Thu Oct 12 19:04:00 EDT 2017 /usr/local/freesurfer/subjects/Han2 /usr/local/freesurfer/bin/recon-all -i 1.dcm -s Han2 -all subjid Han2 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28138 maxlocks unlimited maxsignal 28138 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3616272 2224164 1392108 0 50012 1977868 -/+ buffers/cache: 196284 3419988 Swap: 1944572 0 1944572 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:00-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:00-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:01-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/10/12-23:04:02-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/Han2 mri_convert /usr/local/freesurfer/subjects/Hannah/1.dcm /usr/local/freesurfer/subjects/Han2/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/Hannah/1.dcm /usr/local/freesurfer/subjects/Han2/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/Hannah/1.dcm... Getting Series No INFO: Found 178 files in /usr/local/freesurfer/subjects/Hannah INFO: Scanning for Series Number 5 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. INFO: (256 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /usr/local/freesurfer/subjects/Hannah/59.dcm Identification NumarisVer syngo MR E11 ScannerModel Skyra PatientName Hannah_mentalnav Date and time StudyDate 20170928 StudyTime 172519.086000 SeriesTime 173505.382000 AcqTime 172939.112500 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol t1_mprage_sag_p2_iso_fovph100_Slover20 PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.98 InversionTime 900 RepetitionTime 2300 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 101.5121 149.1488 52.4871 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 176 Vc -0.0341 -0.9791 0.2003 Vr -0.0569 -0.1982 -0.9785 Vs -0.9978 0.0448 0.0490 VolCenter 2.0564 2.3883 -42.8119 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-0.0341078, -0.979136, 0.200324) j_ras = (-0.056905, -0.198213, -0.978506) k_ras = (-0.997797, 0.0447741, 0.0489571) writing to /usr/local/freesurfer/subjects/Han2/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 12 19:04:44 EDT 2017 Found 1 runs /usr/local/freesurfer/subjects/Han2/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 /usr/local/freesurfer/subjects/Han2/mri/orig/001.mgz /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz /usr/local/freesurfer/subjects/Han2 mri_convert /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz /usr/local/freesurfer/subjects/Han2/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz /usr/local/freesurfer/subjects/Han2/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-0.0341078, -0.979136, 0.200324) j_ras = (-0.056905, -0.198213, -0.978506) k_ras = (-0.997797, 0.0447741, 0.0489571) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/Han2/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Han2/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/Han2/mri/orig.mgz /usr/local/freesurfer/subjects/Han2/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 12 19:04:56 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 12 19:06:26 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7565, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/Han2/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/Han2/mri/transforms/talairach_avi.log TalAviQA: 0.98182 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 12 19:06:26 EDT 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/Han2/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux Thu Oct 12 19:06:26 EDT 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.4718 /usr/local/freesurfer/subjects/Han2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4718/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4718/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, -3.72529e-08, 7.45058e-08) j_ras = (6.70552e-08, 2.30502e-08, -1) k_ras = (-1.49012e-08, 1, -4.00469e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4718/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 12 19:06:28 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.4718/nu0.mnc ./tmp.mri_nu_correct.mni.4718/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4718/0/ [fsuser@xubuntu-VirtualBox:/usr/local/freesurfer/subjects/Han2/mri/] [2017-10-12 19:06:29] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4718/0/ ./tmp.mri_nu_correct.mni.4718/nu0.mnc ./tmp.mri_nu_correct.mni.4718/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 28 CV of field change: 0.000960442 [fsuser@xubuntu-VirtualBox:/usr/local/freesurfer/subjects/Han2/mri/] [2017-10-12 19:06:47] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4718/nu0.mnc ./tmp.mri_nu_correct.mni.4718/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Oct 12 19:06:51 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.4718/nu1.mnc ./tmp.mri_nu_correct.mni.4718/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4718/1/ [fsuser@xubuntu-VirtualBox:/usr/local/freesurfer/subjects/Han2/mri/] [2017-10-12 19:06:51] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4718/1/ ./tmp.mri_nu_correct.mni.4718/nu1.mnc ./tmp.mri_nu_correct.mni.4718/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 15 CV of field change: 0.00099578 [fsuser@xubuntu-VirtualBox:/usr/local/freesurfer/subjects/Han2/mri/] [2017-10-12 19:07:01] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4718/nu1.mnc ./tmp.mri_nu_correct.mni.4718/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.4718/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4718/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/Han2/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4718/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4718/ones.mgz sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser input ./tmp.mri_nu_correct.mni.4718/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4718/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4718/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4718/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4718/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4718/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4718/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4718/input.mean.dat sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4718/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4718/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4718/ones.mgz --i ./tmp.mri_nu_correct.mni.4718/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4718/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4718/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4718/ones.mgz --i ./tmp.mri_nu_correct.mni.4718/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4718/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4718/output.mean.dat sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4718/ones.mgz Loading ./tmp.mri_nu_correct.mni.4718/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4718/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.4718/nu2.mnc ./tmp.mri_nu_correct.mni.4718/nu2.mnc mul .99758785166866573097 Saving result to './tmp.mri_nu_correct.mni.4718/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4718/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.4718/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4718/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-08, 7.45058e-08) j_ras = (6.70552e-08, 2.30502e-08, -1) k_ras = (-1.49012e-08, 1, -4.00469e-08) 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 7 seconds. mapping ( 7, 123) to ( 3, 110) Thu Oct 12 19:07:46 EDT 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Han2/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Oct 12 19:07:47 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.027 -0.048 -0.047 -3.486; 0.044 0.989 0.184 -3.909; 0.029 -0.144 1.096 24.791; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 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 70 (70), valley at 57 (57) csf peak at 35, setting threshold to 58 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 75 (75), valley at 56 (56) csf peak at 37, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 0 seconds. #-------------------------------------------- #@# Skull Stripping Thu Oct 12 19:10:47 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (50, 21, 17) --> (213, 255, 218) using (104, 99, 118) as brain centroid... mean wm in atlas = 126, using box (84,70,93) --> (124, 127,142) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.395925 @ (-9.091, 9.091, -9.091) max log p = -4.262088 @ (4.545, 4.545, 4.545) max log p = -4.192747 @ (2.273, -2.273, -2.273) max log p = -4.191823 @ (-1.136, 3.409, 1.136) max log p = -4.171938 @ (1.705, -0.568, 0.568) max log p = -4.171938 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 14.2, -5.1): log p = -4.172 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.2 (thresh=-4.2) 1.064 0.000 0.000 -9.830; 0.000 1.220 0.182 -29.534; 0.000 -0.112 0.997 7.206; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.064 0.000 0.000 -9.830; 0.000 1.220 0.182 -29.534; 0.000 -0.112 0.997 7.206; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.019 -0.087 0.053 -2.868; 0.069 1.220 0.152 -33.150; -0.071 -0.074 1.018 8.124; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.019 -0.087 0.053 -2.868; 0.069 1.220 0.152 -33.150; -0.071 -0.074 1.018 8.124; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.019 -0.077 0.054 -3.496; 0.060 1.221 0.168 -33.382; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.017 -0.077 0.054 -3.345; 0.060 1.220 0.168 -33.200; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.017 -0.077 0.054 -3.345; 0.060 1.220 0.168 -33.200; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01748 -0.07687 0.05390 -3.34472; 0.05965 1.21956 0.16778 -33.20012; -0.07156 -0.09406 1.01382 11.19748; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.01748 -0.07687 0.05390 -3.34472; 0.05965 1.21956 0.16778 -33.20012; -0.07156 -0.09406 1.01382 11.19748; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.017 -0.077 0.054 -3.345; 0.060 1.220 0.168 -33.200; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.5) transform before final EM align: 1.017 -0.077 0.054 -3.345; 0.060 1.220 0.168 -33.200; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01748 -0.07687 0.05390 -3.34472; 0.05965 1.21956 0.16778 -33.20012; -0.07156 -0.09406 1.01382 11.19748; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.01748 -0.07687 0.05390 -3.34472; 0.05965 1.21956 0.16778 -33.20012; -0.07156 -0.09406 1.01382 11.19748; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.017 -0.077 0.054 -3.345; 0.060 1.220 0.168 -33.200; -0.072 -0.094 1.014 11.197; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 28 minutes and 42 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=97 z=118 r=87 first estimation of the main basin volume: 2763882 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=107, y=91, z=77, Imax=255 CSF=19, 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=777330298 voxels, voxel volume =1.000 = 777330298 mmm3 = 777330.304 cm3 done. PostAnalyze...Basin Prior 38 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=128,y=102, z=111, r=9954 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 45342 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=42 , nb = -2147480498 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 2520 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=47 , nb = -1216815980 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = -1080333614 OTHER CSF_MIN=1, CSF_intensity=23, CSF_MAX=47 , nb = 802225708 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 45, 46, 48, 69 after analyzing : 45, 47, 48, 52 RIGHT_CER before analyzing : 42, 48, 53, 77 after analyzing : 42, 51, 53, 57 LEFT_CER before analyzing : 23, 35, 50, 73 after analyzing : 23, 45, 50, 52 RIGHT_BRAIN before analyzing : 47, 47, 48, 69 after analyzing : 36, 47, 48, 52 LEFT_BRAIN before analyzing : 40, 44, 48, 68 after analyzing : 40, 46, 48, 51 OTHER before analyzing : 47, 63, 75, 93 after analyzing : 47, 71, 75, 76 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 71.317, std = 8.545 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.24, sigma = 3.39 after rotation: sse = 2.24, sigma = 3.39 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.31, its var is 3.01 before Erosion-Dilatation 0.20% 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...49 iterations mri_strip_skull: done peeling brain Brain Size = 1797415 voxels, voxel volume = 1.000 mm3 = 1797415 mmm3 = 1797.415 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Oct 12 19:39:54 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (60, 38, 26) --> (198, 161, 203) using (106, 79, 115) as brain centroid... mean wm in atlas = 107, using box (89,64,93) --> (122, 94,136) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.968795 @ (-9.091, 9.091, -9.091) max log p = -3.666585 @ (4.545, 4.545, 4.545) max log p = -3.601269 @ (2.273, 2.273, -2.273) max log p = -3.553163 @ (-1.136, -1.136, -3.409) max log p = -3.548984 @ (0.568, 0.568, 1.705) max log p = -3.548984 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 15.3, -8.5): log p = -3.549 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.000 0.000 0.000 -2.841; 0.000 1.140 0.131 -14.029; 0.000 -0.139 0.917 15.291; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.000 0.000 0.000 -2.841; 0.000 1.140 0.131 -14.029; 0.000 -0.139 0.917 15.291; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.054 -0.047 0.058 -11.563; 0.032 1.155 0.165 -21.889; -0.067 -0.179 0.927 28.786; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.034 -0.047 0.057 -8.968; 0.032 1.134 0.162 -19.250; -0.068 -0.182 0.945 27.351; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.034 -0.047 0.057 -8.968; 0.032 1.134 0.162 -19.250; -0.068 -0.182 0.945 27.351; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.036 -0.047 0.057 -9.133; 0.032 1.136 0.163 -20.048; -0.068 -0.182 0.943 28.003; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.040 -0.055 0.048 -7.831; 0.040 1.135 0.163 -20.989; -0.059 -0.183 0.944 26.799; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04073 -0.05459 0.04820 -7.98872; 0.04029 1.13462 0.16288 -20.98858; -0.05919 -0.18238 0.94304 26.89080; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.04073 -0.05459 0.04820 -7.98872; 0.04029 1.13462 0.16288 -20.98858; -0.05919 -0.18238 0.94304 26.89080; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.2) transform before final EM align: 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04073 -0.05459 0.04820 -7.98872; 0.04029 1.13462 0.16288 -20.98858; -0.05919 -0.18238 0.94304 26.89080; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.04073 -0.05459 0.04820 -7.98872; 0.04029 1.13462 0.16288 -20.98858; -0.05919 -0.18238 0.94304 26.89080; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 27 minutes and 9 seconds. #-------------------------------------- #@# CA Normalize Thu Oct 12 20:07:03 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (60, 38, 26) --> (198, 161, 203) using (106, 79, 115) as brain centroid... mean wm in atlas = 107, using box (89,64,93) --> (122, 94,136) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 44, 31) --> (194, 142, 204) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 224.0 0 of 314 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 29) --> (129, 146, 204) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 224.0 0 of 369 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 120, 60) --> (180, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 224.0 0 of 12 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 120, 55) --> (133, 160, 115) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 224.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 112, 95) --> (146, 173, 127) Brain_Stem: limiting intensities to 83.0 --> 224.0 0 of 8 (0.0%) samples deleted using 715 total control points for intensity normalization... bias field = 1.013 +- 0.056 0 of 715 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 44, 31) --> (194, 142, 204) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 213.0 0 of 334 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 29) --> (129, 146, 204) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 213.0 0 of 420 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 120, 60) --> (180, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 213.0 4 of 35 (11.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 120, 55) --> (133, 160, 115) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 213.0 0 of 56 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 112, 95) --> (146, 173, 127) Brain_Stem: limiting intensities to 74.0 --> 213.0 0 of 81 (0.0%) samples deleted using 926 total control points for intensity normalization... bias field = 1.004 +- 0.050 2 of 922 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 44, 31) --> (194, 142, 204) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 211.0 0 of 395 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 29) --> (129, 146, 204) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 211.0 0 of 458 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 120, 60) --> (180, 158, 115) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 211.0 0 of 74 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 120, 55) --> (133, 160, 115) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 211.0 0 of 40 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 112, 95) --> (146, 173, 127) Brain_Stem: limiting intensities to 70.0 --> 211.0 0 of 164 (0.0%) samples deleted using 1131 total control points for intensity normalization... bias field = 1.005 +- 0.048 4 of 1131 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 13 seconds. #-------------------------------------- #@# CA Reg Thu Oct 12 20:09:17 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.15 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.774, neg=0, invalid=96777 0001: dt=129.472000, rms=0.718 (7.226%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.680 (5.274%), neg=0, invalid=96777 0003: dt=92.480000, rms=0.675 (0.862%), neg=0, invalid=96777 0004: dt=369.920000, rms=0.663 (1.661%), neg=0, invalid=96777 0005: dt=32.368000, rms=0.663 (0.106%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.662 (0.024%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.662 (-0.067%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=96777 0008: dt=32.368000, rms=0.662 (0.022%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.662 (0.075%), neg=0, invalid=96777 0010: dt=517.888000, rms=0.655 (1.047%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.654 (0.065%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.654 (0.008%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.654 (-0.091%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0014: dt=124.416000, rms=0.645 (1.737%), neg=0, invalid=96777 0015: dt=36.288000, rms=0.634 (1.638%), neg=0, invalid=96777 0016: dt=36.288000, rms=0.632 (0.285%), neg=0, invalid=96777 0017: dt=145.152000, rms=0.621 (1.737%), neg=0, invalid=96777 0018: dt=20.736000, rms=0.620 (0.272%), neg=0, invalid=96777 0019: dt=36.288000, rms=0.619 (0.143%), neg=0, invalid=96777 0020: dt=36.288000, rms=0.616 (0.359%), neg=0, invalid=96777 0021: dt=36.288000, rms=0.614 (0.456%), neg=0, invalid=96777 0022: dt=36.288000, rms=0.610 (0.552%), neg=0, invalid=96777 0023: dt=36.288000, rms=0.607 (0.596%), neg=0, invalid=96777 0024: dt=36.288000, rms=0.602 (0.712%), neg=0, invalid=96777 0025: dt=36.288000, rms=0.598 (0.704%), neg=0, invalid=96777 0026: dt=36.288000, rms=0.594 (0.659%), neg=0, invalid=96777 0027: dt=36.288000, rms=0.591 (0.516%), neg=0, invalid=96777 0028: dt=36.288000, rms=0.588 (0.445%), neg=0, invalid=96777 0029: dt=36.288000, rms=0.586 (0.484%), neg=0, invalid=96777 0030: dt=36.288000, rms=0.583 (0.405%), neg=0, invalid=96777 0031: dt=36.288000, rms=0.581 (0.298%), neg=0, invalid=96777 0032: dt=36.288000, rms=0.580 (0.218%), neg=0, invalid=96777 0033: dt=36.288000, rms=0.579 (0.245%), neg=0, invalid=96777 0034: dt=36.288000, rms=0.577 (0.222%), neg=0, invalid=96777 0035: dt=36.288000, rms=0.576 (0.173%), neg=0, invalid=96777 0036: dt=36.288000, rms=0.576 (0.105%), neg=0, invalid=96777 0037: dt=36.288000, rms=0.575 (0.095%), neg=0, invalid=96777 0038: dt=103.680000, rms=0.574 (0.151%), neg=0, invalid=96777 0039: dt=6.480000, rms=0.575 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 0040: dt=20.736000, rms=0.574 (0.068%), neg=0, invalid=96777 0041: dt=145.152000, rms=0.573 (0.287%), neg=0, invalid=96777 0042: dt=36.288000, rms=0.572 (0.097%), neg=0, invalid=96777 0043: dt=36.288000, rms=0.572 (0.012%), neg=0, invalid=96777 0044: dt=36.288000, rms=0.572 (0.037%), neg=0, invalid=96777 0045: dt=36.288000, rms=0.571 (0.053%), neg=0, invalid=96777 0046: dt=36.288000, rms=0.571 (0.062%), neg=0, invalid=96777 0047: dt=36.288000, rms=0.571 (0.065%), neg=0, invalid=96777 0048: dt=36.288000, rms=0.570 (0.066%), neg=0, invalid=96777 0049: dt=36.288000, rms=0.570 (0.076%), neg=0, invalid=96777 0050: dt=36.288000, rms=0.570 (0.056%), neg=0, invalid=96777 0051: dt=36.288000, rms=0.569 (0.030%), neg=0, invalid=96777 0052: dt=0.567000, rms=0.569 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.590, neg=0, invalid=96777 0053: dt=2.000000, rms=0.590 (0.007%), neg=0, invalid=96777 0054: dt=0.700000, rms=0.590 (0.001%), neg=0, invalid=96777 0055: dt=0.700000, rms=0.590 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=96777 0056: dt=0.000000, rms=0.590 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.651, neg=0, invalid=96777 0057: dt=5.525368, rms=0.633 (2.750%), neg=0, invalid=96777 0058: dt=1.760000, rms=0.633 (0.041%), neg=0, invalid=96777 0059: dt=1.760000, rms=0.633 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0060: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.695, neg=0, invalid=96777 0061: dt=1.280000, rms=0.690 (0.745%), neg=0, invalid=96777 0062: dt=2.146067, rms=0.684 (0.924%), neg=0, invalid=96777 0063: dt=0.538462, rms=0.683 (0.141%), neg=0, invalid=96777 0064: dt=0.538462, rms=0.682 (0.049%), neg=0, invalid=96777 0065: dt=0.538462, rms=0.682 (0.058%), neg=0, invalid=96777 0066: dt=0.538462, rms=0.682 (0.033%), neg=0, invalid=96777 0067: dt=0.538462, rms=0.682 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.682, neg=0, invalid=96777 0068: dt=1.792000, rms=0.680 (0.262%), neg=0, invalid=96777 0069: dt=0.080000, rms=0.680 (0.005%), neg=0, invalid=96777 0070: dt=0.080000, rms=0.680 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0071: dt=0.320000, rms=0.629 (1.676%), neg=0, invalid=96777 0072: dt=0.000000, rms=0.629 (0.006%), neg=0, invalid=96777 0073: dt=0.050000, rms=0.629 (-0.218%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.629, neg=0, invalid=96777 0074: dt=0.000000, rms=0.629 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13328 (27) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1715 voxels, overlap=0.791) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1715 voxels, peak = 24), gca=24.4 gca peak = 0.14022 (22) mri peak = 0.11663 (28) Right_Lateral_Ventricle (43): linear fit = 1.21 x + 0.0 (1645 voxels, overlap=0.719) Right_Lateral_Ventricle (43): linear fit = 1.21 x + 0.0 (1645 voxels, peak = 27), gca=26.5 gca peak = 0.24234 (100) mri peak = 0.06557 (98) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (517 voxels, overlap=1.009) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (517 voxels, peak = 102), gca=101.5 gca peak = 0.19192 (97) mri peak = 0.05405 (93) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (462 voxels, overlap=0.906) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (462 voxels, peak = 90), gca=89.7 gca peak = 0.24007 (63) mri peak = 0.08648 (72) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (979 voxels, overlap=0.222) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (979 voxels, peak = 72), gca=71.5 gca peak = 0.29892 (64) mri peak = 0.06781 (73) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (794 voxels, overlap=0.857) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (794 voxels, peak = 71), gca=71.4 gca peak = 0.12541 (104) mri peak = 0.09998 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78208 voxels, overlap=0.633) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78208 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.08139 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81373 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81373 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.04521 (69) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (33014 voxels, overlap=0.881) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (33014 voxels, peak = 66), gca=66.5 gca peak = 0.13270 (63) mri peak = 0.04595 (68) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (34111 voxels, overlap=0.822) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (34111 voxels, peak = 66), gca=66.5 gca peak = 0.15182 (70) mri peak = 0.11739 (83) Right_Caudate (50): linear fit = 1.16 x + 0.0 (351 voxels, overlap=0.048) Right_Caudate (50): linear fit = 1.16 x + 0.0 (351 voxels, peak = 82), gca=81.5 gca peak = 0.14251 (76) mri peak = 0.11321 (89) Left_Caudate (11): linear fit = 1.12 x + 0.0 (925 voxels, overlap=0.217) Left_Caudate (11): linear fit = 1.12 x + 0.0 (925 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.03630 (71) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21404 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21404 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04024 (67) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (26986 voxels, overlap=0.632) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (26986 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.05921 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (8170 voxels, overlap=0.022) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (8170 voxels, peak = 99), gca=99.0 gca peak = 0.21067 (87) mri peak = 0.05343 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (7540 voxels, overlap=0.379) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (7540 voxels, peak = 96), gca=96.1 gca peak = 0.25455 (62) mri peak = 0.09211 (81) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (391 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.24 x + 0.0 (391 voxels, peak = 77), gca=76.6 gca peak = 0.39668 (62) mri peak = 0.09400 (70) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (357 voxels, overlap=0.877) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (357 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.05984 (101) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5917 voxels, overlap=0.868) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5917 voxels, peak = 96), gca=96.3 gca peak = 0.12071 (89) mri peak = 0.05540 (89) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4230 voxels, overlap=0.983) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4230 voxels, peak = 89), gca=88.6 gca peak = 0.13716 (82) mri peak = 0.07946 (94) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2734 voxels, overlap=0.460) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2734 voxels, peak = 90), gca=89.8 gca peak = 0.15214 (84) mri peak = 0.05715 (92) Right_Putamen (51): linear fit = 1.11 x + 0.0 (2740 voxels, overlap=0.676) Right_Putamen (51): linear fit = 1.11 x + 0.0 (2740 voxels, peak = 93), gca=92.8 gca peak = 0.08983 (85) mri peak = 0.09685 (84) Brain_Stem (16): linear fit = 1.02 x + 0.0 (11469 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.02 x + 0.0 (11469 voxels, peak = 87), gca=87.1 gca peak = 0.11809 (92) mri peak = 0.07519 (91) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (808 voxels, overlap=0.901) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (808 voxels, peak = 91), gca=90.6 gca peak = 0.12914 (94) mri peak = 0.07222 (91) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1168 voxels, overlap=0.937) Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1168 voxels, peak = 90), gca=89.8 gca peak = 0.21100 (36) mri peak = 1.00000 (53) Third_Ventricle (14): linear fit = 1.43 x + 0.0 (109 voxels, overlap=2.064) Third_Ventricle (14): linear fit = 1.43 x + 0.0 (109 voxels, peak = 52), gca=51.7 gca peak = 0.13542 (27) mri peak = 0.12305 (24) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (461 voxels, overlap=0.742) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (461 voxels, peak = 24), gca=24.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.14 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.642, neg=0, invalid=96777 0075: dt=32.368000, rms=0.638 (0.573%), neg=0, invalid=96777 0076: dt=32.368000, rms=0.636 (0.395%), neg=0, invalid=96777 0077: dt=32.368000, rms=0.634 (0.292%), neg=0, invalid=96777 0078: dt=8.092000, rms=0.633 (0.057%), neg=0, invalid=96777 0079: dt=8.092000, rms=0.633 (0.050%), neg=0, invalid=96777 0080: dt=2.023000, rms=0.633 (0.013%), neg=0, invalid=96777 0081: dt=2.023000, rms=0.633 (0.013%), neg=0, invalid=96777 0082: dt=1.011500, rms=0.633 (0.006%), neg=0, invalid=96777 0083: dt=0.505750, rms=0.633 (0.003%), neg=0, invalid=96777 0084: dt=0.031609, rms=0.633 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0085: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0086: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0087: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0088: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0089: dt=0.000000, rms=0.633 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0090: dt=1.008000, rms=0.626 (1.093%), neg=0, invalid=96777 0091: dt=4.032000, rms=0.601 (3.992%), neg=0, invalid=96777 0092: dt=4.032000, rms=0.583 (2.988%), neg=0, invalid=96777 0093: dt=13.824000, rms=0.542 (7.093%), neg=0, invalid=96777 0094: dt=4.032000, rms=0.538 (0.645%), neg=0, invalid=96777 0095: dt=4.032000, rms=0.535 (0.537%), neg=0, invalid=96777 0096: dt=13.824000, rms=0.527 (1.562%), neg=0, invalid=96777 0097: dt=4.032000, rms=0.526 (0.233%), neg=0, invalid=96777 0098: dt=4.032000, rms=0.525 (0.225%), neg=0, invalid=96777 0099: dt=11.520000, rms=0.522 (0.512%), neg=0, invalid=96777 0100: dt=4.032000, rms=0.521 (0.162%), neg=0, invalid=96777 0101: dt=4.032000, rms=0.520 (0.109%), neg=0, invalid=96777 0102: dt=4.032000, rms=0.520 (0.135%), neg=0, invalid=96777 0103: dt=13.824000, rms=0.518 (0.305%), neg=0, invalid=96777 0104: dt=4.800000, rms=0.518 (0.116%), neg=0, invalid=96777 0105: dt=2.880000, rms=0.517 (0.021%), neg=0, invalid=96777 0106: dt=2.880000, rms=0.517 (0.086%), neg=0, invalid=96777 0107: dt=2.880000, rms=0.517 (0.099%), neg=0, invalid=96777 0108: dt=2.880000, rms=0.516 (0.109%), neg=0, invalid=96777 0109: dt=2.880000, rms=0.515 (0.147%), neg=0, invalid=96777 0110: dt=2.880000, rms=0.514 (0.167%), neg=0, invalid=96777 0111: dt=2.880000, rms=0.513 (0.179%), neg=0, invalid=96777 0112: dt=2.880000, rms=0.513 (0.170%), neg=0, invalid=96777 0113: dt=2.880000, rms=0.512 (0.154%), neg=0, invalid=96777 0114: dt=2.880000, rms=0.511 (0.146%), neg=0, invalid=96777 0115: dt=2.880000, rms=0.510 (0.132%), neg=0, invalid=96777 0116: dt=2.880000, rms=0.510 (0.109%), neg=0, invalid=96777 0117: dt=2.880000, rms=0.509 (0.090%), neg=0, invalid=96777 0118: dt=2.880000, rms=0.509 (0.067%), neg=0, invalid=96777 0119: dt=2.880000, rms=0.509 (0.058%), neg=0, invalid=96777 0120: dt=2.880000, rms=0.508 (0.048%), neg=0, invalid=96777 0121: dt=2.880000, rms=0.508 (0.045%), neg=0, invalid=96777 0122: dt=2.880000, rms=0.508 (0.037%), neg=0, invalid=96777 0123: dt=2.880000, rms=0.508 (0.030%), neg=0, invalid=96777 0124: dt=2.880000, rms=0.508 (0.030%), neg=0, invalid=96777 0125: dt=2.880000, rms=0.508 (0.026%), neg=0, invalid=96777 0126: dt=2.880000, rms=0.507 (0.027%), neg=0, invalid=96777 0127: dt=2.880000, rms=0.507 (0.023%), neg=0, invalid=96777 0128: dt=2.880000, rms=0.507 (0.013%), neg=0, invalid=96777 0129: dt=4.032000, rms=0.507 (0.005%), neg=0, invalid=96777 0130: dt=4.032000, rms=0.507 (0.006%), neg=0, invalid=96777 0131: dt=4.032000, rms=0.507 (0.004%), neg=0, invalid=96777 0132: dt=4.032000, rms=0.507 (0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.507, neg=0, invalid=96777 0133: dt=0.000000, rms=0.507 (0.001%), neg=0, invalid=96777 0134: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=96777 0135: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=96777 0136: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=96777 0137: dt=0.147380, rms=0.488 (0.901%), neg=0, invalid=96777 0138: dt=0.130631, rms=0.486 (0.577%), neg=0, invalid=96777 0139: dt=0.320000, rms=0.480 (1.076%), neg=0, invalid=96777 0140: dt=0.112000, rms=0.480 (0.183%), neg=0, invalid=96777 0141: dt=0.096065, rms=0.479 (0.134%), neg=0, invalid=96777 0142: dt=0.112000, rms=0.478 (0.142%), neg=0, invalid=96777 0143: dt=0.320000, rms=0.477 (0.348%), neg=0, invalid=96777 0144: dt=0.112000, rms=0.476 (0.082%), neg=0, invalid=96777 0145: dt=0.112000, rms=0.476 (0.076%), neg=0, invalid=96777 0146: dt=0.384000, rms=0.475 (0.232%), neg=0, invalid=96777 0147: dt=0.112000, rms=0.474 (0.047%), neg=0, invalid=96777 0148: dt=0.112000, rms=0.474 (0.046%), neg=0, invalid=96777 0149: dt=0.112000, rms=0.474 (0.084%), neg=0, invalid=96777 0150: dt=0.112000, rms=0.473 (0.113%), neg=0, invalid=96777 0151: dt=0.112000, rms=0.473 (0.128%), neg=0, invalid=96777 0152: dt=0.112000, rms=0.472 (0.140%), neg=0, invalid=96777 0153: dt=0.112000, rms=0.472 (0.015%), neg=0, invalid=96777 0154: dt=0.112000, rms=0.472 (0.033%), neg=0, invalid=96777 0155: dt=0.112000, rms=0.472 (0.041%), neg=0, invalid=96777 0156: dt=0.112000, rms=0.471 (0.050%), neg=0, invalid=96777 0157: dt=0.112000, rms=0.471 (0.060%), neg=0, invalid=96777 0158: dt=0.112000, rms=0.471 (0.065%), neg=0, invalid=96777 0159: dt=0.112000, rms=0.471 (0.011%), neg=0, invalid=96777 0160: dt=0.112000, rms=0.471 (0.017%), neg=0, invalid=96777 0161: dt=0.112000, rms=0.471 (0.005%), neg=0, invalid=96777 0162: dt=0.384000, rms=0.471 (0.030%), neg=0, invalid=96777 0163: dt=0.112000, rms=0.471 (0.006%), neg=0, invalid=96777 0164: dt=0.112000, rms=0.470 (0.005%), neg=0, invalid=96777 0165: dt=0.112000, rms=0.470 (0.019%), neg=0, invalid=96777 0166: dt=0.112000, rms=0.470 (0.004%), neg=0, invalid=96777 0167: dt=0.112000, rms=0.470 (0.013%), neg=0, invalid=96777 0168: dt=0.112000, rms=0.470 (0.015%), neg=0, invalid=96777 0169: dt=0.112000, rms=0.470 (0.019%), neg=0, invalid=96777 0170: dt=0.112000, rms=0.470 (0.027%), neg=0, invalid=96777 0171: dt=0.112000, rms=0.470 (0.025%), neg=0, invalid=96777 0172: dt=0.112000, rms=0.470 (0.026%), neg=0, invalid=96777 0173: dt=0.056000, rms=0.470 (0.003%), neg=0, invalid=96777 0174: dt=0.056000, rms=0.470 (0.002%), neg=0, invalid=96777 0175: dt=0.384000, rms=0.470 (0.013%), neg=0, invalid=96777 0176: dt=0.096000, rms=0.470 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0177: dt=0.101852, rms=0.469 (0.196%), neg=0, invalid=96777 0178: dt=0.112000, rms=0.468 (0.165%), neg=0, invalid=96777 0179: dt=0.384000, rms=0.466 (0.405%), neg=0, invalid=96777 0180: dt=0.112000, rms=0.466 (0.022%), neg=0, invalid=96777 0181: dt=0.112000, rms=0.466 (0.015%), neg=0, invalid=96777 0182: dt=0.112000, rms=0.466 (0.032%), neg=0, invalid=96777 0183: dt=0.112000, rms=0.466 (0.006%), neg=0, invalid=96777 0184: dt=0.112000, rms=0.466 (0.013%), neg=0, invalid=96777 0185: dt=0.112000, rms=0.466 (0.005%), neg=0, invalid=96777 0186: dt=0.448000, rms=0.466 (0.009%), neg=0, invalid=96777 0187: dt=0.112000, rms=0.466 (0.005%), neg=0, invalid=96777 0188: dt=0.056000, rms=0.466 (0.001%), neg=0, invalid=96777 0189: dt=0.056000, rms=0.466 (-0.001%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0190: dt=73.984000, rms=0.463 (0.008%), neg=0, invalid=96777 0191: dt=32.368000, rms=0.463 (0.003%), neg=0, invalid=96777 0192: dt=32.368000, rms=0.463 (0.003%), neg=0, invalid=96777 0193: dt=32.368000, rms=0.463 (0.005%), neg=0, invalid=96777 0194: dt=32.368000, rms=0.463 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 0195: dt=221.952000, rms=0.463 (0.135%), neg=0, invalid=96777 0196: dt=110.976000, rms=0.463 (0.032%), neg=0, invalid=96777 0197: dt=110.976000, rms=0.463 (0.030%), neg=0, invalid=96777 0198: dt=110.976000, rms=0.462 (0.027%), neg=0, invalid=96777 0199: dt=110.976000, rms=0.462 (0.040%), neg=0, invalid=96777 0200: dt=110.976000, rms=0.462 (0.041%), neg=0, invalid=96777 0201: dt=110.976000, rms=0.462 (0.024%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0202: dt=36.288000, rms=0.461 (0.123%), neg=0, invalid=96777 0203: dt=82.944000, rms=0.461 (0.111%), neg=0, invalid=96777 0204: dt=82.944000, rms=0.461 (-0.064%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 0205: dt=36.288000, rms=0.460 (0.231%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.459 (0.125%), neg=0, invalid=96777 0207: dt=36.288000, rms=0.459 (0.113%), neg=0, invalid=96777 0208: dt=36.288000, rms=0.458 (0.179%), neg=0, invalid=96777 0209: dt=36.288000, rms=0.457 (0.193%), neg=0, invalid=96777 0210: dt=36.288000, rms=0.456 (0.197%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0211: dt=36.288000, rms=0.455 (0.187%), neg=0, invalid=96777 0212: dt=36.288000, rms=0.454 (0.168%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0213: dt=36.288000, rms=0.454 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0214: dt=36.288000, rms=0.453 (0.115%), neg=0, invalid=96777 0215: dt=25.920000, rms=0.453 (0.022%), neg=0, invalid=96777 0216: dt=25.920000, rms=0.453 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0217: dt=25.920000, rms=0.453 (0.021%), neg=0, invalid=96777 0218: dt=25.920000, rms=0.453 (0.033%), neg=0, invalid=96777 0219: dt=25.920000, rms=0.453 (0.047%), neg=0, invalid=96777 0220: dt=25.920000, rms=0.452 (0.055%), neg=0, invalid=96777 0221: dt=25.920000, rms=0.452 (0.060%), neg=0, invalid=96777 0222: dt=25.920000, rms=0.452 (0.053%), neg=0, invalid=96777 0223: dt=25.920000, rms=0.452 (0.054%), neg=0, invalid=96777 0224: dt=25.920000, rms=0.452 (0.049%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 12 iterations, nbhd size=1, neg = 0 0225: dt=44.800000, rms=0.449 (0.622%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0226: dt=11.200000, rms=0.448 (0.245%), neg=0, invalid=96777 0227: dt=11.200000, rms=0.447 (0.192%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0228: dt=11.200000, rms=0.446 (0.263%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0229: dt=11.200000, rms=0.445 (0.317%), neg=0, invalid=96777 0230: dt=11.200000, rms=0.443 (0.315%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0231: dt=11.200000, rms=0.442 (0.307%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0232: dt=11.200000, rms=0.441 (0.266%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0233: dt=11.200000, rms=0.440 (0.229%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0234: dt=11.200000, rms=0.439 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 12 iterations, nbhd size=2, neg = 0 0235: dt=11.200000, rms=0.438 (0.211%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0236: dt=11.200000, rms=0.437 (0.209%), neg=0, invalid=96777 0237: dt=11.200000, rms=0.437 (0.079%), neg=0, invalid=96777 0238: dt=11.200000, rms=0.436 (0.171%), neg=0, invalid=96777 0239: dt=11.200000, rms=0.435 (0.193%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0240: dt=11.200000, rms=0.435 (0.141%), neg=0, invalid=96777 0241: dt=11.200000, rms=0.434 (0.080%), neg=0, invalid=96777 0242: dt=11.200000, rms=0.434 (0.103%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0243: dt=11.200000, rms=0.433 (0.169%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0244: dt=11.200000, rms=0.432 (0.131%), neg=0, invalid=96777 0245: dt=11.200000, rms=0.432 (0.075%), neg=0, invalid=96777 0246: dt=11.200000, rms=0.432 (0.060%), neg=0, invalid=96777 0247: dt=11.200000, rms=0.432 (0.068%), neg=0, invalid=96777 0248: dt=11.200000, rms=0.431 (0.042%), neg=0, invalid=96777 0249: dt=11.200000, rms=0.431 (0.005%), neg=0, invalid=96777 0250: dt=11.200000, rms=0.431 (0.027%), neg=0, invalid=96777 0251: dt=11.200000, rms=0.431 (0.026%), neg=0, invalid=96777 0252: dt=11.200000, rms=0.431 (0.025%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 0253: dt=44.800000, rms=0.429 (0.437%), neg=0, invalid=96777 0254: dt=9.600000, rms=0.428 (0.152%), neg=0, invalid=96777 0255: dt=9.600000, rms=0.428 (0.067%), neg=0, invalid=96777 0256: dt=9.600000, rms=0.428 (0.071%), neg=0, invalid=96777 0257: dt=9.600000, rms=0.427 (0.112%), neg=0, invalid=96777 0258: dt=9.600000, rms=0.427 (0.085%), neg=0, invalid=96777 0259: dt=9.600000, rms=0.427 (0.093%), neg=0, invalid=96777 0260: dt=9.600000, rms=0.426 (0.059%), neg=0, invalid=96777 0261: dt=9.600000, rms=0.426 (0.025%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0262: dt=1.008000, rms=0.434 (0.013%), neg=0, invalid=96777 0263: dt=1.008000, rms=0.434 (0.005%), neg=0, invalid=96777 0264: dt=1.008000, rms=0.434 (0.002%), neg=0, invalid=96777 0265: dt=1.008000, rms=0.434 (-0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0266: dt=4.032000, rms=0.434 (0.052%), neg=0, invalid=96777 0267: dt=2.304000, rms=0.434 (0.009%), neg=0, invalid=96777 0268: dt=2.304000, rms=0.434 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=96777 0269: dt=0.907801, rms=0.445 (0.099%), neg=0, invalid=96777 0270: dt=0.320000, rms=0.445 (0.011%), neg=0, invalid=96777 0271: dt=0.320000, rms=0.445 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=96777 0272: dt=1.536000, rms=0.444 (0.162%), neg=0, invalid=96777 0273: dt=0.448000, rms=0.444 (0.010%), neg=0, invalid=96777 0274: dt=0.448000, rms=0.444 (0.004%), neg=0, invalid=96777 0275: dt=0.448000, rms=0.444 (-0.017%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 iter 0, gcam->neg = 538 after 17 iterations, nbhd size=2, neg = 0 0276: dt=1.792000, rms=0.406 (6.330%), neg=0, invalid=96777 0277: dt=0.000438, rms=0.406 (0.001%), neg=0, invalid=96777 0278: dt=0.000438, rms=0.406 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0279: dt=0.000438, rms=0.406 (0.000%), neg=0, invalid=96777 0280: dt=0.000094, rms=0.406 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.394, neg=0, invalid=96777 0281: dt=0.007902, rms=0.395 (-0.151%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 0282: dt=32.368000, rms=0.395 (0.008%), neg=0, invalid=96777 0283: dt=32.368000, rms=0.395 (0.002%), neg=0, invalid=96777 0284: dt=32.368000, rms=0.395 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 0285: dt=0.000000, rms=0.395 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 0286: dt=36.288000, rms=0.395 (0.030%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.395 (0.013%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.395 (0.007%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.395 (-0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 iter 0, gcam->neg = 14 after 18 iterations, nbhd size=2, neg = 0 0290: dt=19.200000, rms=0.394 (0.177%), neg=0, invalid=96777 iter 0, gcam->neg = 34 after 17 iterations, nbhd size=2, neg = 0 0291: dt=11.200000, rms=0.394 (0.089%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 22 iterations, nbhd size=2, neg = 0 0292: dt=11.200000, rms=0.394 (0.055%), neg=0, invalid=96777 iter 0, gcam->neg = 36 after 24 iterations, nbhd size=3, neg = 0 0293: dt=11.200000, rms=0.394 (0.064%), neg=0, invalid=96777 iter 0, gcam->neg = 47 after 38 iterations, nbhd size=4, neg = 0 0294: dt=11.200000, rms=0.394 (-0.044%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=96777 iter 0, gcam->neg = 17 after 31 iterations, nbhd size=4, neg = 0 0295: dt=32.000000, rms=0.392 (0.344%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 34 iterations, nbhd size=4, neg = 0 0296: dt=38.400000, rms=0.391 (0.367%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 27 iterations, nbhd size=3, neg = 0 0297: dt=32.000000, rms=0.390 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 40 iterations, nbhd size=2, neg = 0 0298: dt=32.000000, rms=0.389 (0.189%), neg=0, invalid=96777 iter 0, gcam->neg = 33 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000621: new neg 0, old_neg 1, delta 1, rms=0.003 (22.870%) 0299: dt=32.000000, rms=0.389 (0.062%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 16 iterations, nbhd size=2, neg = 0 0300: dt=32.000000, rms=0.388 (0.154%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 45 iterations, nbhd size=4, neg = 0 0301: dt=32.000000, rms=0.388 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000500: new neg 0, old_neg 1, delta 1, rms=0.002 (26.504%) 0302: dt=32.000000, rms=0.388 (0.217%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 20 iterations, nbhd size=3, neg = 0 0303: dt=32.000000, rms=0.387 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 21 iterations, nbhd size=2, neg = 0 0304: dt=32.000000, rms=0.387 (0.074%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000500: new neg 0, old_neg 1, delta 1, rms=0.003 (29.769%) 0305: dt=32.000000, rms=0.386 (0.101%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0306: dt=32.000000, rms=0.386 (-0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0307: dt=11.200000, rms=0.386 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 24 iterations, nbhd size=3, neg = 0 0308: dt=44.800000, rms=0.386 (0.123%), neg=0, invalid=96777 0309: dt=11.200000, rms=0.385 (0.022%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0310: dt=2.476190, rms=0.389 (0.026%), neg=0, invalid=96777 0311: dt=1.008000, rms=0.389 (0.004%), neg=0, invalid=96777 0312: dt=1.008000, rms=0.389 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0313: dt=1.008000, rms=0.389 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 21 iterations, nbhd size=3, neg = 0 0314: dt=1.008000, rms=0.389 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0315: dt=4.032000, rms=0.388 (0.049%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 23 iterations, nbhd size=3, neg = 0 0316: dt=9.216000, rms=0.388 (0.130%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0317: dt=1.728000, rms=0.388 (0.010%), neg=0, invalid=96777 0318: dt=1.728000, rms=0.388 (0.018%), neg=0, invalid=96777 0319: dt=1.728000, rms=0.388 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0320: dt=1.728000, rms=0.387 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0321: dt=1.728000, rms=0.387 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 25 iterations, nbhd size=3, neg = 0 0322: dt=1.728000, rms=0.387 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0323: dt=1.728000, rms=0.387 (0.041%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 25 iterations, nbhd size=3, neg = 0 0324: dt=1.728000, rms=0.387 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 23 iterations, nbhd size=2, neg = 0 0325: dt=1.728000, rms=0.387 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 29 iterations, nbhd size=3, neg = 0 0326: dt=1.728000, rms=0.386 (0.055%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0327: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0328: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=96777 iter 0, gcam->neg = 334 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.009, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.009 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0329: dt=0.768000, rms=0.383 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.383, neg=0, invalid=96777 iter 0, gcam->neg = 547 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.008, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.008 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0330: dt=0.989644, rms=0.383 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 0 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Inv Thu Oct 12 22:09:24 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Oct 12 22:10:50 EDT 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10786421 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 34 seconds. #-------------------------------------- #@# SkullLTA Thu Oct 12 22:12:24 EDT 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (47, 21, 13) --> (210, 203, 221) using (101, 82, 117) as brain centroid... mean wm in atlas = 126, using box (81,60,91) --> (121, 104,142) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.8 (thresh=-3.8) 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.064 -0.196 1.014 20.955; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.021 -0.054 0.047 -5.481; 0.045 1.205 0.140 -26.272; -0.059 -0.147 0.962 20.991; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.021 -0.054 0.047 -5.481; 0.045 1.205 0.140 -26.272; -0.060 -0.150 0.980 19.396; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.8) 1.023 -0.055 0.055 -6.505; 0.045 1.209 0.132 -25.433; -0.068 -0.140 0.983 18.590; 0.000 0.000 0.000 1.000; **************************************** 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) 1.022 -0.055 0.055 -6.350; 0.045 1.210 0.132 -25.605; -0.068 -0.140 0.985 18.488; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02189 -0.05477 0.05539 -6.34952; 0.04525 1.21032 0.13198 -25.60458; -0.06804 -0.14023 0.98456 18.48758; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02189 -0.05477 0.05539 -6.34952; 0.04525 1.21032 0.13198 -25.60458; -0.06804 -0.14023 0.98456 18.48758; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.022 -0.055 0.055 -6.350; 0.045 1.210 0.132 -25.605; -0.068 -0.140 0.985 18.488; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.8) transform before final EM align: 1.022 -0.055 0.055 -6.350; 0.045 1.210 0.132 -25.605; -0.068 -0.140 0.985 18.488; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02189 -0.05477 0.05539 -6.34952; 0.04525 1.21032 0.13198 -25.60458; -0.06804 -0.14023 0.98456 18.48758; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02189 -0.05477 0.05539 -6.34952; 0.04525 1.21032 0.13198 -25.60458; -0.06804 -0.14023 0.98456 18.48758; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = 4.2 tol 0.000000 final transform: 1.022 -0.055 0.055 -6.350; 0.045 1.210 0.132 -25.605; -0.068 -0.140 0.985 18.488; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 20 minutes and 53 seconds. #-------------------------------------- #@# SubCort Seg Thu Oct 12 22:33:17 EDT 2017 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname xubuntu-VirtualBox machine i686 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Han2/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13311 (28) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1773 voxels, overlap=0.852) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1773 voxels, peak = 27), gca=27.4 gca peak = 0.14982 (20) mri peak = 0.13391 (28) Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (2093 voxels, overlap=0.524) Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (2093 voxels, peak = 26), gca=25.5 gca peak = 0.28003 (97) mri peak = 0.10000 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (320 voxels, overlap=1.023) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (320 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.11765 (98) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (405 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (405 voxels, peak = 97), gca=97.4 gca peak = 0.27536 (62) mri peak = 0.09859 (72) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (703 voxels, overlap=0.221) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (703 voxels, peak = 73), gca=73.5 gca peak = 0.32745 (63) mri peak = 0.09016 (73) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (838 voxels, overlap=0.426) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (838 voxels, peak = 72), gca=71.5 gca peak = 0.08597 (105) mri peak = 0.10409 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49337 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49337 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.08872 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (47657 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (47657 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.05078 (67) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (33055 voxels, overlap=0.826) Left_Cerebral_Cortex (3): linear fit = 1.07 x + 0.0 (33055 voxels, peak = 67), gca=67.1 gca peak = 0.08598 (64) mri peak = 0.05021 (68) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (29736 voxels, overlap=0.794) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (29736 voxels, peak = 68), gca=67.5 gca peak = 0.24164 (71) mri peak = 0.12077 (85) Right_Caudate (50): linear fit = 1.17 x + 0.0 (828 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.17 x + 0.0 (828 voxels, peak = 83), gca=83.4 gca peak = 0.18227 (75) mri peak = 0.13048 (87) Left_Caudate (11): linear fit = 1.12 x + 0.0 (958 voxels, overlap=0.240) Left_Caudate (11): linear fit = 1.12 x + 0.0 (958 voxels, peak = 84), gca=83.6 gca peak = 0.10629 (62) mri peak = 0.04783 (71) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (20017 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (20017 voxels, peak = 70), gca=70.4 gca peak = 0.11668 (59) mri peak = 0.05048 (67) Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (23135 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (23135 voxels, peak = 68), gca=67.6 gca peak = 0.17849 (88) mri peak = 0.08777 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.13 x + 0.0 (5255 voxels, overlap=0.123) Left_Cerebellum_White_Matter (7): linear fit = 1.13 x + 0.0 (5255 voxels, peak = 100), gca=99.9 gca peak = 0.16819 (86) mri peak = 0.09444 (98) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5302 voxels, overlap=0.279) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5302 voxels, peak = 94), gca=94.2 gca peak = 0.41688 (64) mri peak = 0.09375 (77) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (318 voxels, overlap=0.073) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (318 voxels, peak = 76), gca=76.5 gca peak = 0.42394 (62) mri peak = 0.12202 (70) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (264 voxels, overlap=0.055) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (264 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.07143 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3648 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3648 voxels, peak = 96), gca=96.5 gca peak = 0.13978 (88) mri peak = 0.05902 (89) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3296 voxels, overlap=0.999) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3296 voxels, peak = 89), gca=89.3 gca peak = 0.08514 (81) mri peak = 0.09516 (94) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1897 voxels, overlap=0.548) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1897 voxels, peak = 89), gca=88.7 gca peak = 0.09624 (82) mri peak = 0.07868 (92) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2237 voxels, overlap=0.635) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2237 voxels, peak = 89), gca=89.0 gca peak = 0.07543 (88) mri peak = 0.09951 (84) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10768 voxels, overlap=0.754) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10768 voxels, peak = 87), gca=86.7 gca peak = 0.12757 (95) mri peak = 0.07914 (92) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (976 voxels, overlap=0.837) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (976 voxels, peak = 94), gca=93.6 gca peak = 0.17004 (92) mri peak = 0.08333 (91) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1171 voxels, overlap=0.941) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1171 voxels, peak = 90), gca=89.7 gca peak = 0.21361 (36) mri peak = 0.12500 (19) gca peak = 0.26069 (23) mri peak = 0.13919 (27) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (189 voxels, overlap=0.829) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (189 voxels, peak = 24), gca=24.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.13 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.12 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15235 (28) mri peak = 0.13311 (28) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1773 voxels, overlap=0.859) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1773 voxels, peak = 28), gca=28.4 gca peak = 0.15999 (26) mri peak = 0.13391 (28) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (2093 voxels, overlap=0.668) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (2093 voxels, peak = 26), gca=26.4 gca peak = 0.30364 (100) mri peak = 0.10000 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (320 voxels, overlap=1.023) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (320 voxels, peak = 100), gca=100.5 gca peak = 0.16572 (97) mri peak = 0.11765 (98) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (405 voxels, overlap=1.010) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (405 voxels, peak = 95), gca=94.6 gca peak = 0.21758 (74) mri peak = 0.09859 (72) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (703 voxels, overlap=0.900) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (703 voxels, peak = 72), gca=72.2 gca peak = 0.21544 (71) mri peak = 0.09016 (73) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (838 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (838 voxels, peak = 69), gca=69.2 gca peak = 0.08344 (108) mri peak = 0.10409 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49337 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49337 voxels, peak = 109), gca=108.5 gca peak = 0.08576 (111) mri peak = 0.08872 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47657 voxels, overlap=0.743) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47657 voxels, peak = 111), gca=111.0 gca peak = 0.07405 (67) mri peak = 0.05078 (67) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33055 voxels, overlap=0.849) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (33055 voxels, peak = 66), gca=66.0 gca peak = 0.08488 (67) mri peak = 0.05021 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29736 voxels, overlap=0.892) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29736 voxels, peak = 67), gca=67.0 gca peak = 0.21726 (83) mri peak = 0.12077 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (828 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (828 voxels, peak = 83), gca=83.0 gca peak = 0.16044 (83) mri peak = 0.13048 (87) Left_Caudate (11): linear fit = 1.02 x + 0.0 (958 voxels, overlap=0.907) Left_Caudate (11): linear fit = 1.02 x + 0.0 (958 voxels, peak = 85), gca=85.1 gca peak = 0.09360 (69) mri peak = 0.04783 (71) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (20017 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (20017 voxels, peak = 71), gca=71.4 gca peak = 0.10879 (69) mri peak = 0.05048 (67) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23135 voxels, overlap=0.984) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (23135 voxels, peak = 68), gca=68.0 gca peak = 0.16242 (99) mri peak = 0.08777 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5255 voxels, overlap=0.991) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5255 voxels, peak = 99), gca=99.5 gca peak = 0.13939 (94) mri peak = 0.09444 (98) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5302 voxels, overlap=0.981) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5302 voxels, peak = 95), gca=95.4 gca peak = 0.29977 (76) mri peak = 0.09375 (77) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (318 voxels, overlap=1.023) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (318 voxels, peak = 76), gca=76.0 gca peak = 0.31935 (71) mri peak = 0.12202 (70) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (264 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (264 voxels, peak = 72), gca=72.1 gca peak = 0.10682 (95) mri peak = 0.07143 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3648 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3648 voxels, peak = 95), gca=95.5 gca peak = 0.11870 (89) mri peak = 0.05902 (89) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3296 voxels, overlap=0.970) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3296 voxels, peak = 89), gca=88.6 gca peak = 0.09561 (90) mri peak = 0.09516 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1897 voxels, overlap=0.915) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1897 voxels, peak = 90), gca=89.6 gca peak = 0.10257 (82) mri peak = 0.07868 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2237 voxels, overlap=0.985) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2237 voxels, peak = 82), gca=81.6 gca peak = 0.07868 (87) mri peak = 0.09951 (84) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10768 voxels, overlap=0.723) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10768 voxels, peak = 87), gca=86.6 gca peak = 0.14030 (93) mri peak = 0.07914 (92) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (976 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (976 voxels, peak = 94), gca=94.4 gca peak = 0.16356 (90) mri peak = 0.08333 (91) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1171 voxels, overlap=0.943) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1171 voxels, peak = 90), gca=89.6 gca peak = 0.14773 (41) mri peak = 0.12500 (19) gca peak = 0.20195 (25) mri peak = 0.13919 (27) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (189 voxels, overlap=0.780) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (189 voxels, peak = 25), gca=24.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26012 (40) gca peak Third_Ventricle = 0.14773 (41) gca peak CSF = 0.19515 (51) gca peak Left_Accumbens_area = 0.56763 (78) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65116 (62) gca peak Left_choroid_plexus = 0.09085 (48) gca peak Right_Inf_Lat_Vent = 0.22069 (38) gca peak Right_Accumbens_area = 0.27366 (84) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.68165 (47) gca peak WM_hypointensities = 0.15236 (84) gca peak non_WM_hypointensities = 0.10275 (55) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 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 20782 gm and wm labels changed (%22 to gray, %78 to white out of all changed labels) 291 hippocampal voxels changed. 5 amygdala voxels changed. pass 1: 78899 changed. image ll: -2.208, PF=1.000 pass 2: 11520 changed. image ll: -2.205, PF=1.000 pass 3: 3665 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 24 minutes and 14 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/Han2/mri/transforms/cc_up.lta Han2 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/Han2/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/Han2/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/Han2/mri/norm.mgz 58729 voxels in left wm, 45464 in right wm, xrange [123, 134] searching rotation angles z=[-5 9], y=[-4 10] searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 global minimum found at slice 127.5, rotations (2.62, 2.01) final transformation (x=127.5, yr=2.615, zr=2.008): 0.998 -0.035 0.046 -1.325; 0.035 0.999 0.002 34.412; -0.046 0.000 0.999 21.937; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 142 112 eigenvectors: 0.001 0.003 1.000; 0.021 -1.000 0.003; 1.000 0.021 -0.002; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/subjects/Han2/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Thu Oct 12 22:58:28 EDT 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Oct 12 22:58:28 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1924 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 73 (73), valley at 36 (36) csf peak at 36, setting threshold to 60 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 74 (74), valley at 36 (36) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 20 seconds. #-------------------------------------------- #@# Mask BFS Thu Oct 12 23:02:49 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1765264 voxels in mask (pct= 10.52) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Oct 12 23:02:51 EDT 2017 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 (103.0): 102.9 +- 7.0 [80.0 --> 125.0] GM (75.0) : 74.0 +- 9.1 [30.0 --> 96.0] setting bottom of white matter range to 83.2 setting top of gray matter range to 92.3 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... 6358 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4217 filled 2750 bright non-wm voxels segmented. 3852 diagonally connected voxels added... white matter segmentation took 2.0 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.62 minutes reading wm segmentation from wm.seg.mgz... 124 voxels added to wm to prevent paths from MTL structures to cortex 2084 additional wm voxels added 0 additional wm voxels added SEG EDIT: 56072 voxels turned on, 44759 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+): 24 found - 24 modified | TOTAL: 24 pass 2 (xy+): 0 found - 24 modified | TOTAL: 24 pass 1 (xy-): 37 found - 37 modified | TOTAL: 61 pass 2 (xy-): 0 found - 37 modified | TOTAL: 61 pass 1 (yz+): 27 found - 27 modified | TOTAL: 88 pass 2 (yz+): 0 found - 27 modified | TOTAL: 88 pass 1 (yz-): 32 found - 32 modified | TOTAL: 120 pass 2 (yz-): 0 found - 32 modified | TOTAL: 120 pass 1 (xz+): 29 found - 29 modified | TOTAL: 149 pass 2 (xz+): 0 found - 29 modified | TOTAL: 149 pass 1 (xz-): 29 found - 29 modified | TOTAL: 178 pass 2 (xz-): 0 found - 29 modified | TOTAL: 178 Iteration Number : 1 pass 1 (+++): 17 found - 17 modified | TOTAL: 17 pass 2 (+++): 0 found - 17 modified | TOTAL: 17 pass 1 (+++): 24 found - 24 modified | TOTAL: 41 pass 2 (+++): 0 found - 24 modified | TOTAL: 41 pass 1 (+++): 27 found - 27 modified | TOTAL: 68 pass 2 (+++): 0 found - 27 modified | TOTAL: 68 pass 1 (+++): 21 found - 21 modified | TOTAL: 89 pass 2 (+++): 0 found - 21 modified | TOTAL: 89 Iteration Number : 1 pass 1 (++): 151 found - 151 modified | TOTAL: 151 pass 2 (++): 0 found - 151 modified | TOTAL: 151 pass 1 (+-): 129 found - 129 modified | TOTAL: 280 pass 2 (+-): 0 found - 129 modified | TOTAL: 280 pass 1 (--): 155 found - 155 modified | TOTAL: 435 pass 2 (--): 1 found - 156 modified | TOTAL: 436 pass 3 (--): 0 found - 156 modified | TOTAL: 436 pass 1 (-+): 108 found - 108 modified | TOTAL: 544 pass 2 (-+): 0 found - 108 modified | TOTAL: 544 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 4 found - 4 modified | TOTAL: 9 pass 2 (xy-): 0 found - 4 modified | TOTAL: 9 pass 1 (yz+): 5 found - 5 modified | TOTAL: 14 pass 2 (yz+): 0 found - 5 modified | TOTAL: 14 pass 1 (yz-): 8 found - 8 modified | TOTAL: 22 pass 2 (yz-): 0 found - 8 modified | TOTAL: 22 pass 1 (xz+): 5 found - 5 modified | TOTAL: 27 pass 2 (xz+): 0 found - 5 modified | TOTAL: 27 pass 1 (xz-): 10 found - 10 modified | TOTAL: 37 pass 2 (xz-): 0 found - 10 modified | TOTAL: 37 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 2 found - 2 modified | TOTAL: 9 pass 2 (+-): 0 found - 2 modified | TOTAL: 9 pass 1 (--): 3 found - 3 modified | TOTAL: 12 pass 2 (--): 0 found - 3 modified | TOTAL: 12 pass 1 (-+): 3 found - 3 modified | TOTAL: 15 pass 2 (-+): 0 found - 3 modified | TOTAL: 15 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 868 (out of 622093: 0.139529) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Oct 12 23:05:36 EDT 2017 /usr/local/freesurfer/subjects/Han2/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.041 -0.055 0.048 -7.989; 0.040 1.135 0.163 -20.989; -0.059 -0.182 0.943 26.891; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1092 (min = 350, max = 1400), aspect = 0.65 (min = 0.10, max = 0.75) no need to search using seed (126, 108, 94), TAL = (2.0, -34.0, 20.0) talairach voxel to voxel transform 0.956 0.037 -0.055 9.905; -0.041 0.856 -0.146 21.553; 0.052 0.168 1.029 -23.725; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 108, 94) --> (2.0, -34.0, 20.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, -34.00, 20.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -34.00, 20.00) SRC: (112.00, 95.82, 96.72) search lh wm seed point around talairach space (-16.00, -34.00, 20.00), SRC: (146.42, 94.33, 98.60) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Oct 12 23:06:34 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 3 found - 3 modified | TOTAL: 5 pass 2 (yz-): 0 found - 3 modified | TOTAL: 5 pass 1 (xz+): 3 found - 3 modified | TOTAL: 8 pass 2 (xz+): 0 found - 3 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 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 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 12 (out of 299308: 0.004009) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 54 vertices, 66 faces slice 40: 3139 vertices, 3323 faces slice 50: 10554 vertices, 10860 faces slice 60: 20243 vertices, 20573 faces slice 70: 30357 vertices, 30719 faces slice 80: 40656 vertices, 41026 faces slice 90: 51450 vertices, 51808 faces slice 100: 62869 vertices, 63290 faces slice 110: 74767 vertices, 75173 faces slice 120: 87082 vertices, 87503 faces slice 130: 98552 vertices, 98969 faces slice 140: 110904 vertices, 111334 faces slice 150: 121808 vertices, 122197 faces slice 160: 131076 vertices, 131408 faces slice 170: 139413 vertices, 139716 faces slice 180: 146343 vertices, 146581 faces slice 190: 152537 vertices, 152771 faces slice 200: 156473 vertices, 156567 faces slice 210: 156686 vertices, 156732 faces slice 220: 156686 vertices, 156732 faces slice 230: 156686 vertices, 156732 faces slice 240: 156686 vertices, 156732 faces slice 250: 156686 vertices, 156732 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 156686 voxel in cpt #1: X=-46 [v=156686,e=470196,f=313464] located at (-28.379108, -15.810908, 32.065022) For the whole surface: X=-46 [v=156686,e=470196,f=313464] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Oct 12 23:06:40 EDT 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /usr/local/freesurfer/subjects/Han2/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Oct 12 23:06:44 EDT 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /usr/local/freesurfer/subjects/Han2/scripts avg radius = 49.2 mm, total surface area = 82878 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Oct 12 23:07:15 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.55 (0.00-->6.60) (max @ vno 112753 --> 112754) face area 0.02 +- 0.03 (-0.08-->0.57) scaling brain by 0.290... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.917, avgs=0 005/300: dt: 0.9000, rms radial error=176.658, avgs=0 010/300: dt: 0.9000, rms radial error=176.102, avgs=0 015/300: dt: 0.9000, rms radial error=175.372, avgs=0 020/300: dt: 0.9000, rms radial error=174.540, avgs=0 025/300: dt: 0.9000, rms radial error=173.650, avgs=0 030/300: dt: 0.9000, rms radial error=172.728, avgs=0 035/300: dt: 0.9000, rms radial error=171.789, avgs=0 040/300: dt: 0.9000, rms radial error=170.842, avgs=0 045/300: dt: 0.9000, rms radial error=169.892, avgs=0 050/300: dt: 0.9000, rms radial error=168.943, avgs=0 055/300: dt: 0.9000, rms radial error=167.997, avgs=0 060/300: dt: 0.9000, rms radial error=167.054, avgs=0 065/300: dt: 0.9000, rms radial error=166.115, avgs=0 070/300: dt: 0.9000, rms radial error=165.180, avgs=0 075/300: dt: 0.9000, rms radial error=164.254, avgs=0 080/300: dt: 0.9000, rms radial error=163.334, avgs=0 085/300: dt: 0.9000, rms radial error=162.419, avgs=0 090/300: dt: 0.9000, rms radial error=161.509, avgs=0 095/300: dt: 0.9000, rms radial error=160.604, avgs=0 100/300: dt: 0.9000, rms radial error=159.704, avgs=0 105/300: dt: 0.9000, rms radial error=158.809, avgs=0 110/300: dt: 0.9000, rms radial error=157.918, avgs=0 115/300: dt: 0.9000, rms radial error=157.033, avgs=0 120/300: dt: 0.9000, rms radial error=156.152, avgs=0 125/300: dt: 0.9000, rms radial error=155.275, avgs=0 130/300: dt: 0.9000, rms radial error=154.404, avgs=0 135/300: dt: 0.9000, rms radial error=153.537, avgs=0 140/300: dt: 0.9000, rms radial error=152.675, avgs=0 145/300: dt: 0.9000, rms radial error=151.817, avgs=0 150/300: dt: 0.9000, rms radial error=150.965, avgs=0 155/300: dt: 0.9000, rms radial error=150.116, avgs=0 160/300: dt: 0.9000, rms radial error=149.273, avgs=0 165/300: dt: 0.9000, rms radial error=148.434, avgs=0 170/300: dt: 0.9000, rms radial error=147.599, avgs=0 175/300: dt: 0.9000, rms radial error=146.769, avgs=0 180/300: dt: 0.9000, rms radial error=145.944, avgs=0 185/300: dt: 0.9000, rms radial error=145.123, avgs=0 190/300: dt: 0.9000, rms radial error=144.307, avgs=0 195/300: dt: 0.9000, rms radial error=143.495, avgs=0 200/300: dt: 0.9000, rms radial error=142.687, avgs=0 205/300: dt: 0.9000, rms radial error=141.885, avgs=0 210/300: dt: 0.9000, rms radial error=141.086, avgs=0 215/300: dt: 0.9000, rms radial error=140.292, avgs=0 220/300: dt: 0.9000, rms radial error=139.502, avgs=0 225/300: dt: 0.9000, rms radial error=138.717, avgs=0 230/300: dt: 0.9000, rms radial error=137.936, avgs=0 235/300: dt: 0.9000, rms radial error=137.159, avgs=0 240/300: dt: 0.9000, rms radial error=136.387, avgs=0 245/300: dt: 0.9000, rms radial error=135.619, avgs=0 250/300: dt: 0.9000, rms radial error=134.855, avgs=0 255/300: dt: 0.9000, rms radial error=134.096, avgs=0 260/300: dt: 0.9000, rms radial error=133.341, avgs=0 265/300: dt: 0.9000, rms radial error=132.590, avgs=0 270/300: dt: 0.9000, rms radial error=131.843, avgs=0 275/300: dt: 0.9000, rms radial error=131.100, avgs=0 280/300: dt: 0.9000, rms radial error=130.362, avgs=0 285/300: dt: 0.9000, rms radial error=129.627, avgs=0 290/300: dt: 0.9000, rms radial error=128.897, avgs=0 295/300: dt: 0.9000, rms radial error=128.171, avgs=0 300/300: dt: 0.9000, rms radial error=127.449, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18723.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 3259.76 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 356.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00768 epoch 4 (K=640.0), pass 1, starting sse = 21.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/18 = 0.00882 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Oct 12 23:11:43 EDT 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /usr/local/freesurfer/subjects/Han2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Han2 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-46 (nv=156686, nf=313464, ne=470196, g=24) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4310 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 25 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/Han2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2502 (-4.6251) -vertex loglikelihood: -5.9144 (-2.9572) -normal dot loglikelihood: -3.6061 (-3.6061) -quad curv loglikelihood: -6.4835 (-3.2418) Total Loglikelihood : -25.2543 CORRECTING DEFECT 0 (vertices=18, convex hull=17) Warning - incorrect dp selected!!!!(-70.923437 >= -70.923439 ) After retessellation of defect 0, euler #=-20 (154183,461797,307594) : difference with theory (-22) = -2 CORRECTING DEFECT 1 (vertices=38, convex hull=67) After retessellation of defect 1, euler #=-19 (154207,461898,307672) : difference with theory (-21) = -2 CORRECTING DEFECT 2 (vertices=5, convex hull=19) After retessellation of defect 2, euler #=-18 (154207,461906,307681) : difference with theory (-20) = -2 CORRECTING DEFECT 3 (vertices=9, convex hull=27) After retessellation of defect 3, euler #=-17 (154212,461931,307702) : difference with theory (-19) = -2 CORRECTING DEFECT 4 (vertices=636, convex hull=279) After retessellation of defect 4, euler #=-17 (154379,462582,308186) : difference with theory (-18) = -1 CORRECTING DEFECT 5 (vertices=15, convex hull=21) After retessellation of defect 5, euler #=-16 (154382,462596,308198) : difference with theory (-17) = -1 CORRECTING DEFECT 6 (vertices=37, convex hull=36) After retessellation of defect 6, euler #=-15 (154386,462622,308221) : difference with theory (-16) = -1 CORRECTING DEFECT 7 (vertices=15, convex hull=18) After retessellation of defect 7, euler #=-14 (154388,462638,308236) : difference with theory (-15) = -1 CORRECTING DEFECT 8 (vertices=29, convex hull=31) After retessellation of defect 8, euler #=-13 (154396,462672,308263) : difference with theory (-14) = -1 CORRECTING DEFECT 9 (vertices=33, convex hull=30) After retessellation of defect 9, euler #=-12 (154399,462690,308279) : difference with theory (-13) = -1 CORRECTING DEFECT 10 (vertices=365, convex hull=129) After retessellation of defect 10, euler #=-12 (154441,462885,308432) : difference with theory (-12) = 0 CORRECTING DEFECT 11 (vertices=18, convex hull=31) After retessellation of defect 11, euler #=-11 (154447,462914,308456) : difference with theory (-11) = 0 CORRECTING DEFECT 12 (vertices=564, convex hull=194) After retessellation of defect 12, euler #=-10 (154489,463127,308628) : difference with theory (-10) = 0 CORRECTING DEFECT 13 (vertices=38, convex hull=20) After retessellation of defect 13, euler #=-9 (154492,463140,308639) : difference with theory (-9) = 0 CORRECTING DEFECT 14 (vertices=34, convex hull=27) After retessellation of defect 14, euler #=-8 (154494,463156,308654) : difference with theory (-8) = 0 CORRECTING DEFECT 15 (vertices=24, convex hull=36) After retessellation of defect 15, euler #=-7 (154496,463175,308672) : difference with theory (-7) = 0 CORRECTING DEFECT 16 (vertices=193, convex hull=108) After retessellation of defect 16, euler #=-6 (154520,463293,308767) : difference with theory (-6) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=71) After retessellation of defect 17, euler #=-5 (154539,463375,308831) : difference with theory (-5) = 0 CORRECTING DEFECT 18 (vertices=62, convex hull=101) After retessellation of defect 18, euler #=-4 (154562,463485,308919) : difference with theory (-4) = 0 CORRECTING DEFECT 19 (vertices=147, convex hull=178) After retessellation of defect 19, euler #=-3 (154613,463732,309116) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=39, convex hull=63) After retessellation of defect 20, euler #=-2 (154630,463812,309180) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=76, convex hull=57) After retessellation of defect 21, euler #=-1 (154651,463899,309247) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=31, convex hull=40) After retessellation of defect 22, euler #=0 (154658,463933,309275) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=19, convex hull=42) After retessellation of defect 23, euler #=1 (154667,463972,309306) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=30, convex hull=57) After retessellation of defect 24, euler #=2 (154676,464022,309348) : 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-->8.41) (max @ vno 77934 --> 87358) 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-->8.41) (max @ vno 77934 --> 87358) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 96 mutations (34.4%), 183 crossovers (65.6%), 183 vertices were eliminated building final representation... 2010 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=154676, nf=309348, ne=464022, g=0) writing corrected surface to /usr/local/freesurfer/subjects/Han2/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.1 minutes 0 defective edges removing intersecting faces 000: 229 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 154676 - 464022 + 309348 = 2 --> 0 holes F =2V-4: 309348 = 309352-4 (0) 2E=3F: 928044 = 928044 (0) total defect index = 0 /usr/local/freesurfer/subjects/Han2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 30 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Oct 12 23:28:57 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Han2 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/Han2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Han2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Han2/mri/wm.mgz... 15541 bright wm thresholded. 2797 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Han2/surf/lh.orig... computing class statistics... border white: 293896 voxels (1.75%) border gray 325611 voxels (1.94%) WM (96.0): 97.1 +- 7.3 [70.0 --> 110.0] GM (85.0) : 83.3 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/Han2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->3.75) (max @ vno 74188 --> 154221) face area 0.28 +- 0.12 (0.00-->4.14) mean absolute distance = 0.73 +- 0.89 4403 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=74 mean inside = 96.6, mean outside = 80.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=83.1, 70 (70) missing vertices, mean dist 0.3 [0.6 (%32.6)->0.8 (%67.4))] %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=xubun, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.07-->5.48) (max @ vno 154259 --> 73069) face area 0.28 +- 0.13 (0.00-->5.27) mean absolute distance = 0.35 +- 0.52 3102 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5508881.0, rms=9.53 001: dt: 0.5000, sse=6251863.0, rms=6.828 (0.000%) 002: dt: 0.5000, sse=6613212.5, rms=5.191 (0.000%) 003: dt: 0.5000, sse=6979209.5, rms=4.188 (0.000%) 004: dt: 0.5000, sse=7206554.0, rms=3.578 (0.000%) 005: dt: 0.5000, sse=7368280.0, rms=3.273 (0.000%) 006: dt: 0.5000, sse=7417300.0, rms=3.085 (0.000%) 007: dt: 0.5000, sse=7484842.0, rms=3.008 (0.000%) 008: dt: 0.5000, sse=7481327.5, rms=2.934 (0.000%) rms = 2.93, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7495599.5, rms=2.926 (0.000%) 010: dt: 0.2500, sse=4501375.5, rms=2.062 (0.000%) 011: dt: 0.2500, sse=4194112.2, rms=1.876 (0.000%) rms = 1.84, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4050557.8, rms=1.838 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3984062.8, rms=1.816 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.5, 77 (21) missing vertices, mean dist -0.2 [0.4 (%77.3)->0.3 (%22.7))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=xubun, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.09-->5.27) (max @ vno 65114 --> 61313) face area 0.35 +- 0.16 (0.00-->6.77) mean absolute distance = 0.23 +- 0.30 3941 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4698470.5, rms=4.76 014: dt: 0.5000, sse=4915993.5, rms=2.934 (0.000%) 015: dt: 0.5000, sse=5341099.5, rms=2.704 (0.000%) 016: dt: 0.5000, sse=5854515.0, rms=2.571 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4809078.5, rms=1.947 (0.000%) 018: dt: 0.2500, sse=4467546.5, rms=1.677 (0.000%) 019: dt: 0.2500, sse=4343599.5, rms=1.616 (0.000%) rms = 1.61, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4288539.0, rms=1.608 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4245045.0, rms=1.592 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.0, 78 (10) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=xubun, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.43) (max @ vno 65114 --> 61313) face area 0.34 +- 0.16 (0.00-->6.64) mean absolute distance = 0.18 +- 0.25 3004 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4465156.5, rms=3.31 022: dt: 0.5000, sse=4685795.0, rms=2.240 (0.000%) rms = 2.42, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4431140.0, rms=1.613 (0.000%) 024: dt: 0.2500, sse=4357962.5, rms=1.288 (0.000%) 025: dt: 0.2500, sse=4334990.5, rms=1.218 (0.000%) rms = 1.23, time step reduction 2 of 3 to 0.125... rms = 1.21, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4311318.5, rms=1.208 (0.000%) positioning took 0.7 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=89.8, 85 (5) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=xubun, 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 /usr/local/freesurfer/subjects/Han2/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4320449.0, rms=1.46 rms = 1.47, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4373752.5, rms=1.092 (0.000%) 028: dt: 0.2500, sse=4550539.0, rms=0.910 (0.000%) rms = 0.94, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4543925.0, rms=0.910 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 15 non-cortical segments detected only using segment with 2234 vertices erasing segment 1 (vno[0] = 88431) erasing segment 2 (vno[0] = 100799) erasing segment 3 (vno[0] = 101966) erasing segment 4 (vno[0] = 103267) erasing segment 5 (vno[0] = 104503) erasing segment 6 (vno[0] = 105630) erasing segment 7 (vno[0] = 105697) erasing segment 8 (vno[0] = 105766) erasing segment 9 (vno[0] = 105800) erasing segment 10 (vno[0] = 109440) erasing segment 11 (vno[0] = 112379) erasing segment 12 (vno[0] = 113396) erasing segment 13 (vno[0] = 114496) erasing segment 14 (vno[0] = 114527) writing cortex label to /usr/local/freesurfer/subjects/Han2/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Han2/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/Han2/surf/lh.area vertex spacing 0.89 +- 0.25 (0.07-->5.49) (max @ vno 65114 --> 61313) face area 0.33 +- 0.16 (0.00-->6.58) refinement took 5.8 minutes #-------------------------------------------- #@# Smooth2 lh Thu Oct 12 23:34:43 EDT 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /usr/local/freesurfer/subjects/Han2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Oct 12 23:34:47 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 49.4 mm, total surface area = 94018 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 274 vertices thresholded to be in k1 ~ [-0.25 0.32], k2 ~ [-0.09 0.06] total integrated curvature = 0.575*4pi (7.226) --> 0 handles ICI = 1.8, FI = 14.6, variation=233.385 147 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 190 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.026 done. #----------------------------------------- #@# Curvature Stats lh Thu Oct 12 23:37:07 EDT 2017 /usr/local/freesurfer/subjects/Han2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Han2 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 [ Han2/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 [ 273 ] Gb_filter = 0 WARN: S lookup min: -0.008779 WARN: S explicit min: 0.000000 vertex = 111 #-------------------------------------------- #@# Sphere lh Thu Oct 12 23:37:11 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=xubun, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.05 pass 1: epoch 2 of 3 starting distance error %19.98 unfolding complete - removing small folds... starting distance error %19.89 removing remaining folds... final distance error %19.90 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.87 hours #-------------------------------------------- #@# Surf Reg lh Fri Oct 13 00:29:09 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/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=xubun, 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=xubun, 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 = 0.574 curvature mean = 0.027, std = 0.931 curvature mean = 0.027, std = 0.840 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 8.00) sse = 237743.4, tmin=1.9068 d=8.00 min @ (0.00, 2.00, -2.00) sse = 234611.7, tmin=3.8119 d=4.00 min @ (0.00, -1.00, 1.00) sse = 230790.2, tmin=4.7712 d=2.00 min @ (0.50, 0.50, -0.50) sse = 230594.8, tmin=5.7353 d=1.00 min @ (0.00, -0.25, 0.25) sse = 230350.9, tmin=6.7042 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 230314.1, tmin=7.6886 tol=1.0e+00, sigma=0.5, host=xubun, 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 7.69 min curvature mean = 0.014, std = 0.932 curvature mean = 0.014, std = 0.929 curvature mean = 0.013, std = 0.943 curvature mean = 0.006, std = 0.967 curvature mean = 0.011, std = 0.944 curvature mean = 0.002, std = 0.986 2 Reading smoothwm curvature mean = -0.025, std = 0.302 curvature mean = 0.003, std = 0.067 curvature mean = 0.071, std = 0.306 curvature mean = 0.004, std = 0.079 curvature mean = 0.032, std = 0.497 curvature mean = 0.004, std = 0.084 curvature mean = 0.017, std = 0.639 curvature mean = 0.005, std = 0.086 curvature mean = 0.004, std = 0.754 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Oct 13 00:57:14 EDT 2017 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Oct 13 00:57:16 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mrisp_paint -a 5 /usr/local/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 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Oct 13 00:57:17 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Han2 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 1356 labels changed using aseg relabeling using gibbs priors... 000: 3392 changed, 154676 examined... 001: 797 changed, 14490 examined... 002: 191 changed, 4356 examined... 003: 74 changed, 1173 examined... 004: 34 changed, 444 examined... 005: 7 changed, 196 examined... 006: 3 changed, 41 examined... 007: 2 changed, 22 examined... 008: 2 changed, 12 examined... 009: 1 changed, 10 examined... 010: 0 changed, 8 examined... 227 labels changed using aseg 000: 126 total segments, 76 labels (273 vertices) changed 001: 51 total segments, 7 labels (19 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 55 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2188 vertices marked for relabeling... 2188 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 46 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Oct 13 00:58:03 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Han2 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/Han2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Han2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Han2/mri/wm.mgz... 15541 bright wm thresholded. 2797 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Han2/surf/lh.orig... computing class statistics... border white: 293896 voxels (1.75%) border gray 325611 voxels (1.94%) WM (96.0): 97.1 +- 7.3 [70.0 --> 110.0] GM (85.0) : 83.3 +- 10.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=74 mean inside = 96.6, mean outside = 80.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/Han2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->3.75) (max @ vno 74188 --> 154221) face area 0.28 +- 0.12 (0.00-->4.14) mean absolute distance = 0.73 +- 0.90 4444 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 392 points - only 0.00% unknown deleting segment 3 with 74 points - only 0.00% unknown deleting segment 4 with 18 points - only 0.00% unknown mean border=83.1, 70 (70) missing vertices, mean dist 0.3 [0.6 (%32.7)->0.8 (%67.3))] %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=xubun, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->5.48) (max @ vno 154259 --> 73069) face area 0.28 +- 0.13 (0.00-->5.27) mean absolute distance = 0.35 +- 0.52 3128 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5518663.5, rms=9.52 001: dt: 0.5000, sse=6274899.0, rms=6.820 (0.000%) 002: dt: 0.5000, sse=6635855.5, rms=5.186 (0.000%) 003: dt: 0.5000, sse=7003585.0, rms=4.185 (0.000%) 004: dt: 0.5000, sse=7230795.0, rms=3.575 (0.000%) 005: dt: 0.5000, sse=7395480.5, rms=3.271 (0.000%) 006: dt: 0.5000, sse=7442410.0, rms=3.083 (0.000%) 007: dt: 0.5000, sse=7512533.5, rms=3.007 (0.000%) 008: dt: 0.5000, sse=7506847.5, rms=2.933 (0.000%) rms = 2.92, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7523433.5, rms=2.924 (0.000%) 010: dt: 0.2500, sse=4520293.5, rms=2.062 (0.000%) 011: dt: 0.2500, sse=4213189.5, rms=1.877 (0.000%) rms = 1.84, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4069195.5, rms=1.839 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4002722.2, rms=1.817 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 362 points - only 0.00% unknown deleting segment 2 with 13 points - only 53.85% unknown deleting segment 3 with 76 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 6 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=86.5, 79 (21) missing vertices, mean dist -0.2 [0.4 (%77.3)->0.3 (%22.7))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=xubun, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.09-->5.27) (max @ vno 65114 --> 61313) face area 0.35 +- 0.16 (0.00-->6.77) mean absolute distance = 0.23 +- 0.30 4001 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4719104.0, rms=4.76 014: dt: 0.5000, sse=4936268.5, rms=2.932 (0.000%) 015: dt: 0.5000, sse=5365876.5, rms=2.701 (0.000%) 016: dt: 0.5000, sse=5877591.5, rms=2.569 (0.000%) rms = 2.80, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4830065.0, rms=1.946 (0.000%) 018: dt: 0.2500, sse=4488442.0, rms=1.677 (0.000%) 019: dt: 0.2500, sse=4363860.5, rms=1.617 (0.000%) rms = 1.61, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4308415.5, rms=1.608 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4265502.0, rms=1.592 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 390 points - only 0.00% unknown deleting segment 1 with 13 points - only 53.85% unknown deleting segment 2 with 90 points - only 0.00% unknown deleting segment 3 with 31 points - only 0.00% unknown deleting segment 4 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown mean border=89.0, 102 (14) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))] %91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=xubun, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.48) (max @ vno 65114 --> 61313) face area 0.34 +- 0.16 (0.00-->6.65) mean absolute distance = 0.18 +- 0.25 2976 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4503381.5, rms=3.37 022: dt: 0.5000, sse=4723745.5, rms=2.340 (0.000%) rms = 2.51, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4468637.5, rms=1.750 (0.000%) 024: dt: 0.2500, sse=4394741.0, rms=1.446 (0.000%) 025: dt: 0.2500, sse=4369566.5, rms=1.372 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4332273.5, rms=1.365 (0.000%) rms = 1.35, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4307729.5, rms=1.345 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 397 points - only 0.00% unknown deleting segment 1 with 92 points - only 0.00% unknown deleting segment 2 with 9 points - only 33.33% unknown deleting segment 3 with 31 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown mean border=89.8, 119 (10) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=xubun, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4313502.5, rms=1.55 rms = 1.52, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=5357565.0, rms=1.520 (0.000%) 029: dt: 0.2500, sse=4645038.0, rms=1.236 (0.000%) 030: dt: 0.2500, sse=4825764.0, rms=1.110 (0.000%) rms = 1.15, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4802949.0, rms=1.098 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=64.0, 168 (168) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.5 (%100.0))] %24 local maxima, %46 large gradients and %27 min vals, 2085 gradients ignored tol=1.0e-04, sigma=2.0, host=xubun, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=23146750.0, rms=26.04 001: dt: 0.5000, sse=17836972.0, rms=22.333 (0.000%) 002: dt: 0.5000, sse=13910055.0, rms=19.175 (0.000%) 003: dt: 0.5000, sse=11076944.0, rms=16.537 (0.000%) 004: dt: 0.5000, sse=9199718.0, rms=14.374 (0.000%) 005: dt: 0.5000, sse=8064080.5, rms=12.651 (0.000%) 006: dt: 0.5000, sse=7348950.5, rms=11.281 (0.000%) 007: dt: 0.5000, sse=6919249.5, rms=10.092 (0.000%) 008: dt: 0.5000, sse=6615870.5, rms=9.003 (0.000%) 009: dt: 0.5000, sse=6435176.0, rms=7.985 (0.000%) 010: dt: 0.5000, sse=6306335.0, rms=7.018 (0.000%) 011: dt: 0.5000, sse=6257838.0, rms=6.107 (0.000%) 012: dt: 0.5000, sse=6215163.0, rms=5.266 (0.000%) 013: dt: 0.5000, sse=6288484.5, rms=4.552 (0.000%) 014: dt: 0.5000, sse=6381819.0, rms=4.019 (0.000%) 015: dt: 0.5000, sse=6498482.5, rms=3.700 (0.000%) 016: dt: 0.5000, sse=6605128.0, rms=3.515 (0.000%) 017: dt: 0.5000, sse=6637985.5, rms=3.424 (0.000%) 018: dt: 0.5000, sse=6661890.0, rms=3.372 (0.000%) rms = 3.33, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6697258.5, rms=3.332 (0.000%) 020: dt: 0.2500, sse=4583154.0, rms=2.667 (0.000%) 021: dt: 0.2500, sse=4392720.5, rms=2.489 (0.000%) rms = 2.46, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4290466.0, rms=2.465 (0.000%) 023: dt: 0.1250, sse=4142660.5, rms=2.391 (0.000%) rms = 2.38, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4122756.2, rms=2.381 (0.000%) positioning took 2.6 minutes mean border=61.2, 955 (41) missing vertices, mean dist 0.2 [0.2 (%40.9)->0.5 (%59.1))] %44 local maxima, %32 large gradients and %20 min vals, 674 gradients ignored tol=1.0e-04, sigma=1.0, host=xubun, 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=4956109.5, rms=5.05 025: dt: 0.5000, sse=4960731.0, rms=3.559 (0.000%) 026: dt: 0.5000, sse=6253201.5, rms=3.387 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5215962.5, rms=2.745 (0.000%) 028: dt: 0.2500, sse=4787808.0, rms=2.469 (0.000%) 029: dt: 0.2500, sse=4719012.0, rms=2.394 (0.000%) rms = 2.37, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4689095.5, rms=2.367 (0.000%) 031: dt: 0.1250, sse=4564257.0, rms=2.277 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4555413.0, rms=2.262 (0.000%) positioning took 1.0 minutes mean border=59.4, 1257 (29) missing vertices, mean dist 0.1 [0.2 (%35.8)->0.3 (%64.2))] %60 local maxima, %16 large gradients and %20 min vals, 723 gradients ignored tol=1.0e-04, sigma=0.5, host=xubun, 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=4739388.5, rms=3.26 rms = 3.21, time step reduction 1 of 3 to 0.250... 033: dt: 0.5000, sse=4996305.5, rms=3.213 (0.000%) 034: dt: 0.2500, sse=4847465.0, rms=2.431 (0.000%) 035: dt: 0.2500, sse=4884836.0, rms=2.278 (0.000%) rms = 2.27, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4835042.5, rms=2.269 (0.000%) 037: dt: 0.1250, sse=4707119.5, rms=2.144 (0.000%) rms = 2.13, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4702376.5, rms=2.130 (0.000%) positioning took 0.7 minutes mean border=58.7, 2536 (25) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.2 (%56.0))] %64 local maxima, %12 large gradients and %19 min vals, 576 gradients ignored tol=1.0e-04, sigma=0.2, host=xubun, 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 /usr/local/freesurfer/subjects/Han2/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4729623.5, rms=2.36 rms = 2.75, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4639610.5, rms=2.174 (0.000%) 040: dt: 0.2500, sse=4778392.5, rms=2.110 (0.000%) rms = 2.10, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4832016.5, rms=2.102 (0.000%) 042: dt: 0.1250, sse=4754551.5, rms=2.034 (0.000%) rms = 2.02, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4771009.5, rms=2.023 (0.000%) positioning took 0.6 minutes writing curvature file /usr/local/freesurfer/subjects/Han2/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/Han2/surf/lh.area.pial vertex spacing 0.99 +- 0.41 (0.11-->6.75) (max @ vno 65114 --> 61313) face area 0.39 +- 0.29 (0.00-->7.26) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 154676 vertices processed 25000 of 154676 vertices processed 50000 of 154676 vertices processed 75000 of 154676 vertices processed 100000 of 154676 vertices processed 125000 of 154676 vertices processed 150000 of 154676 vertices processed 0 of 154676 vertices processed 25000 of 154676 vertices processed 50000 of 154676 vertices processed 75000 of 154676 vertices processed 100000 of 154676 vertices processed 125000 of 154676 vertices processed 150000 of 154676 vertices processed thickness calculation complete, 626:863 truncations. 33631 vertices at 0 distance 101134 vertices at 1 distance 98667 vertices at 2 distance 43907 vertices at 3 distance 14649 vertices at 4 distance 4325 vertices at 5 distance 1268 vertices at 6 distance 396 vertices at 7 distance 157 vertices at 8 distance 92 vertices at 9 distance 56 vertices at 10 distance 42 vertices at 11 distance 27 vertices at 12 distance 27 vertices at 13 distance 8 vertices at 14 distance 12 vertices at 15 distance 16 vertices at 16 distance 12 vertices at 17 distance 5 vertices at 18 distance 7 vertices at 19 distance 12 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Han2/surf/lh.thickness positioning took 11.9 minutes #-------------------------------------------- #@# Surf Volume lh Fri Oct 13 01:09:56 EDT 2017 /usr/local/freesurfer/subjects/Han2/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Fri Oct 13 01:09:56 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts pctsurfcon --s Han2 --lh-only Log file is /usr/local/freesurfer/subjects/Han2/scripts/pctsurfcon.log Fri Oct 13 01:09:56 EDT 2017 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Han2/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.wm.mgh --regheader Han2 --cortex srcvol = /usr/local/freesurfer/subjects/Han2/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 /usr/local/freesurfer/subjects/Han2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/Han2/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/Han2/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 = 84674 Masking with /usr/local/freesurfer/subjects/Han2/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.wm.mgh Dim: 154676 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/Han2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.gm.mgh --projfrac 0.3 --regheader Han2 --cortex srcvol = /usr/local/freesurfer/subjects/Han2/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 /usr/local/freesurfer/subjects/Han2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/Han2/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/Han2/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/Han2/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 = 101382 Masking with /usr/local/freesurfer/subjects/Han2/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.gm.mgh Dim: 154676 1 1 mri_concat /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.wm.mgh /usr/local/freesurfer/subjects/Han2/surf/tmp.pctsurfcon.6148/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/Han2/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 /usr/local/freesurfer/subjects/Han2/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/Han2/surf/lh.w-g.pct.mgh --annot Han2 lh aparc --sum /usr/local/freesurfer/subjects/Han2/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /usr/local/freesurfer/subjects/Han2/surf/lh.w-g.pct.mgh --annot Han2 lh aparc --sum /usr/local/freesurfer/subjects/Han2/stats/lh.w-g.pct.stats --snr sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /usr/local/freesurfer/subjects/Han2/surf/lh.w-g.pct.mgh Vertex Area is 0.65967 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1743 1238.832 2 1002 caudalanteriorcingulate 1386 884.569 3 1003 caudalmiddlefrontal 3468 2316.776 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2495 1618.354 6 1006 entorhinal 530 369.717 7 1007 fusiform 5484 3637.042 8 1008 inferiorparietal 7839 5223.378 9 1009 inferiortemporal 6143 4064.670 10 1010 isthmuscingulate 1916 1208.557 11 1011 lateraloccipital 9298 6001.525 12 1012 lateralorbitofrontal 4761 3142.498 13 1013 lingual 4466 2868.841 14 1014 medialorbitofrontal 2828 1897.818 15 1015 middletemporal 5816 3916.452 16 1016 parahippocampal 1101 715.482 17 1017 paracentral 1692 1044.525 18 1018 parsopercularis 3151 2125.625 19 1019 parsorbitalis 951 616.591 20 1020 parstriangularis 2129 1404.580 21 1021 pericalcarine 2054 1394.068 22 1022 postcentral 7026 4561.418 23 1023 posteriorcingulate 2059 1377.927 24 1024 precentral 8356 5328.855 25 1025 precuneus 6718 4425.676 26 1026 rostralanteriorcingulate 1645 1102.453 27 1027 rostralmiddlefrontal 11440 7722.105 28 1028 superiorfrontal 11991 8047.325 29 1029 superiorparietal 8904 5815.742 30 1030 superiortemporal 6496 4327.211 31 1031 supramarginal 6628 4485.877 32 1032 frontalpole 355 229.176 33 1033 temporalpole 629 447.242 34 1034 transversetemporal 831 517.044 35 1035 insula 4430 2838.814 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Oct 13 01:10:04 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Han2 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/Han2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Han2/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Han2/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Han2/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1743 1239 3159 2.681 0.415 0.117 0.027 14 2.0 bankssts 1386 885 2572 2.658 0.767 0.135 0.043 21 2.3 caudalanteriorcingulate 3468 2317 6922 2.791 0.558 0.125 0.042 36 5.2 caudalmiddlefrontal 2495 1618 3119 1.832 0.369 0.152 0.056 41 5.3 cuneus 530 370 1572 3.449 0.756 0.134 0.044 6 1.0 entorhinal 5484 3637 11298 2.662 0.700 0.135 0.046 83 10.6 fusiform 7839 5223 14509 2.470 0.553 0.136 0.056 140 15.8 inferiorparietal 6143 4065 12643 2.818 0.678 0.144 0.056 135 14.0 inferiortemporal 1916 1209 2980 2.303 0.863 0.148 0.124 47 12.9 isthmuscingulate 9298 6002 15440 2.312 0.579 0.149 0.053 157 18.6 lateraloccipital 4761 3142 8988 2.678 0.715 0.148 0.067 115 12.9 lateralorbitofrontal 4466 2869 6675 2.210 0.648 0.157 0.066 85 12.2 lingual 2828 1898 4982 2.356 0.638 0.156 0.077 126 9.1 medialorbitofrontal 5816 3916 13932 2.952 0.696 0.137 0.049 103 11.4 middletemporal 1101 715 2492 3.030 0.738 0.132 0.133 66 6.7 parahippocampal 1692 1045 2920 2.489 0.562 0.133 0.881 737 4.8 paracentral 3151 2126 6840 2.879 0.529 0.133 0.047 49 6.1 parsopercularis 951 617 2327 2.900 0.542 0.163 0.065 23 2.2 parsorbitalis 2129 1405 3874 2.540 0.438 0.136 0.045 33 3.9 parstriangularis 2054 1394 2277 1.776 0.435 0.134 0.042 25 3.7 pericalcarine 7026 4561 11483 2.272 0.645 0.130 0.052 133 17.3 postcentral 2059 1378 3827 2.564 0.621 0.164 0.069 48 6.1 posteriorcingulate 8356 5329 16493 2.833 0.553 0.116 0.034 76 12.6 precentral 6718 4426 11368 2.384 0.519 0.133 0.047 96 13.0 precuneus 1645 1102 3781 2.970 0.667 0.164 0.083 39 5.1 rostralanteriorcingulate 11440 7722 21664 2.446 0.596 0.143 0.055 206 22.0 rostralmiddlefrontal 11991 8047 26754 2.866 0.565 0.132 0.056 246 27.3 superiorfrontal 8904 5816 14265 2.223 0.431 0.126 0.038 108 13.7 superiorparietal 6496 4327 15419 3.094 0.624 0.122 0.037 73 10.0 superiortemporal 6628 4486 13386 2.712 0.528 0.144 0.055 136 12.6 supramarginal 355 229 910 2.784 0.570 0.167 0.065 9 1.0 frontalpole 629 447 2350 3.818 0.843 0.214 0.267 240 3.3 temporalpole 831 517 1796 3.078 0.464 0.147 0.050 13 1.6 transversetemporal 4430 2839 8786 3.085 0.922 0.146 0.115 149 16.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Oct 13 01:10:19 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Han2 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 4 labels changed using aseg relabeling using gibbs priors... 000: 10379 changed, 154676 examined... 001: 2575 changed, 39732 examined... 002: 774 changed, 13206 examined... 003: 335 changed, 4329 examined... 004: 183 changed, 1880 examined... 005: 94 changed, 990 examined... 006: 61 changed, 513 examined... 007: 25 changed, 309 examined... 008: 12 changed, 143 examined... 009: 6 changed, 78 examined... 010: 8 changed, 35 examined... 011: 3 changed, 34 examined... 012: 0 changed, 13 examined... 1 labels changed using aseg 000: 328 total segments, 244 labels (2820 vertices) changed 001: 105 total segments, 22 labels (78 vertices) changed 002: 84 total segments, 1 labels (1 vertices) changed 003: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 159 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1398 vertices marked for relabeling... 1398 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 54 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Oct 13 01:11:13 EDT 2017 /usr/local/freesurfer/subjects/Han2/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Han2 lh white Segmentation fault (core dumped) Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s Han2 exited with ERRORS at Fri Oct 13 01:11:13 EDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting