (27) missing vertices, mean dist 0.2 [0.2 (%41.4)->0.4 (%58.6))] %49 local maxima, %34 large gradients and %12 min vals, 188 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, 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=4399138.5, rms=5.443 023: dt: 0.5000, sse=4625921.0, rms=4.298 (21.028%) rms = 4.40, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4238624.0, rms=3.466 (19.366%) 025: dt: 0.2500, sse=4260460.0, rms=3.079 (11.151%) 026: dt: 0.2500, sse=4212998.5, rms=2.934 (4.727%) 027: dt: 0.2500, sse=4239433.5, rms=2.856 (2.637%) rms = 2.82, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4221647.0, rms=2.816 (1.402%) 029: dt: 0.1250, sse=4055531.5, rms=2.634 (6.479%) rms = 2.60, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4034392.5, rms=2.602 (1.198%) positioning took 0.7 minutes mean border=51.2, 893 (23) missing vertices, mean dist 0.1 [0.2 (%36.4)->0.3 (%63.6))] %63 local maxima, %20 large gradients and %12 min vals, 210 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, 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=4288697.0, rms=4.089 rms = 4.29, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4084695.0, rms=3.265 (20.145%) 032: dt: 0.2500, sse=4076740.5, rms=2.847 (12.815%) 033: dt: 0.2500, sse=4232749.0, rms=2.694 (5.372%) rms = 2.66, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4300095.5, rms=2.660 (1.244%) 035: dt: 0.1250, sse=4138258.8, rms=2.487 (6.517%) rms = 2.45, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4132269.2, rms=2.450 (1.483%) positioning took 0.5 minutes mean border=50.0, 1597 (21) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.2 (%57.0))] %67 local maxima, %16 large gradients and %12 min vals, 184 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4187602.5, rms=2.890 rms = 3.86, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4076207.8, rms=2.528 (12.545%) 038: dt: 0.2500, sse=4202007.5, rms=2.446 (3.206%) rms = 2.40, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4242587.5, rms=2.405 (1.715%) 040: dt: 0.1250, sse=4161733.2, rms=2.280 (5.184%) rms = 2.26, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4156224.5, rms=2.261 (0.834%) positioning took 0.4 minutes writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial vertex spacing 0.99 +- 0.40 (0.09-->5.75) (max @ vno 78879 --> 79903) face area 0.40 +- 0.28 (0.00-->5.63) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 123586 vertices processed 25000 of 123586 vertices processed 50000 of 123586 vertices processed 75000 of 123586 vertices processed 100000 of 123586 vertices processed 0 of 123586 vertices processed 25000 of 123586 vertices processed 50000 of 123586 vertices processed 75000 of 123586 vertices processed 100000 of 123586 vertices processed thickness calculation complete, 165:421 truncations. 43666 vertices at 0 distance 100975 vertices at 1 distance 65619 vertices at 2 distance 20521 vertices at 3 distance 5071 vertices at 4 distance 1319 vertices at 5 distance 393 vertices at 6 distance 133 vertices at 7 distance 60 vertices at 8 distance 24 vertices at 9 distance 16 vertices at 10 distance 7 vertices at 11 distance 6 vertices at 12 distance 4 vertices at 13 distance 6 vertices at 14 distance 8 vertices at 15 distance 2 vertices at 16 distance 7 vertices at 17 distance 3 vertices at 18 distance 4 vertices at 19 distance 2 vertices at 20 distance writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness positioning took 4.9 minutes #-------------------------------------------- #@# Make Pial Surf rh Tue Jan 12 19:59:32 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs MRM_003_w_070655_171011_0000FD62 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 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/filled.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/brain.finalsurfs.mgz... reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... 10185 bright wm thresholded. 1430 bright non-wm voxels segmented. reading original surface position from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.orig... computing class statistics... border white: 230601 voxels (1.37%) border gray 248839 voxels (1.48%) WM (94.0): 94.6 +- 8.0 [70.0 --> 110.0] GM (82.0) : 79.0 +- 12.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.3 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.6 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=69+-11.3 mean inside = 93.5, mean outside = 74.7 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/../mri/aseg.presurf.mgz... 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 0 with 21 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=57.8, 90 (90) missing vertices, mean dist 1.8 [0.3 (%0.0)->2.0 (%100.0))] %35 local maxima, %49 large gradients and %12 min vals, 482 gradients ignored tol=1.0e-04, sigma=2.0, host=eddie, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25114960.0, rms=30.348 001: dt: 0.5000, sse=18810006.0, rms=25.459 (16.110%) 002: dt: 0.5000, sse=13972790.0, rms=21.103 (17.110%) 003: dt: 0.5000, sse=10425691.0, rms=17.558 (16.797%) 004: dt: 0.5000, sse=8379192.0, rms=15.116 (13.905%) 005: dt: 0.5000, sse=7614194.5, rms=13.097 (13.362%) 006: dt: 0.5000, sse=7017754.0, rms=11.320 (13.565%) 007: dt: 0.5000, sse=6627511.5, rms=9.601 (15.183%) 008: dt: 0.5000, sse=6352554.5, rms=8.163 (14.983%) 009: dt: 0.5000, sse=6281152.5, rms=6.931 (15.091%) 010: dt: 0.5000, sse=6294402.5, rms=6.165 (11.052%) 011: dt: 0.5000, sse=6361133.0, rms=5.561 (9.796%) 012: dt: 0.5000, sse=6410154.5, rms=5.315 (4.416%) 013: dt: 0.5000, sse=6467220.0, rms=5.024 (5.484%) rms = 4.98, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=6495806.0, rms=4.980 (0.870%) 015: dt: 0.2500, sse=4308549.5, rms=3.721 (25.284%) 016: dt: 0.2500, sse=4026868.0, rms=3.321 (10.740%) 017: dt: 0.2500, sse=3876226.0, rms=3.204 (3.547%) 018: dt: 0.2500, sse=3830697.2, rms=3.122 (2.549%) rms = 3.08, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3790052.0, rms=3.075 (1.492%) 020: dt: 0.1250, sse=3568557.2, rms=2.846 (7.471%) rms = 2.81, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3535874.5, rms=2.811 (1.211%) positioning took 1.5 minutes mean border=54.4, 345 (6) missing vertices, mean dist 0.2 [0.2 (%38.7)->0.4 (%61.3))] %56 local maxima, %31 large gradients and % 8 min vals, 145 gradients ignored tol=1.0e-04, sigma=1.0, host=eddie, 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=4259810.5, rms=5.874 022: dt: 0.5000, sse=4442807.5, rms=4.707 (19.867%) rms = 4.85, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4025607.8, rms=3.689 (21.626%) 024: dt: 0.2500, sse=4054501.2, rms=3.234 (12.351%) 025: dt: 0.2500, sse=4012526.0, rms=3.057 (5.464%) 026: dt: 0.2500, sse=4045449.5, rms=2.960 (3.160%) rms = 2.92, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=4026414.0, rms=2.917 (1.450%) 028: dt: 0.1250, sse=3846175.5, rms=2.656 (8.949%) rms = 2.61, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=3817568.5, rms=2.610 (1.761%) positioning took 0.6 minutes mean border=51.8, 492 (2) missing vertices, mean dist 0.1 [0.1 (%34.9)->0.3 (%65.1))] %69 local maxima, %18 large gradients and % 8 min vals, 180 gradients ignored tol=1.0e-04, sigma=0.5, host=eddie, 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=4079012.0, rms=4.171 rms = 4.75, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3869750.2, rms=3.230 (22.560%) 031: dt: 0.2500, sse=3867138.0, rms=2.870 (11.153%) 032: dt: 0.2500, sse=4003167.2, rms=2.700 (5.923%) rms = 2.68, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4083518.5, rms=2.680 (0.728%) 034: dt: 0.1250, sse=3907828.5, rms=2.439 (9.015%) rms = 2.39, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3887037.8, rms=2.392 (1.894%) positioning took 0.5 minutes mean border=50.5, 1117 (1) missing vertices, mean dist 0.1 [0.2 (%43.1)->0.2 (%56.9))] %73 local maxima, %14 large gradients and % 8 min vals, 152 gradients ignored tol=1.0e-04, sigma=0.2, host=eddie, 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3939512.2, rms=2.838 rms = 4.16, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3832655.2, rms=2.424 (14.583%) 037: dt: 0.2500, sse=3946432.5, rms=2.366 (2.415%) rms = 2.33, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=3998715.0, rms=2.330 (1.500%) 039: dt: 0.1250, sse=3924500.2, rms=2.183 (6.328%) rms = 2.16, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=3909894.0, rms=2.165 (0.837%) positioning took 0.4 minutes writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial vertex spacing 0.99 +- 0.39 (0.10-->6.59) (max @ vno 67760 --> 68680) face area 0.40 +- 0.28 (0.00-->5.43) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119567 vertices processed 25000 of 119567 vertices processed 50000 of 119567 vertices processed 75000 of 119567 vertices processed 100000 of 119567 vertices processed 0 of 119567 vertices processed 25000 of 119567 vertices processed 50000 of 119567 vertices processed 75000 of 119567 vertices processed 100000 of 119567 vertices processed thickness calculation complete, 110:457 truncations. 46925 vertices at 0 distance 99147 vertices at 1 distance 59583 vertices at 2 distance 17456 vertices at 3 distance 3920 vertices at 4 distance 1052 vertices at 5 distance 383 vertices at 6 distance 133 vertices at 7 distance 57 vertices at 8 distance 31 vertices at 9 distance 18 vertices at 10 distance 9 vertices at 11 distance 5 vertices at 12 distance 6 vertices at 13 distance 2 vertices at 14 distance 8 vertices at 15 distance 4 vertices at 16 distance 6 vertices at 17 distance 2 vertices at 18 distance 2 vertices at 19 distance 3 vertices at 20 distance writing curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness positioning took 4.6 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jan 12 20:04:08 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Total face volume 189776 Total vertex volume 185900 (mask=0) #@# MRM_003_w_070655_171011_0000FD62 lh 185900 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Jan 12 20:04:12 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Total face volume 176473 Total vertex volume 172518 (mask=0) #@# MRM_003_w_070655_171011_0000FD62 rh 172518 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Jan 12 20:04:15 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 SUBJECTS_DIR is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 56 writing volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Tue Jan 12 20:12:41 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189776 Total vertex volume 185900 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1154 815 1559 2.007 0.416 0.091 0.017 5 0.7 bankssts 1069 720 1775 2.432 0.577 0.139 0.022 19 0.9 caudalanteriorcingulate 3490 2384 5640 2.157 0.473 0.128 0.028 37 4.0 caudalmiddlefrontal 2125 1359 2362 1.656 0.369 0.146 0.036 32 3.1 cuneus 480 356 1508 3.497 0.681 0.128 0.033 3 0.8 entorhinal 4030 2719 6993 2.284 0.633 0.134 0.031 57 5.0 fusiform 5544 3701 7824 1.960 0.469 0.133 0.031 68 6.8 inferiorparietal 4719 3187 9484 2.509 0.742 0.134 0.034 77 6.4 inferiortemporal 1439 933 1964 1.974 0.664 0.118 0.030 20 1.6 isthmuscingulate 6008 3795 7137 1.779 0.470 0.144 0.035 92 8.2 lateraloccipital 3524 2389 6175 2.432 0.624 0.144 0.038 49 5.3 lateralorbitofrontal 4898 3204 5762 1.737 0.473 0.147 0.043 70 8.1 lingual 2919 1923 4291 2.078 0.660 0.133 0.045 57 6.3 medialorbitofrontal 3682 2469 7478 2.608 0.614 0.131 0.030 51 4.4 middletemporal 810 553 1934 3.057 0.874 0.115 0.032 9 0.9 parahippocampal 2037 1265 3139 2.275 0.537 0.100 0.023 17 1.7 paracentral 1955 1322 2877 2.068 0.469 0.125 0.027 22 2.1 parsopercularis 872 609 2017 2.594 0.614 0.166 0.045 16 1.6 parsorbitalis 1533 1048 2359 2.054 0.513 0.147 0.035 23 2.1 parstriangularis 2429 1614 2111 1.449 0.410 0.133 0.031 28 3.2 pericalcarine 5856 3848 7852 1.895 0.561 0.109 0.023 57 5.3 postcentral 1733 1167 2670 2.101 0.641 0.123 0.025 23 1.5 posteriorcingulate 7143 4514 11848 2.392 0.573 0.106 0.024 57 6.7 precentral 4891 3249 6972 2.005 0.525 0.127 0.032 66 5.9 precuneus 1243 852 2413 2.445 0.682 0.140 0.037 23 2.1 rostralanteriorcingulate 8140 5609 13323 2.063 0.536 0.148 0.038 139 12.6 rostralmiddlefrontal 10116 6874 18629 2.377 0.557 0.125 0.029 109 11.5 superiorfrontal 8288 5457 11039 1.834 0.450 0.114 0.022 82 7.2 superiorparietal 4319 3001 8695 2.494 0.655 0.104 0.018 35 3.2 superiortemporal 5161 3441 7921 2.084 0.525 0.128 0.027 66 5.5 supramarginal 319 217 783 2.625 0.390 0.177 0.055 10 0.7 frontalpole 588 418 2072 3.435 0.861 0.131 0.032 8 0.8 temporalpole 686 395 1035 2.334 0.330 0.117 0.027 8 0.6 transversetemporal 3152 2098 6259 2.930 0.862 0.116 0.031 31 3.6 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 MRM_003_w_070655_171011_0000FD62 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189776 Total vertex volume 185900 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1154 741 1559 2.007 0.416 0.102 0.023 10 1.2 bankssts 1069 788 1775 2.432 0.577 0.180 0.054 52 2.4 caudalanteriorcingulate 3490 2789 5640 2.157 0.473 0.135 0.024 36 3.6 caudalmiddlefrontal 2125 1607 2362 1.656 0.369 0.137 0.029 24 2.7 cuneus 480 539 1508 3.497 0.681 0.175 0.040 12 0.9 entorhinal 4030 3303 6993 2.284 0.633 0.149 0.035 67 6.5 fusiform 5544 4297 7824 1.960 0.469 0.137 0.028 58 6.8 inferiorparietal 4719 4199 9484 2.509 0.742 0.152 0.035 75 7.2 inferiortemporal 1439 1113 1964 1.974 0.664 0.147 0.040 23 2.6 isthmuscingulate 6008 4485 7137 1.779 0.470 0.141 0.031 116 7.7 lateraloccipital 3524 2680 6175 2.432 0.624 0.144 0.036 51 5.6 lateralorbitofrontal 4898 3694 5762 1.737 0.473 0.142 0.039 101 8.4 lingual 2919 2269 4291 2.078 0.660 0.146 0.043 57 5.7 medialorbitofrontal 3682 3199 7478 2.608 0.614 0.141 0.028 49 4.4 middletemporal 810 737 1934 3.057 0.874 0.137 0.034 11 1.1 parahippocampal 2037 1498 3139 2.275 0.537 0.105 0.019 19 1.6 paracentral 1955 1505 2877 2.068 0.469 0.136 0.025 22 2.0 parsopercularis 872 904 2017 2.594 0.614 0.167 0.034 9 1.3 parsorbitalis 1533 1260 2359 2.054 0.513 0.163 0.035 22 2.3 parstriangularis 2429 1408 2111 1.449 0.410 0.123 0.032 36 3.3 pericalcarine 5856 4612 7852 1.895 0.561 0.114 0.020 47 4.9 postcentral 1733 1309 2670 2.101 0.641 0.136 0.030 28 2.3 posteriorcingulate 7143 5282 11848 2.392 0.573 0.108 0.018 61 5.7 precentral 4891 3667 6972 2.005 0.525 0.134 0.031 89 6.3 precuneus 1243 1130 2413 2.445 0.682 0.156 0.040 15 2.3 rostralanteriorcingulate 8140 7113 13323 2.063 0.536 0.161 0.033 108 11.9 rostralmiddlefrontal 10116 8389 18629 2.377 0.557 0.141 0.029 112 12.3 superiorfrontal 8288 6488 11039 1.834 0.450 0.126 0.021 77 7.0 superiorparietal 4319 3729 8695 2.494 0.655 0.126 0.021 35 4.0 superiortemporal 5161 4019 7921 2.084 0.525 0.133 0.027 65 5.8 supramarginal 319 366 783 2.625 0.390 0.206 0.043 3 0.7 frontalpole 588 749 2072 3.435 0.861 0.187 0.039 7 1.0 temporalpole 686 514 1035 2.334 0.330 0.108 0.022 4 0.6 transversetemporal 3152 1988 6259 2.930 0.862 0.127 0.032 55 4.3 insula #----------------------------------------- #@# Parcellation Stats rh Tue Jan 12 20:13:40 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176473 Total vertex volume 172518 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 898 628 1040 1.733 0.314 0.110 0.020 7 0.7 bankssts 1245 854 2251 2.199 0.786 0.134 0.026 20 1.2 caudalanteriorcingulate 2913 2014 4585 2.004 0.497 0.123 0.026 29 2.9 caudalmiddlefrontal 2540 1489 2731 1.649 0.434 0.140 0.040 41 4.2 cuneus 389 273 1267 3.308 0.789 0.124 0.040 4 0.6 entorhinal 3477 2270 5705 2.217 0.771 0.136 0.034 49 4.5 fusiform 5965 3963 8000 1.796 0.465 0.121 0.026 67 6.2 inferiorparietal 3980 2610 7167 2.294 0.676 0.132 0.031 59 4.9 inferiortemporal 1220 764 1815 2.186 0.688 0.130 0.040 19 1.8 isthmuscingulate 6107 3695 6656 1.641 0.431 0.137 0.035 93 8.2 lateraloccipital 3681 2475 5919 2.177 0.560 0.143 0.040 65 5.5 lateralorbitofrontal 4651 2926 5136 1.731 0.497 0.140 0.039 69 7.6 lingual 2675 1720 4090 2.136 0.620 0.132 0.030 49 3.2 medialorbitofrontal 4097 2740 7698 2.414 0.645 0.126 0.028 54 4.7 middletemporal 873 594 1825 2.736 0.770 0.111 0.026 9 0.8 parahippocampal 2254 1388 3429 2.229 0.570 0.104 0.022 15 1.9 paracentral 1925 1294 3040 2.169 0.487 0.113 0.025 20 1.9 parsopercularis 989 665 1693 2.366 0.553 0.165 0.040 18 1.6 parsorbitalis 2194 1485 3477 2.096 0.438 0.130 0.029 29 2.5 parstriangularis 2480 1590 2141 1.438 0.402 0.123 0.034 27 3.4 pericalcarine 5833 3764 8141 1.909 0.619 0.103 0.021 51 5.1 postcentral 1567 1058 2481 2.130 0.698 0.145 0.031 25 1.9 posteriorcingulate 6395 4095 10602 2.373 0.603 0.106 0.021 47 5.5 precentral 4884 3193 6521 1.927 0.524 0.122 0.027 53 5.1 precuneus 945 635 1799 2.545 0.525 0.139 0.030 16 1.2 rostralanteriorcingulate 7807 5408 12291 1.989 0.522 0.150 0.038 133 11.5 rostralmiddlefrontal 9739 6577 17504 2.294 0.562 0.130 0.031 118 12.1 superiorfrontal 6599 4353 8410 1.741 0.458 0.121 0.024 73 6.3 superiorparietal 4537 3054 8427 2.433 0.582 0.102 0.019 38 3.3 superiortemporal 4175 2707 6320 2.147 0.471 0.125 0.028 50 4.6 supramarginal 398 277 965 2.447 0.608 0.194 0.050 10 0.9 frontalpole 500 333 2118 3.799 0.656 0.133 0.038 7 0.7 temporalpole 621 348 810 2.065 0.347 0.106 0.023 7 0.5 transversetemporal 3543 2315 6464 2.691 0.839 0.121 0.043 47 6.3 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 MRM_003_w_070655_171011_0000FD62 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176473 Total vertex volume 172518 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 898 564 1040 1.733 0.314 0.107 0.022 9 0.8 bankssts 1245 1090 2251 2.199 0.786 0.171 0.048 35 3.0 caudalanteriorcingulate 2913 2490 4585 2.004 0.497 0.136 0.023 29 2.7 caudalmiddlefrontal 2540 1879 2731 1.649 0.434 0.142 0.030 30 3.3 cuneus 389 446 1267 3.308 0.789 0.172 0.042 7 0.6 entorhinal 3477 2706 5705 2.217 0.771 0.141 0.033 47 5.0 fusiform 5965 4890 8000 1.796 0.465 0.137 0.023 60 6.4 inferiorparietal 3980 3405 7167 2.294 0.676 0.147 0.033 50 5.5 inferiortemporal 1220 904 1815 2.186 0.688 0.152 0.042 43 2.3 isthmuscingulate 6107 4550 6656 1.641 0.431 0.138 0.028 77 7.5 lateraloccipital 3681 2950 5919 2.177 0.560 0.155 0.039 63 6.3 lateralorbitofrontal 4651 3278 5136 1.731 0.497 0.130 0.032 72 6.5 lingual 2675 2166 4090 2.136 0.620 0.139 0.030 38 3.5 medialorbitofrontal 4097 3588 7698 2.414 0.645 0.141 0.026 43 4.5 middletemporal 873 734 1825 2.736 0.770 0.131 0.028 8 1.1 parahippocampal 2254 1642 3429 2.229 0.570 0.113 0.020 19 1.9 paracentral 1925 1490 3040 2.169 0.487 0.128 0.024 21 2.0 parsopercularis 989 786 1693 2.366 0.553 0.152 0.035 14 1.4 parsorbitalis 2194 1864 3477 2.096 0.438 0.146 0.029 26 2.8 parstriangularis 2480 1508 2141 1.438 0.402 0.110 0.027 29 2.8 pericalcarine 5833 4705 8141 1.909 0.619 0.116 0.018 44 4.7 postcentral 1567 1210 2481 2.130 0.698 0.150 0.031 28 2.1 posteriorcingulate 6395 4742 10602 2.373 0.603 0.105 0.017 50 4.6 precentral 4884 3559 6521 1.927 0.524 0.130 0.027 53 5.2 precuneus 945 782 1799 2.545 0.525 0.166 0.039 24 1.6 rostralanteriorcingulate 7807 6886 12291 1.989 0.522 0.164 0.035 101 11.3 rostralmiddlefrontal 9739 8373 17504 2.294 0.562 0.147 0.031 112 12.8 superiorfrontal 6599 5236 8410 1.741 0.458 0.133 0.023 62 6.1 superiorparietal 4537 3777 8427 2.433 0.582 0.119 0.020 39 3.8 superiortemporal 4175 3058 6320 2.147 0.471 0.128 0.026 45 4.3 supramarginal 398 489 965 2.447 0.608 0.233 0.042 7 0.8 frontalpole 500 723 2118 3.799 0.656 0.187 0.032 4 0.8 temporalpole 621 434 810 2.065 0.347 0.096 0.015 3 0.3 transversetemporal 3543 2332 6464 2.691 0.839 0.135 0.039 88 5.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jan 12 20:14:40 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/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... 36 labels changed using aseg relabeling using gibbs priors... 000: 8382 changed, 123586 examined... 001: 2107 changed, 32051 examined... 002: 618 changed, 10858 examined... 003: 269 changed, 3409 examined... 004: 118 changed, 1529 examined... 005: 75 changed, 692 examined... 006: 42 changed, 407 examined... 007: 27 changed, 244 examined... 008: 13 changed, 136 examined... 009: 3 changed, 63 examined... 010: 1 changed, 16 examined... 011: 1 changed, 7 examined... 012: 2 changed, 9 examined... 013: 2 changed, 12 examined... 014: 1 changed, 13 examined... 015: 1 changed, 8 examined... 016: 0 changed, 6 examined... 15 labels changed using aseg 000: 262 total segments, 178 labels (2216 vertices) changed 001: 93 total segments, 11 labels (67 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 150 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 960 vertices marked for relabeling... 960 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 51 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Tue Jan 12 20:15:32 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/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.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 2 labels changed using aseg relabeling using gibbs priors... 000: 8297 changed, 119567 examined... 001: 1915 changed, 32057 examined... 002: 543 changed, 10004 examined... 003: 244 changed, 3023 examined... 004: 120 changed, 1362 examined... 005: 46 changed, 680 examined... 006: 17 changed, 272 examined... 007: 8 changed, 90 examined... 008: 4 changed, 34 examined... 009: 5 changed, 23 examined... 010: 2 changed, 20 examined... 011: 1 changed, 10 examined... 012: 3 changed, 7 examined... 013: 3 changed, 13 examined... 014: 0 changed, 17 examined... 2 labels changed using aseg 000: 228 total segments, 145 labels (1425 vertices) changed 001: 86 total segments, 3 labels (38 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 132 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 927 vertices marked for relabeling... 927 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 49 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jan 12 20:16:21 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189776 Total vertex volume 185900 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1058 724 1709 2.135 0.532 0.155 0.038 20 1.7 G_and_S_frontomargin 1499 978 1803 1.744 0.426 0.149 0.036 23 2.0 G_and_S_occipital_inf 1577 932 2388 2.164 0.579 0.111 0.031 17 1.7 G_and_S_paracentral 1439 944 2748 2.576 0.493 0.134 0.030 18 1.5 G_and_S_subcentral 618 450 1538 2.520 0.447 0.178 0.055 14 1.3 G_and_S_transv_frontopol 2435 1662 3919 2.222 0.579 0.123 0.029 31 3.1 G_and_S_cingul-Ant 1738 1182 2924 2.279 0.571 0.128 0.024 22 1.6 G_and_S_cingul-Mid-Ant 1213 844 2041 2.344 0.506 0.108 0.019 10 0.8 G_and_S_cingul-Mid-Post 523 345 1067 2.473 0.605 0.155 0.043 10 0.8 G_cingul-Post-dorsal 346 192 426 1.904 0.690 0.120 0.041 5 0.5 G_cingul-Post-ventral 1980 1246 2228 1.638 0.406 0.153 0.037 33 3.0 G_cuneus 1182 785 2211 2.274 0.495 0.131 0.028 18 1.4 G_front_inf-Opercular 343 227 919 2.851 0.439 0.148 0.030 5 0.4 G_front_inf-Orbital 1067 710 1767 2.078 0.522 0.157 0.043 20 1.9 G_front_inf-Triangul 4764 3277 9101 2.220 0.505 0.155 0.040 87 7.8 G_front_middle 6489 4351 13696 2.557 0.520 0.133 0.033 86 8.7 G_front_sup 424 268 1023 3.430 0.852 0.107 0.034 5 0.4 G_Ins_lg_and_S_cent_ins 667 448 2082 3.504 0.770 0.151 0.049 13 1.3 G_insular_short 1972 1251 2914 2.026 0.528 0.154 0.040 36 3.0 G_occipital_middle 1475 938 2116 1.926 0.423 0.136 0.032 19 1.9 G_occipital_sup 1387 907 2446 2.258 0.560 0.131 0.032 22 1.7 G_oc-temp_lat-fusifor 3501 2186 4133 1.709 0.473 0.154 0.049 57 6.9 G_oc-temp_med-Lingual 1199 828 3371 3.359 0.715 0.133 0.040 16 2.0 G_oc-temp_med-Parahip 2527 1707 5154 2.471 0.553 0.160 0.049 53 4.4 G_orbital 2034 1358 3339 2.030 0.438 0.146 0.035 32 2.8 G_pariet_inf-Angular 2671 1781 4948 2.284 0.500 0.141 0.030 42 3.2 G_pariet_inf-Supramar 3292 2183 5120 1.942 0.511 0.128 0.026 44 3.3 G_parietal_sup 2064 1314 3040 1.948 0.474 0.121 0.031 30 2.3 G_postcentral 2440 1486 4937 2.574 0.470 0.107 0.026 23 2.5 G_precentral 2271 1492 3907 2.119 0.568 0.145 0.039 43 3.1 G_precuneus 1006 652 1866 2.191 0.560 0.139 0.040 20 1.6 G_rectus 468 312 630 2.263 0.890 0.139 0.093 18 2.4 G_subcallosal 523 301 921 2.473 0.340 0.129 0.032 8 0.5 G_temp_sup-G_T_transv 1707 1166 4605 2.765 0.619 0.130 0.025 22 1.6 G_temp_sup-Lateral 402 271 981 3.398 0.537 0.084 0.025 2 0.3 G_temp_sup-Plan_polar 677 503 946 1.847 0.393 0.076 0.013 3 0.3 G_temp_sup-Plan_tempo 2759 1841 6182 2.598 0.725 0.147 0.040 60 4.3 G_temporal_inf 2470 1619 5668 2.709 0.624 0.141 0.033 44 3.2 G_temporal_middle 297 204 382 1.938 0.398 0.132 0.026 3 0.3 Lat_Fis-ant-Horizont 236 160 236 1.690 0.522 0.128 0.021 2 0.1 Lat_Fis-ant-Vertical 1036 693 1156 2.013 0.411 0.114 0.023 7 1.0 Lat_Fis-post 1927 1125 2319 1.940 0.491 0.146 0.040 31 3.0 Pole_occipital 1589 1139 4942 3.276 0.745 0.142 0.039 23 2.4 Pole_temporal 3065 2134 3088 1.642 0.547 0.127 0.031 35 3.9 S_calcarine 3250 2145 3511 1.856 0.672 0.091 0.018 15 2.5 S_central 1091 761 1427 1.934 0.475 0.089 0.015 5 0.6 S_cingul-Marginalis 352 234 584 2.941 0.668 0.119 0.032 3 0.4 S_circular_insula_ant 1328 893 2109 2.577 0.720 0.080 0.012 5 0.7 S_circular_insula_inf 1616 1107 2184 2.367 0.415 0.109 0.021 8 1.5 S_circular_insula_sup 1251 870 2012 2.273 0.559 0.113 0.021 11 1.2 S_collat_transv_ant 372 249 419 1.616 0.351 0.155 0.038 5 0.5 S_collat_transv_post 1840 1268 2361 1.842 0.442 0.118 0.025 15 1.9 S_front_inf 1784 1205 2345 1.908 0.442 0.135 0.035 26 2.5 S_front_middle 3108 2119 4453 2.041 0.486 0.115 0.024 24 3.2 S_front_sup 657 426 537 1.460 0.342 0.096 0.012 4 0.4 S_interm_prim-Jensen 3146 2068 3327 1.682 0.354 0.103 0.018 23 2.4 S_intrapariet_and_P_trans 821 555 659 1.314 0.252 0.115 0.018 7 0.6 S_oc_middle_and_Lunatus 1117 740 1218 1.689 0.349 0.119 0.025 10 1.2 S_oc_sup_and_transversal 332 233 413 1.917 0.486 0.142 0.029 5 0.4 S_occipital_ant 818 540 1112 2.046 0.518 0.120 0.021 8 0.7 S_oc-temp_lat 1628 1133 2172 2.050 0.556 0.123 0.026 15 1.6 S_oc-temp_med_and_Lingual 440 295 458 1.754 0.390 0.117 0.022 3 0.4 S_orbital_lateral 729 520 928 2.018 0.684 0.127 0.026 8 0.8 S_orbital_med-olfact 1148 803 2002 2.498 0.780 0.151 0.038 14 2.0 S_orbital-H_Shaped 1757 1149 2086 1.919 0.482 0.106 0.022 11 1.7 S_parieto_occipital 1402 896 1205 1.818 0.718 0.127 0.025 23 1.3 S_pericallosal 2728 1826 3214 1.867 0.383 0.094 0.017 14 2.0 S_postcentral 1378 944 1790 2.054 0.393 0.110 0.022 9 1.2 S_precentral-inf-part 1059 710 1375 2.215 0.505 0.094 0.016 5 0.8 S_precentral-sup-part 492 323 746 2.269 0.757 0.138 0.032 7 0.6 S_suborbital 873 593 1089 1.853 0.429 0.123 0.023 9 0.8 S_subparietal 1190 821 1536 2.206 0.529 0.122 0.026 9 1.4 S_temporal_inf 4048 2771 5344 2.033 0.418 0.105 0.022 29 3.4 S_temporal_sup 240 188 347 2.195 0.351 0.116 0.013 2 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jan 12 20:16:50 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176473 Total vertex volume 172518 (mask=0) 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 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 871 594 1303 1.889 0.611 0.159 0.043 18 1.5 G_and_S_frontomargin 1213 732 1416 1.759 0.465 0.144 0.038 19 1.7 G_and_S_occipital_inf 1399 802 2001 2.082 0.532 0.113 0.028 14 1.5 G_and_S_paracentral 1093 714 2058 2.635 0.466 0.120 0.028 11 1.1 G_and_S_subcentral 1143 790 2052 2.105 0.566 0.158 0.042 24 1.9 G_and_S_transv_frontopol 2573 1755 4278 2.339 0.495 0.137 0.030 38 3.1 G_and_S_cingul-Ant 1607 1090 3111 2.488 0.576 0.129 0.032 19 2.0 G_and_S_cingul-Mid-Ant 1433 982 2380 2.289 0.532 0.125 0.021 14 1.2 G_and_S_cingul-Mid-Post 489 317 1053 2.550 0.502 0.159 0.049 9 1.0 G_cingul-Post-dorsal 265 149 563 2.803 0.619 0.130 0.053 5 0.6 G_cingul-Post-ventral 2327 1348 2549 1.633 0.461 0.136 0.037 35 3.5 G_cuneus 1158 760 2328 2.445 0.442 0.129 0.030 18 1.4 G_front_inf-Opercular 388 260 745 2.280 0.369 0.163 0.041 8 0.7 G_front_inf-Orbital 1139 763 2126 2.201 0.419 0.138 0.034 20 1.6 G_front_inf-Triangul 3923 2755 7709 2.191 0.543 0.154 0.037 71 5.7 G_front_middle 6473 4255 13281 2.430 0.577 0.136 0.034 98 8.7 G_front_sup 465 312 1164 3.288 1.086 0.121 0.050 11 0.9 G_Ins_lg_and_S_cent_ins 598 369 1727 3.313 0.684 0.151 0.053 10 1.4 G_insular_short 1989 1213 2746 1.822 0.437 0.139 0.032 33 2.6 G_occipital_middle 1782 1118 2294 1.782 0.443 0.135 0.029 24 2.0 G_occipital_sup 1205 734 2010 2.129 0.610 0.134 0.036 21 1.6 G_oc-temp_lat-fusifor 3243 1931 3725 1.750 0.516 0.140 0.040 53 5.5 G_oc-temp_med-Lingual 1329 857 3259 3.011 0.785 0.132 0.051 18 2.5 G_oc-temp_med-Parahip 2611 1743 5244 2.415 0.532 0.157 0.049 60 4.5 G_orbital 2115 1350 3557 2.067 0.511 0.135 0.029 32 2.4 G_pariet_inf-Angular 2153 1343 3925 2.331 0.417 0.136 0.033 35 2.8 G_pariet_inf-Supramar 1754 1186 2860 1.944 0.493 0.125 0.027 23 2.0 G_parietal_sup 2156 1299 3571 2.127 0.531 0.109 0.025 25 2.1 G_postcentral 2325 1323 4750 2.674 0.481 0.102 0.024 20 2.1 G_precentral 1973 1259 3230 2.071 0.483 0.135 0.031 32 2.2 G_precuneus 810 484 1320 2.106 0.574 0.135 0.033 19 1.2 G_rectus 369 228 549 2.449 0.772 0.100 0.039 3 0.5 G_subcallosal 437 238 662 2.181 0.395 0.122 0.028 7 0.5 G_temp_sup-G_T_transv 1474 937 3284 2.616 0.614 0.126 0.027 20 1.5 G_temp_sup-Lateral 714 483 1580 2.875 0.525 0.081 0.017 3 0.4 G_temp_sup-Plan_polar 640 462 1026 1.985 0.454 0.074 0.013 2 0.3 G_temp_sup-Plan_tempo 2023 1311 4339 2.504 0.638 0.140 0.036 37 2.9 G_temporal_inf 2484 1622 5290 2.509 0.654 0.135 0.033 41 3.4 G_temporal_middle 296 198 308 1.917 0.412 0.101 0.017 2 0.2 Lat_Fis-ant-Horizont 241 167 330 2.104 0.616 0.159 0.027 3 0.3 Lat_Fis-ant-Vertical 1367 917 1703 2.077 0.424 0.109 0.024 9 1.3 Lat_Fis-post 3134 1823 3436 1.694 0.437 0.142 0.039 47 4.9 Pole_occipital 1420 980 4919 3.326 0.850 0.147 0.038 24 2.2 Pole_temporal 2911 1903 2845 1.657 0.528 0.122 0.033 31 4.0 S_calcarine 2921 2028 3379 1.836 0.651 0.096 0.016 13 2.2 S_central 1213 853 1398 1.728 0.441 0.108 0.019 7 1.0 S_cingul-Marginalis 591 391 755 2.328 0.407 0.100 0.020 3 0.4 S_circular_insula_ant 1131 744 1626 2.475 0.646 0.079 0.017 5 0.8 S_circular_insula_inf 1425 962 1990 2.349 0.403 0.102 0.022 11 1.4 S_circular_insula_sup 863 576 1274 2.241 0.597 0.113 0.026 9 0.8 S_collat_transv_ant 463 329 426 1.442 0.346 0.137 0.029 3 0.6 S_collat_transv_post 1643 1147 2015 1.784 0.412 0.120 0.024 13 1.6 S_front_inf 2043 1395 2534 1.809 0.395 0.142 0.035 27 2.9 S_front_middle 2409 1667 3256 1.915 0.419 0.116 0.031 22 2.9 S_front_sup 126 82 139 1.890 0.318 0.149 0.039 1 0.2 S_interm_prim-Jensen 2388 1627 2368 1.539 0.312 0.102 0.017 17 1.5 S_intrapariet_and_P_trans 883 602 694 1.302 0.271 0.131 0.031 8 1.1 S_oc_middle_and_Lunatus 1425 964 1375 1.508 0.321 0.121 0.025 12 1.5 S_oc_sup_and_transversal 504 346 512 1.469 0.465 0.108 0.023 11 0.4 S_occipital_ant 796 542 826 1.659 0.393 0.132 0.022 9 0.8 S_oc-temp_lat 1495 1061 1933 2.119 0.592 0.124 0.026 13 1.6 S_oc-temp_med_and_Lingual 390 265 413 1.916 0.479 0.124 0.024 3 0.4 S_orbital_lateral 839 576 952 1.807 0.589 0.120 0.033 8 1.2 S_orbital_med-olfact 1350 923 1918 2.024 0.549 0.140 0.033 19 1.9 S_orbital-H_Shaped 2113 1380 2306 1.775 0.474 0.118 0.026 21 2.2 S_parieto_occipital 1436 914 1284 1.803 0.697 0.133 0.028 27 1.3 S_pericallosal 2379 1620 2448 1.598 0.395 0.106 0.019 17 1.8 S_postcentral 1439 1008 1848 1.949 0.444 0.108 0.017 10 1.0 S_precentral-inf-part 1242 859 1456 1.889 0.486 0.111 0.019 8 1.1 S_precentral-sup-part 352 223 462 2.143 0.745 0.124 0.019 5 0.3 S_suborbital 901 603 1157 1.835 0.488 0.142 0.039 11 1.4 S_subparietal 1164 777 1427 2.043 0.485 0.132 0.025 13 1.2 S_temporal_inf 4398 3043 5411 1.880 0.441 0.099 0.017 26 3.2 S_temporal_sup 262 188 325 2.122 0.515 0.109 0.013 2 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Jan 12 20:17:20 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 lh ../surf/lh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 804 labels changed using aseg relabeling using gibbs priors... 000: 2532 changed, 123586 examined... 001: 613 changed, 10808 examined... 002: 178 changed, 3394 examined... 003: 83 changed, 1017 examined... 004: 42 changed, 455 examined... 005: 9 changed, 233 examined... 006: 8 changed, 54 examined... 007: 6 changed, 48 examined... 008: 2 changed, 29 examined... 009: 2 changed, 13 examined... 010: 1 changed, 10 examined... 011: 0 changed, 7 examined... 114 labels changed using aseg 000: 61 total segments, 28 labels (212 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 873 vertices marked for relabeling... 873 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Tue Jan 12 20:18:07 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 MRM_003_w_070655_171011_0000FD62 rh ../surf/rh.sphere.reg /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.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 1.767.2.2 2015/07/06 21:59:21 greve Exp $ reading atlas from /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 931 labels changed using aseg relabeling using gibbs priors... 000: 2395 changed, 119567 examined... 001: 536 changed, 10392 examined... 002: 129 changed, 3018 examined... 003: 68 changed, 780 examined... 004: 29 changed, 383 examined... 005: 14 changed, 176 examined... 006: 8 changed, 81 examined... 007: 5 changed, 43 examined... 008: 3 changed, 30 examined... 009: 0 changed, 13 examined... 140 labels changed using aseg 000: 65 total segments, 32 labels (106 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 702 vertices marked for relabeling... 702 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Jan 12 20:18:52 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 189776 Total vertex volume 185900 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1742 1174 2874 2.426 0.528 0.130 0.024 27 1.5 caudalanteriorcingulate 3575 2435 5812 2.163 0.473 0.128 0.028 38 4.1 caudalmiddlefrontal 2802 1808 3174 1.671 0.370 0.138 0.032 38 3.6 cuneus 452 340 1387 3.423 0.665 0.126 0.032 3 0.7 entorhinal 3578 2397 5744 2.196 0.564 0.130 0.029 48 4.0 fusiform 5486 3655 7655 1.946 0.472 0.134 0.031 68 6.7 inferiorparietal 4834 3265 9916 2.537 0.771 0.136 0.036 80 6.9 inferiortemporal 1406 907 1900 1.966 0.649 0.119 0.031 20 1.6 isthmuscingulate 6289 3968 7551 1.794 0.474 0.144 0.035 96 8.7 lateraloccipital 3810 2584 6818 2.425 0.666 0.150 0.041 62 6.2 lateralorbitofrontal 4915 3212 5763 1.736 0.473 0.147 0.043 71 8.2 lingual 2455 1642 3869 2.091 0.652 0.131 0.037 40 3.9 medialorbitofrontal 4673 3175 9182 2.521 0.630 0.126 0.028 59 5.2 middletemporal 834 573 2031 3.080 0.876 0.115 0.032 9 0.9 parahippocampal 2321 1459 3573 2.296 0.521 0.100 0.022 18 2.0 paracentral 1692 1138 2424 2.095 0.468 0.121 0.025 18 1.5 parsopercularis 965 646 1977 2.456 0.601 0.135 0.031 11 1.1 parsorbitalis 1940 1336 2899 1.991 0.487 0.146 0.035 29 2.9 parstriangularis 2418 1605 2109 1.454 0.409 0.132 0.032 27 3.2 pericalcarine 6670 4407 9000 1.902 0.553 0.110 0.023 64 6.2 postcentral 1859 1260 2834 2.132 0.646 0.123 0.024 24 1.6 posteriorcingulate 7090 4484 11726 2.398 0.572 0.106 0.024 56 6.7 precentral 4724 3143 6975 2.036 0.528 0.131 0.033 69 5.9 precuneus 1769 1170 2940 2.316 0.704 0.141 0.046 39 4.3 rostralanteriorcingulate 5641 3882 9187 2.071 0.561 0.147 0.038 98 8.8 rostralmiddlefrontal 11405 7785 21273 2.331 0.566 0.133 0.032 143 14.6 superiorfrontal 6717 4422 8852 1.826 0.448 0.110 0.020 61 5.5 superiorparietal 5965 4141 12330 2.536 0.741 0.107 0.021 53 4.9 superiortemporal 4952 3306 7565 2.088 0.527 0.128 0.027 60 5.2 supramarginal 655 375 989 2.333 0.331 0.116 0.026 7 0.5 transversetemporal 2718 1810 5571 2.957 0.866 0.116 0.030 27 3.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Tue Jan 12 20:19:20 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 176473 Total vertex volume 172518 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 1254 861 2261 2.203 0.775 0.134 0.026 20 1.3 caudalanteriorcingulate 2957 2045 4628 2.005 0.497 0.123 0.026 29 2.9 caudalmiddlefrontal 3007 1798 3277 1.662 0.421 0.141 0.038 47 4.7 cuneus 422 295 1401 3.346 0.806 0.122 0.039 4 0.6 entorhinal 3031 1972 4664 2.130 0.679 0.137 0.036 46 4.1 fusiform 5611 3706 7583 1.812 0.471 0.124 0.026 63 6.0 inferiorparietal 4342 2866 8292 2.367 0.760 0.133 0.030 61 5.4 inferiortemporal 1243 774 1818 2.177 0.681 0.130 0.040 19 1.9 isthmuscingulate 6470 3923 7009 1.632 0.432 0.137 0.034 98 8.6 lateraloccipital 4316 2890 7051 2.180 0.609 0.150 0.045 83 7.4 lateralorbitofrontal 4629 2912 5107 1.731 0.495 0.140 0.039 69 7.6 lingual 2279 1453 3478 2.125 0.653 0.122 0.028 36 2.5 medialorbitofrontal 4795 3222 8492 2.309 0.661 0.123 0.028 60 5.4 middletemporal 877 598 1817 2.735 0.757 0.111 0.026 8 0.8 parahippocampal 2371 1461 3653 2.246 0.567 0.105 0.022 16 2.2 paracentral 2019 1356 3218 2.181 0.484 0.118 0.028 28 2.3 parsopercularis 1179 785 1876 2.257 0.489 0.143 0.034 17 1.6 parsorbitalis 2062 1403 3170 2.041 0.448 0.126 0.027 26 2.2 parstriangularis 2505 1609 2160 1.434 0.397 0.122 0.034 26 3.4 pericalcarine 6283 4055 8708 1.908 0.623 0.106 0.022 57 5.6 postcentral 1713 1157 2792 2.160 0.694 0.142 0.030 26 2.0 posteriorcingulate 6194 3951 10393 2.389 0.600 0.107 0.021 47 5.4 precentral 4901 3196 6668 1.933 0.530 0.121 0.027 53 5.2 precuneus 1068 713 2001 2.525 0.513 0.143 0.031 19 1.4 rostralanteriorcingulate 4683 3272 7384 1.994 0.515 0.150 0.036 75 6.7 rostralmiddlefrontal 13050 8857 22785 2.222 0.564 0.136 0.034 186 17.6 superiorfrontal 5593 3701 7175 1.748 0.456 0.117 0.024 60 5.2 superiorparietal 5805 3901 11323 2.496 0.711 0.106 0.022 51 4.9 superiortemporal 3965 2588 5966 2.137 0.447 0.123 0.028 46 4.2 supramarginal 599 331 784 2.062 0.354 0.105 0.023 7 0.5 transversetemporal 2873 1902 5581 2.773 0.821 0.117 0.035 33 4.2 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Jan 12 20:19:51 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts pctsurfcon --s MRM_003_w_070655_171011_0000FD62 --lh-only Log file is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/pctsurfcon.log Tue Jan 12 20:19:51 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux eddie412 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.wm.mgh --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 68446 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.wm.mgh Dim: 123586 1 1 mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.gm.mgh --projfrac 0.3 --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Done reading source surface Reading thickness /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 81260 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.gm.mgh Dim: 123586 1 1 mri_concat /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.wm.mgh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9582/lh.gm.mgh --paired-diff-norm --mul 100 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 lh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 lh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/lh.w-g.pct.stats --snr sysname Linux hostname eddie412 machine x86_64 user s1158296 UseRobust 0 Constructing seg from annotation Reading annotation /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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) Seg base 1000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh Vertex Area is 0.665518 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 Tue Jan 12 20:19:59 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts pctsurfcon --s MRM_003_w_070655_171011_0000FD62 --rh-only Log file is /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts/pctsurfcon.log Tue Jan 12 20:19:59 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/scripts /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux eddie412 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.wm.mgh --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 64825 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.wm.mgh Dim: 119567 1 1 mri_vol2surf --mov /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.gm.mgh --projfrac 0.3 --regheader MRM_003_w_070655_171011_0000FD62 --cortex srcvol = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 INFO: changing type to float Done loading volume Computing registration from header. Using /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/orig.mgz as target reference. -------- original matrix ----------- -0.08017 0.99678 0.00000 0.00002; -0.99611 -0.08012 0.03661 0.00000; 0.03650 0.00294 0.99933 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Reading surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Done reading source surface Reading thickness /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 78853 Masking with /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.cortex.label Writing to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.gm.mgh Dim: 119567 1 1 mri_concat /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.wm.mgh /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/tmp.pctsurfcon.9634/rh.gm.mgh --paired-diff-norm --mul 100 --o /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 rh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --in /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --annot MRM_003_w_070655_171011_0000FD62 rh aparc --sum /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/stats/rh.w-g.pct.stats --snr sysname Linux hostname eddie412 machine x86_64 user s1158296 UseRobust 0 Constructing seg from annotation Reading annotation /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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) Seg base 2000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh Vertex Area is 0.655927 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 Tue Jan 12 20:20:05 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 452 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 270 voxels changed to hypointensity... 669 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg Tue Jan 12 20:20:23 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_aparc2aseg --s MRM_003_w_070655_171011_0000FD62 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer subject MRM_003_w_070655_171011_0000FD62 outvol /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 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/exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 357357 Used brute-force search on 0 voxels Writing output aseg to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Tue Jan 12 20:22:51 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Jan 12 20:22:51 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 $Id: apas2aseg,v 1.1 2014/08/14 22:25:53 greve Exp $ Linux eddie412 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 14:01:59 CDT 2014 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 1.41 2014/08/17 17:47:29 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri cmdline 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 sysname Linux hostname eddie412 machine x86_64 user s1158296 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 Tue Jan 12 20:22:51 GMT 2016 Ended at Tue Jan 12 20:22:58 GMT 2016 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Jan 12 20:22:58 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/ASegStatsLUT.txt --subject MRM_003_w_070655_171011_0000FD62 $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/ASegStatsLUT.txt --subject MRM_003_w_070655_171011_0000FD62 sysname Linux hostname eddie412 machine x86_64 user s1158296 UseRobust 0 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) Computing euler number orig.nofix lheno = -28, rheno = -28 orig.nofix lhholes = 15, rhholes = 15 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 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 Tue Jan 12 20:25:26 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 mri_aparc2aseg --s MRM_003_w_070655_171011_0000FD62 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer subject MRM_003_w_070655_171011_0000FD62 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aparc+aseg.mgz Reading lh white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading lh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial Loading lh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading rh pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial Loading rh annotations from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz Loading filled from /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7234 vertices from left hemi Ripped 7471 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/aseg.mgz Loading Ctx Seg File /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 = 763965 Used brute-force search on 32 voxels Fixing Parahip LH WM Found 4 clusters 0 k 1.000000 1 k 3.000000 2 k 19.000000 3 k 1212.000000 Fixing Parahip RH WM Found 7 clusters 0 k 4.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 1.000000 5 k 1224.000000 6 k 1.000000 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 MRM_003_w_070655_171011_0000FD62 --surf-wm-vol --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 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 MRM_003_w_070655_171011_0000FD62 --surf-wm-vol --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname eddie412 machine x86_64 user s1158296 UseRobust 0 atlas_icv (eTIV) = 1377205 mm^3 (det: 1.414535 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label #-------------------------------------------- #@# BA_exvivo Labels lh Tue Jan 12 20:33:54 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4339 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 460 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4254 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 907 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 301 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4482 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 451 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 1917 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6558 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 2733 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10847 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2201 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1345 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1267 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2218 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1672 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7252 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 214 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1365 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 1538 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4943 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 1248 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4582 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 487 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 123586 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 462 mri_label2label: Done mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie412 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi lh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 84616 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/lh.BA_exvivo.annot mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi lh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie412 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi lh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 100286 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189776 Total vertex volume 185900 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 948 589 1535 2.079 0.445 0.148 0.041 21 1.4 BA1_exvivo 3849 2541 5075 1.938 0.421 0.100 0.019 27 2.9 BA2_exvivo 1034 701 871 1.524 0.308 0.122 0.024 7 1.0 BA3a_exvivo 2288 1541 2840 1.693 0.568 0.107 0.023 21 2.2 BA3b_exvivo 1662 906 2867 2.667 0.496 0.096 0.029 14 1.5 BA4a_exvivo 1421 856 2089 2.485 0.503 0.086 0.021 6 1.3 BA4p_exvivo 8300 5516 15691 2.418 0.548 0.117 0.027 81 8.7 BA6_exvivo 2213 1497 3547 2.145 0.476 0.123 0.026 26 2.2 BA44_exvivo 2527 1743 3798 1.947 0.535 0.142 0.033 36 3.4 BA45_exvivo 4189 2639 4174 1.584 0.477 0.133 0.037 55 6.3 V1_exvivo 8011 5129 9242 1.759 0.462 0.155 0.042 131 13.3 V2_exvivo 1450 989 1785 1.783 0.456 0.136 0.029 19 1.6 MT_exvivo 496 306 1147 3.420 0.721 0.118 0.028 8 0.5 perirhinal_exvivo 582 444 1812 3.614 0.767 0.144 0.040 7 1.0 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab MRM_003_w_070655_171011_0000FD62 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 189776 Total vertex volume 185900 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 556 314 885 2.140 0.395 0.157 0.050 14 0.9 BA1_exvivo 1466 971 2066 1.984 0.424 0.092 0.017 10 1.0 BA2_exvivo 848 578 685 1.507 0.299 0.126 0.024 6 0.9 BA3a_exvivo 1425 997 1418 1.391 0.308 0.079 0.014 6 0.9 BA3b_exvivo 1719 931 2830 2.639 0.489 0.086 0.026 12 1.5 BA4a_exvivo 1155 697 1626 2.439 0.510 0.089 0.022 6 1.1 BA4p_exvivo 4220 2782 8371 2.538 0.521 0.113 0.027 40 4.0 BA6_exvivo 1334 907 2084 2.095 0.462 0.130 0.028 17 1.4 BA44_exvivo 1063 727 1798 2.061 0.525 0.155 0.045 20 1.8 BA45_exvivo 4535 2830 4621 1.609 0.479 0.136 0.040 64 7.2 V1_exvivo 4089 2651 4489 1.693 0.455 0.161 0.044 69 7.4 V2_exvivo 372 270 464 1.695 0.418 0.153 0.031 7 0.4 MT_exvivo 239 157 784 3.609 0.529 0.098 0.015 1 0.2 perirhinal_exvivo 279 228 848 3.486 0.711 0.114 0.027 2 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Tue Jan 12 20:38:27 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 222 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4184 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6970 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4769 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5981 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4602 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 638 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12894 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 488 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 718 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 1867 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 2908 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10924 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1145 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 809 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 929 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 163 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1446 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 126 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1382 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 1397 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 1325 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4762 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 49 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 317 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 732 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject MRM_003_w_070655_171011_0000FD62 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = MRM_003_w_070655_171011_0000FD62 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 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white Reading target registration /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 119567 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 321 mri_label2label: Done mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie412 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi rh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 80584 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label/rh.BA_exvivo.annot mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/label cmdline mris_label2annot --s MRM_003_w_070655_171011_0000FD62 --hemi rh --ctab /exports/work/mcm_cric_nas/Kaiming/freesurfer/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 eddie412 machine x86_64 user s1158296 subject MRM_003_w_070655_171011_0000FD62 hemi rh SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer ColorTable /exports/work/mcm_cric_nas/Kaiming/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 96842 unhit vertices Writing annot to /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 176473 Total vertex volume 172518 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 791 426 1385 2.331 0.453 0.127 0.034 14 1.0 BA1_exvivo 3074 2087 3820 1.740 0.486 0.100 0.017 21 2.2 BA2_exvivo 1030 731 910 1.534 0.411 0.127 0.024 7 1.1 BA3a_exvivo 1999 1290 2426 1.669 0.520 0.096 0.020 16 1.7 BA3b_exvivo 1469 785 2451 2.576 0.468 0.093 0.021 8 1.4 BA4a_exvivo 1126 738 1868 2.536 0.513 0.087 0.016 5 0.7 BA4p_exvivo 7266 4737 13246 2.346 0.595 0.115 0.025 68 7.1 BA6_exvivo 3165 2149 5112 2.230 0.495 0.114 0.024 31 2.9 BA44_exvivo 3877 2630 6008 2.050 0.490 0.134 0.031 52 4.8 BA45_exvivo 4408 2683 4365 1.577 0.447 0.132 0.039 61 6.9 V1_exvivo 8230 5024 8814 1.690 0.468 0.139 0.037 118 12.5 V2_exvivo 1749 1163 1781 1.504 0.448 0.121 0.025 27 1.7 MT_exvivo 447 286 1201 3.336 0.662 0.147 0.055 8 1.0 perirhinal_exvivo 352 243 851 3.074 0.806 0.125 0.028 4 0.4 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 MRM_003_w_070655_171011_0000FD62 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/mri/wm.mgz... reading input surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... reading input pial surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.pial... reading input white surface /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 176473 Total vertex volume 172518 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /exports/work/mcm_cric_nas/Kaiming/freesurfer/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) = 1377205 mm^3 (det: 1.414535 ) lhCtxGM: 186468.223 186373.000 diff= 95.2 pctdiff= 0.051 rhCtxGM: 172744.995 172410.000 diff= 335.0 pctdiff= 0.194 lhCtxWM: 209553.609 209908.000 diff= -354.4 pctdiff=-0.169 rhCtxWM: 197161.939 197432.000 diff= -270.1 pctdiff=-0.137 SubCortGMVol 48444.000 SupraTentVol 835181.766 (834418.000) diff=763.766 pctdiff=0.091 SupraTentVolNotVent 815433.766 (814670.000) diff=763.766 pctdiff=0.094 BrainSegVol 964223.000 (960454.000) diff=3769.000 pctdiff=0.391 BrainSegVolNotVent 939451.000 (939061.766) diff=389.234 pctdiff=0.041 BrainSegVolNotVent 939451.000 CerebellumVol 124586.000 VentChorVol 19748.000 3rd4th5thCSF 5024.000 CSFVol 1262.000, OptChiasmVol 188.000 MaskVol 1437477.000 584 298 1014 2.352 0.387 0.124 0.030 9 0.7 BA1_exvivo 1913 1270 2474 1.785 0.535 0.093 0.016 13 1.2 BA2_exvivo 890 647 730 1.484 0.356 0.134 0.026 6 1.0 BA3a_exvivo 1624 1092 1727 1.519 0.414 0.084 0.015 8 1.1 BA3b_exvivo 896 459 1514 2.645 0.517 0.091 0.023 5 0.9 BA4a_exvivo 976 649 1657 2.586 0.509 0.084 0.015 4 0.6 BA4p_exvivo 4519 2932 8283 2.379 0.605 0.116 0.025 42 4.6 BA6_exvivo 880 588 1592 2.269 0.454 0.124 0.029 13 1.0 BA44_exvivo 1132 772 2115 2.214 0.440 0.145 0.036 20 1.5 BA45_exvivo 4260 2610 4111 1.558 0.440 0.130 0.038 56 6.6 V1_exvivo 4327 2632 4658 1.676 0.477 0.145 0.039 68 7.2 V2_exvivo 271 191 229 1.288 0.276 0.114 0.018 2 0.2 MT_exvivo 218 149 778 3.404 0.634 0.129 0.033 3 0.2 perirhinal_exvivo 235 154 534 3.021 0.644 0.098 0.034 1 0.3 entorhinal_exvivo #------------------------------------------ Started at Tue Jan 12 16:30:08 GMT 2016 Ended at Tue Jan 12 20:42:52 GMT 2016 #@#%# recon-all-run-time-hours 4.212 recon-all -s MRM_003_w_070655_171011_0000FD62 finished without error at Tue Jan 12 20:42:52 GMT 2016 New invocation of recon-all Mon Feb 22 22:45:20 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62 /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/recon-all -s MRM_003_w_070655_171011_0000FD62 -qcache subjid MRM_003_w_070655_171011_0000FD62 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer Actual FREESURFER_HOME /exports/work/mcm_cric_nas/Kaiming/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 122880 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 27033600 kbytes descriptors 1024 memorylocked 301989888 kbytes maxproc 191986 total used free shared buffers cached Mem: 24594416 2573656 22020760 0 3768 30004 -/+ buffers/cache: 2539884 22054532 Swap: 50331644 143248 50188396 ######################################## program versions used $Id: recon-all,v 1.515.2.24 2015/10/01 21:23:52 greve 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: $ TimeStamp: 2016/02/22-22:45:21-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:21-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.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: 2016/02/22-22:45:22-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-22:45:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize.c,v 1.84.2.1 2015/08/13 17:12:10 zkaufman Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:23-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_watershed.cpp,v 1.100.2.1 2015/07/10 18:57:54 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:24-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:25-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_em_register.c,v 1.101.2.1 2015/06/24 20:18:26 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:25-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_normalize.c,v 1.62.2.1 2015/06/24 20:18:24 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:26-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_register.c,v 1.92.2.1 2015/06/24 20:18:25 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:26-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_ca_label.c,v 1.108 2014/11/24 20:09:20 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:27-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:27-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:28-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:28-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_concatenate_lta.c,v 1.13.2.2 2015/08/19 16:36:35 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:29-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:29-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:30-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:30-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:30-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:31-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:31-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:31-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:32-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/02/22-22:45:32-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_make_surfaces.c,v 1.154.2.5 2015/08/13 17:10:46 zkaufman Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:33-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:33-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:34-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_anatomical_stats.c,v 1.76.2.2 2015/07/06 21:59:22 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:34-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:34-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_curvature_stats.c,v 1.64.4.1 2015/06/04 21:12:38 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:34-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mris_calc.c,v 1.51.2.2 2015/06/04 21:12:37 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:35-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:35-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:35-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:36-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:36-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:37-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2016/02/22-22:45:37-GMT BuildTimeStamp: Oct 15 2015 01:03:13 CVS: $Id: mri_relabel_hypointensities.c,v 1.11.2.1 2015/05/15 18:45:54 nicks Exp $ User: s1158296 Machine: eddie521 Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /exports/work/mcm_cric_nas/Kaiming/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Mon Feb 22 22:45:37 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.8700 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.thickness.fsaverage.mris_preproc.log Mon Feb 22 22:45:37 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.8700 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:45:37 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8700/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8700/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.8700/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.thickness Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.8700/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.8700/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.8700 Mon Feb 22 22:45:44 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area fsaverage Mon Feb 22 22:45:44 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.8809 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.area.fsaverage.mris_preproc.log Mon Feb 22 22:45:44 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.8809 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:45:44 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8809/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8809/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.8809/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (123586) Reverse Loop had 17496 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.8809/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.8809/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.8809 Mon Feb 22 22:45:52 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area.pial fsaverage Mon Feb 22 22:45:52 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.8918 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Mon Feb 22 22:45:52 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.8918 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:45:52 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8918/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.8918/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.8918/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.area.pial Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (123586) Reverse Loop had 17496 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.8918/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.8918/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.8918 Mon Feb 22 22:46:00 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh volume fsaverage Mon Feb 22 22:46:00 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.9031 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.volume.fsaverage.mris_preproc.log Mon Feb 22 22:46:00 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9031 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:00 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9031/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9031/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9031/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.volume Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (123586) Reverse Loop had 17496 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9031/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9031/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9031 Mon Feb 22 22:46:07 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh curv fsaverage Mon Feb 22 22:46:07 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9140 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.curv.fsaverage.mris_preproc.log Mon Feb 22 22:46:07 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9140 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:07 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9140/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9140/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9140/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.curv Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9140/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9140/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9140 Mon Feb 22 22:46:13 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh sulc fsaverage Mon Feb 22 22:46:13 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9300 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.sulc.fsaverage.mris_preproc.log Mon Feb 22 22:46:13 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9300 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:13 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9300/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sulc --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9300/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sulc --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9300/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sulc Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9300/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9300/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9300 Mon Feb 22 22:46:19 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh white.K fsaverage Mon Feb 22 22:46:19 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9409 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.white.K.fsaverage.mris_preproc.log Mon Feb 22 22:46:19 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9409 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:19 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9409/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.K --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9409/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.K --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.K srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9409/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.K Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9409/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9409/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.white.K.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.white.K.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9409 Mon Feb 22 22:46:25 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh white.H fsaverage Mon Feb 22 22:46:25 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas white.H --target fsaverage --out lh.white.H.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9519 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.white.H.fsaverage.mris_preproc.log Mon Feb 22 22:46:25 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas white.H --target fsaverage --out lh.white.H.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9519 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:25 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9519/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.H --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9519/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.H --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.H srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9519/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.white.H Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9519/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9519/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.white.H.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.white.H.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9519 Mon Feb 22 22:46:31 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh jacobian_white fsaverage Mon Feb 22 22:46:31 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9666 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.jacobian_white.fsaverage.mris_preproc.log Mon Feb 22 22:46:31 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9666 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:31 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9666/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.jacobian_white --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9666/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.jacobian_white --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9666/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.jacobian_white Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9666/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9666/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9666 Mon Feb 22 22:46:37 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh w-g.pct.mgh fsaverage Mon Feb 22 22:46:37 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9776 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is lh.w-g.pct.mgh.fsaverage.mris_preproc.log Mon Feb 22 22:46:37 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9776 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:37 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9776/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9776/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9776/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/lh.w-g.pct.mgh Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (123586) Reverse Loop had 17496 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 149984, nTrgMulti = 13858, MnTrgMultiHits = 2.26252 nSrc121 = 81326, nSrcLost = 0, nSrcMulti = 42260, MnSrcMultiHits = 2.36659 Saving target data Saving to ./tmp.mris_preproc.9776/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9776/MRM_003_w_070655_171011_0000FD62.1.mgh --o lh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9776 Mon Feb 22 22:46:43 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh thickness fsaverage Mon Feb 22 22:46:43 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.9888 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.thickness.fsaverage.mris_preproc.log Mon Feb 22 22:46:43 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.9888 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:43 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9888/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.9888/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.9888/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.thickness Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.9888/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.9888/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.9888 Mon Feb 22 22:46:48 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh area fsaverage Mon Feb 22 22:46:48 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.10000 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.area.fsaverage.mris_preproc.log Mon Feb 22 22:46:48 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10000 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:48 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10000/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10000/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10000/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (119567) Reverse Loop had 15809 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10000/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10000/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10000 Mon Feb 22 22:46:56 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh area.pial fsaverage Mon Feb 22 22:46:56 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.10171 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.area.pial.fsaverage.mris_preproc.log Mon Feb 22 22:46:56 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10171 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:46:56 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10171/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10171/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10171/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.area.pial Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (119567) Reverse Loop had 15809 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10171/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10171/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10171 Mon Feb 22 22:47:03 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh volume fsaverage Mon Feb 22 22:47:03 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.10301 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.volume.fsaverage.mris_preproc.log Mon Feb 22 22:47:03 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10301 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:03 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10301/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10301/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume --jac --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10301/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.volume Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (119567) Reverse Loop had 15809 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10301/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10301/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10301 Mon Feb 22 22:47:11 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh curv fsaverage Mon Feb 22 22:47:11 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10421 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.curv.fsaverage.mris_preproc.log Mon Feb 22 22:47:11 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10421 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:11 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10421/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10421/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10421/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.curv Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10421/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10421/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10421 Mon Feb 22 22:47:17 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh sulc fsaverage Mon Feb 22 22:47:17 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10529 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.sulc.fsaverage.mris_preproc.log Mon Feb 22 22:47:17 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10529 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:17 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10529/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sulc --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10529/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sulc --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10529/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sulc Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10529/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10529/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10529 Mon Feb 22 22:47:22 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh white.K fsaverage Mon Feb 22 22:47:22 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas white.K --target fsaverage --out rh.white.K.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10652 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.white.K.fsaverage.mris_preproc.log Mon Feb 22 22:47:22 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas white.K --target fsaverage --out rh.white.K.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10652 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:22 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10652/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.K --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10652/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.K --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.K srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10652/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.K Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10652/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10652/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.white.K.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.white.K.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10652 Mon Feb 22 22:47:28 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh white.H fsaverage Mon Feb 22 22:47:28 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas white.H --target fsaverage --out rh.white.H.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10765 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.white.H.fsaverage.mris_preproc.log Mon Feb 22 22:47:28 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas white.H --target fsaverage --out rh.white.H.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10765 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:28 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10765/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.H --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10765/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.H --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.H srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10765/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.white.H Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10765/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10765/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.white.H.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.white.H.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10765 Mon Feb 22 22:47:34 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh jacobian_white fsaverage Mon Feb 22 22:47:34 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10874 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.jacobian_white.fsaverage.mris_preproc.log Mon Feb 22 22:47:34 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10874 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:34 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10874/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.jacobian_white --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10874/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.jacobian_white --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10874/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.jacobian_white Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10874/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10874/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10874 Mon Feb 22 22:47:39 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh w-g.pct.mgh fsaverage Mon Feb 22 22:47:40 GMT 2016 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.10984 /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf Log file is rh.w-g.pct.mgh.fsaverage.mris_preproc.log Mon Feb 22 22:47:40 GMT 2016 setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf /exports/work/mcm_cric_nas/Kaiming/freesurfer/bin/mris_preproc --s MRM_003_w_070655_171011_0000FD62 --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh Linux eddie521 2.6.32-504.3.3.el6.x86_64 #1 SMP Tue Dec 16 14:29:22 CST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.72.2.1 2015/05/21 17:41:38 greve Exp $ freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 tmpdir is ./tmp.mris_preproc.10984 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 MRM_003_w_070655_171011_0000FD62 Mon Feb 22 22:47:40 GMT 2016 -------------- ----------------------- mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10984/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --srcsubject MRM_003_w_070655_171011_0000FD62 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.10984/MRM_003_w_070655_171011_0000FD62.1.mgh --sval /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = MRM_003_w_070655_171011_0000FD62 srcval = /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.10984/MRM_003_w_070655_171011_0000FD62.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.sphere.reg Loading source data Reading curvature file /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf/rh.w-g.pct.mgh Reading target surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (119567) Reverse Loop had 15809 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 151270, nTrgMulti = 12572, MnTrgMultiHits = 2.25748 nSrc121 = 76549, nSrcLost = 0, nSrcMulti = 43018, MnSrcMultiHits = 2.39672 Saving target data Saving to ./tmp.mris_preproc.10984/MRM_003_w_070655_171011_0000FD62.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.10984/MRM_003_w_070655_171011_0000FD62.1.mgh --o rh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.10984 Mon Feb 22 22:47:45 GMT 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm0 fsaverage Mon Feb 22 22:47:45 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm5 fsaverage Mon Feb 22 22:47:47 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm10 fsaverage Mon Feb 22 22:47:53 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm15 fsaverage Mon Feb 22 22:47:58 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm20 fsaverage Mon Feb 22 22:48:03 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm25 fsaverage Mon Feb 22 22:48:09 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm0 fsaverage Mon Feb 22 22:48:15 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm5 fsaverage Mon Feb 22 22:48:17 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm10 fsaverage Mon Feb 22 22:48:22 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm15 fsaverage Mon Feb 22 22:48:27 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm20 fsaverage Mon Feb 22 22:48:32 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm25 fsaverage Mon Feb 22 22:48:37 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm0 fsaverage Mon Feb 22 22:48:43 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm5 fsaverage Mon Feb 22 22:48:46 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm10 fsaverage Mon Feb 22 22:48:50 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm15 fsaverage Mon Feb 22 22:48:55 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm20 fsaverage Mon Feb 22 22:49:01 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm25 fsaverage Mon Feb 22 22:49:06 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm0 fsaverage Mon Feb 22 22:49:12 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm5 fsaverage Mon Feb 22 22:49:14 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm10 fsaverage Mon Feb 22 22:49:19 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm15 fsaverage Mon Feb 22 22:49:24 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm20 fsaverage Mon Feb 22 22:49:29 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm25 fsaverage Mon Feb 22 22:49:35 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm0 fsaverage Mon Feb 22 22:49:41 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm5 fsaverage Mon Feb 22 22:49:43 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm10 fsaverage Mon Feb 22 22:49:48 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm15 fsaverage Mon Feb 22 22:49:53 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm20 fsaverage Mon Feb 22 22:49:58 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm25 fsaverage Mon Feb 22 22:50:04 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm0 fsaverage Mon Feb 22 22:50:10 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm5 fsaverage Mon Feb 22 22:50:12 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm10 fsaverage Mon Feb 22 22:50:17 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm15 fsaverage Mon Feb 22 22:50:22 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm20 fsaverage Mon Feb 22 22:50:27 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm25 fsaverage Mon Feb 22 22:50:33 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm0 fsaverage Mon Feb 22 22:50:39 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.white.K.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm5 fsaverage Mon Feb 22 22:50:41 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.white.K.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm10 fsaverage Mon Feb 22 22:50:46 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.white.K.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm15 fsaverage Mon Feb 22 22:50:51 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.white.K.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm20 fsaverage Mon Feb 22 22:50:56 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.white.K.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm25 fsaverage Mon Feb 22 22:51:01 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.K.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.white.K.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm0 fsaverage Mon Feb 22 22:51:07 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.white.H.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm5 fsaverage Mon Feb 22 22:51:09 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.white.H.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm10 fsaverage Mon Feb 22 22:51:14 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.white.H.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm15 fsaverage Mon Feb 22 22:51:19 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.white.H.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm20 fsaverage Mon Feb 22 22:51:24 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.white.H.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm25 fsaverage Mon Feb 22 22:51:30 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.white.H.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.white.H.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm0 fsaverage Mon Feb 22 22:51:36 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm5 fsaverage Mon Feb 22 22:51:38 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm10 fsaverage Mon Feb 22 22:51:43 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm15 fsaverage Mon Feb 22 22:51:48 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm20 fsaverage Mon Feb 22 22:51:53 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm25 fsaverage Mon Feb 22 22:51:59 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm0 fsaverage Mon Feb 22 22:52:05 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm5 fsaverage Mon Feb 22 22:52:07 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm10 fsaverage Mon Feb 22 22:52:12 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm15 fsaverage Mon Feb 22 22:52:17 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm20 fsaverage Mon Feb 22 22:52:22 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm25 fsaverage Mon Feb 22 22:52:27 GMT 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.w-g.pct.mgh.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm0 fsaverage Mon Feb 22 22:52:33 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm5 fsaverage Mon Feb 22 22:52:36 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm10 fsaverage Mon Feb 22 22:52:41 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm15 fsaverage Mon Feb 22 22:52:46 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm20 fsaverage Mon Feb 22 22:52:51 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm25 fsaverage Mon Feb 22 22:52:56 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.thickness.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm0 fsaverage Mon Feb 22 22:53:02 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm5 fsaverage Mon Feb 22 22:53:05 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm10 fsaverage Mon Feb 22 22:53:09 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm15 fsaverage Mon Feb 22 22:53:14 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm20 fsaverage Mon Feb 22 22:53:20 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm25 fsaverage Mon Feb 22 22:53:25 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm0 fsaverage Mon Feb 22 22:53:31 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm5 fsaverage Mon Feb 22 22:53:33 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm10 fsaverage Mon Feb 22 22:53:38 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm15 fsaverage Mon Feb 22 22:53:43 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm20 fsaverage Mon Feb 22 22:53:48 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm25 fsaverage Mon Feb 22 22:53:54 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.area.pial.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm0 fsaverage Mon Feb 22 22:54:00 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm5 fsaverage Mon Feb 22 22:54:02 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm10 fsaverage Mon Feb 22 22:54:07 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm15 fsaverage Mon Feb 22 22:54:12 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm20 fsaverage Mon Feb 22 22:54:17 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm25 fsaverage Mon Feb 22 22:54:23 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.volume.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm0 fsaverage Mon Feb 22 22:54:28 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm5 fsaverage Mon Feb 22 22:54:31 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm10 fsaverage Mon Feb 22 22:54:36 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm15 fsaverage Mon Feb 22 22:54:40 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm20 fsaverage Mon Feb 22 22:54:46 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm25 fsaverage Mon Feb 22 22:54:51 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.curv.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm0 fsaverage Mon Feb 22 22:54:57 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm5 fsaverage Mon Feb 22 22:54:59 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm10 fsaverage Mon Feb 22 22:55:04 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm15 fsaverage Mon Feb 22 22:55:09 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm20 fsaverage Mon Feb 22 22:55:14 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm25 fsaverage Mon Feb 22 22:55:20 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.sulc.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm0 fsaverage Mon Feb 22 22:55:26 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.white.K.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm5 fsaverage Mon Feb 22 22:55:28 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.white.K.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm10 fsaverage Mon Feb 22 22:55:33 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.white.K.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm15 fsaverage Mon Feb 22 22:55:38 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.white.K.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm20 fsaverage Mon Feb 22 22:55:43 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.white.K.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm25 fsaverage Mon Feb 22 22:55:49 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.K.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.white.K.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm0 fsaverage Mon Feb 22 22:55:55 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.white.H.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm5 fsaverage Mon Feb 22 22:55:57 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.white.H.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm10 fsaverage Mon Feb 22 22:56:02 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.white.H.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm15 fsaverage Mon Feb 22 22:56:07 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.white.H.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm20 fsaverage Mon Feb 22 22:56:12 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.white.H.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm25 fsaverage Mon Feb 22 22:56:17 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.white.H.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.white.H.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm0 fsaverage Mon Feb 22 22:56:23 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm5 fsaverage Mon Feb 22 22:56:26 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm10 fsaverage Mon Feb 22 22:56:30 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm15 fsaverage Mon Feb 22 22:56:35 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm20 fsaverage Mon Feb 22 22:56:41 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm25 fsaverage Mon Feb 22 22:56:46 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.jacobian_white.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm0 fsaverage Mon Feb 22 22:56:52 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm5 fsaverage Mon Feb 22 22:56:54 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm10 fsaverage Mon Feb 22 22:56:59 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm15 fsaverage Mon Feb 22 22:57:04 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm20 fsaverage Mon Feb 22 22:57:09 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm25 fsaverage Mon Feb 22 22:57:15 GMT 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.101 2014/01/24 21:40:28 greve Exp $ setenv SUBJECTS_DIR /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer cd /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/MRM_003_w_070655_171011_0000FD62/surf mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex sysname Linux hostname eddie521 machine x86_64 user s1158296 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /exports/work/mcm_cric_nas/Kaiming/Alzheimer_Munich/Freesurfer/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.w-g.pct.mgh.fwhm25.fsaverage.mgh #------------------------------------------ Started at Mon Feb 22 22:45:19 GMT 2016 Ended at Mon Feb 22 22:57:21 GMT 2016 #@#%# recon-all-run-time-hours 0.201 recon-all -s MRM_003_w_070655_171011_0000FD62 finished without error at Mon Feb 22 22:57:21 GMT 2016