Fri Jun 9 13:29:07 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz /home/brainmind-engineer/freesurfer/bin/recon-all -all -i MM_T1_BL.nii -s fsMM.nii.mgz subjid fsMM.nii.mgz setenv SUBJECTS_DIR /home/brainmind-engineer/freesurfer/subjects FREESURFER_HOME /home/brainmind-engineer/freesurfer Actual FREESURFER_HOME /home/brainmind-engineer/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 2061427 maxlocks unlimited maxsignal 2061427 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 264076400 19602704 244473696 6549544 586828 13977760 -/+ buffers/cache: 5038116 259038284 Swap: 268354556 0 268354556 ######################################## 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: 2017/06/09-03:29:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 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: 2017/06/09-03:29:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 $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: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 $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: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/06/09-03:29:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: brainmind-engineer Machine: brainmindengineer-Precision-Tower-7910 Platform: Linux PlatformVersion: 3.13.0-117-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/brainmind-engineer/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/brainmind-engineer/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz mri_convert /home/brainmind-engineer/DataAnalysis/MM_T1_BL.nii /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig/001.mgz mri_convert /home/brainmind-engineer/DataAnalysis/MM_T1_BL.nii /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/brainmind-engineer/DataAnalysis/MM_T1_BL.nii... TR=7.12, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999249, -0.0320883, -0.0216997) j_ras = (-0.0302638, 0.996356, -0.0797359) k_ras = (-0.0241792, 0.0790193, 0.99658) writing to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Jun 9 13:29:54 AEST 2017 Found 1 runs /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig/001.mgz /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz mri_convert /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz --conform mri_convert /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz... TR=7.12, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999249, -0.0320883, -0.0216997) j_ras = (-0.0302638, 0.996356, -0.0797359) k_ras = (-0.0241792, 0.0790193, 0.99658) Original Data has (0.4688, 0.4688, 0.700027) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz... mri_add_xform_to_header -c /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/talairach.xfm /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Jun 9 13:30:20 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 Fri Jun 9 13:31:28 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6576, pval=0.3663 >= threshold=0.0050) awk -f /home/brainmind-engineer/freesurfer/bin/extract_talairach_avi_QA.awk /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/talairach_avi.log tal_QC_AZS /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/talairach_avi.log TalAviQA: 0.97954 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Jun 9 13:31:28 AEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri /home/brainmind-engineer/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 brainmindengineer-Precision-Tower-7910 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Fri Jun 9 13:31:28 AEST 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.11712 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11712/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11712/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=7.12, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.00586e-09, 1.86265e-09) j_ras = (0, 7.45058e-09, -1) k_ras = (-3.49246e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.11712/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Jun 9 13:31:29 AEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.11712/nu0.mnc ./tmp.mri_nu_correct.mni.11712/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11712/0/ defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [brainmind-engineer@brainmindengineer-Precision-Tower-7910:/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/] [2017-06-09 13:31:29] running: /home/brainmind-engineer/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.11712/0/ ./tmp.mri_nu_correct.mni.11712/nu0.mnc ./tmp.mri_nu_correct.mni.11712/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.00096716 [brainmind-engineer@brainmindengineer-Precision-Tower-7910:/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/] [2017-06-09 13:31:46] running: /home/brainmind-engineer/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11712/nu0.mnc ./tmp.mri_nu_correct.mni.11712/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Jun 9 13:31:48 AEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.11712/nu1.mnc ./tmp.mri_nu_correct.mni.11712/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11712/1/ defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [brainmind-engineer@brainmindengineer-Precision-Tower-7910:/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/] [2017-06-09 13:31:48] running: /home/brainmind-engineer/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.11712/1/ ./tmp.mri_nu_correct.mni.11712/nu1.mnc ./tmp.mri_nu_correct.mni.11712/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /home/brainmind-engineer/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000995218 [brainmind-engineer@brainmindengineer-Precision-Tower-7910:/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/] [2017-06-09 13:31:57] running: /home/brainmind-engineer/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11712/nu1.mnc ./tmp.mri_nu_correct.mni.11712/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.11712/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11712/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.11712/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11712/ones.mgz sysname Linux hostname brainmindengineer-Precision-Tower-7910 machine x86_64 user brainmind-engineer input ./tmp.mri_nu_correct.mni.11712/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.11712/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.11712/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11712/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11712/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.11712/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11712/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11712/input.mean.dat sysname Linux hostname brainmindengineer-Precision-Tower-7910 machine x86_64 user brainmind-engineer UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11712/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.11712/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11712/ones.mgz --i ./tmp.mri_nu_correct.mni.11712/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11712/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11712/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.11712/ones.mgz --i ./tmp.mri_nu_correct.mni.11712/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11712/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11712/output.mean.dat sysname Linux hostname brainmindengineer-Precision-Tower-7910 machine x86_64 user brainmind-engineer UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11712/ones.mgz Loading ./tmp.mri_nu_correct.mni.11712/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.11712/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.11712/nu2.mnc ./tmp.mri_nu_correct.mni.11712/nu2.mnc mul .99044074173277525220 Saving result to './tmp.mri_nu_correct.mni.11712/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.11712/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11712/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.11712/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.00586e-09, 1.86265e-09) j_ras = (0, 7.45058e-09, -1) k_ras = (-3.49246e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. mapping (13, 101) to ( 3, 110) Fri Jun 9 13:32:29 AEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Jun 9 13:32:30 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.096 0.027 0.035 -1.990; -0.054 1.024 -0.005 -43.317; -0.025 0.045 1.149 -57.193; 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 = 13 Starting OpenSpline(): npoints = 13 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 103 gm peak at 70 (70), valley at 49 (49) 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 102 gm peak at 69 (69), valley at 48 (48) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 31 seconds. #-------------------------------------------- #@# Skull Stripping Fri Jun 9 13:34:01 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_em_register -skull nu.mgz /home/brainmind-engineer/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/brainmind-engineer/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=11.0 skull bounding box = (47, 52, 11) --> (205, 213, 217) using (100, 106, 114) as brain centroid... mean wm in atlas = 126, using box (81,86,89) --> (119, 125,139) to find MRI wm before smoothing, mri peak at 101 after smoothing, mri peak at 102, scaling input intensities by 1.235 scaling channel 0 by 1.23529 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.688576 @ (-9.091, -27.273, -9.091) max log p = -4.562162 @ (13.636, 13.636, 4.545) max log p = -4.510594 @ (-2.273, -2.273, 6.818) max log p = -4.466645 @ (-1.136, -5.682, -5.682) max log p = -4.466645 @ (0.000, 0.000, 0.000) max log p = -4.461531 @ (-1.420, -2.557, -0.852) Found translation: (-0.3, -24.1, -4.3): log p = -4.462 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.5 (thresh=-4.5) 1.150 0.000 0.000 -19.191; 0.000 1.236 0.000 -49.840; 0.000 0.000 1.236 -37.819; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.055 0.149 0.000 -27.812; -0.161 1.318 0.000 -33.250; 0.000 0.000 1.329 -41.108; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.055 0.149 0.000 -27.812; -0.161 1.318 0.000 -33.250; 0.000 0.000 1.329 -41.108; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.045 0.027 -0.016 -8.489; -0.059 1.298 0.079 -54.245; 0.011 -0.076 1.253 -24.256; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.028 -0.016 -11.006; -0.060 1.322 0.081 -59.408; 0.011 -0.076 1.253 -24.256; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.028 -0.016 -11.006; -0.060 1.322 0.081 -59.408; 0.011 -0.076 1.253 -24.256; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.063 0.028 -0.016 -11.315; -0.061 1.324 0.070 -58.082; 0.011 -0.065 1.251 -25.896; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.063 0.028 -0.016 -11.315; -0.061 1.324 0.070 -58.082; 0.011 -0.065 1.251 -25.896; 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 1.06309 0.02779 -0.01637 -11.31491; -0.06052 1.32414 0.07038 -58.08196; 0.01053 -0.06497 1.25068 -25.89571; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06309 0.02779 -0.01637 -11.31491; -0.06052 1.32414 0.07038 -58.08196; 0.01053 -0.06497 1.25068 -25.89571; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.063 0.028 -0.016 -11.315; -0.061 1.324 0.070 -58.082; 0.011 -0.065 1.251 -25.896; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.7) transform before final EM align: 1.063 0.028 -0.016 -11.315; -0.061 1.324 0.070 -58.082; 0.011 -0.065 1.251 -25.896; 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 1.06309 0.02779 -0.01637 -11.31491; -0.06052 1.32414 0.07038 -58.08196; 0.01053 -0.06497 1.25068 -25.89571; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06309 0.02779 -0.01637 -11.31491; -0.06052 1.32414 0.07038 -58.08196; 0.01053 -0.06497 1.25068 -25.89571; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.063 0.028 -0.016 -11.315; -0.061 1.324 0.070 -58.082; 0.011 -0.065 1.251 -25.896; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 22 minutes and 54 seconds. mri_watershed -T1 -brain_atlas /home/brainmind-engineer/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=123 y=133 z=112 r=68 first estimation of the main basin volume: 1371728 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=152, y=112, z=97, Imax=255 CSF=20, 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=16681876790 voxels, voxel volume =1.000 = 16681876790 mmm3 = 16681876.480 cm3 done. PostAnalyze...Basin Prior 154 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=126,y=134, z=107, r=10164 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=4, CSF_MAX=15 , nb = 45656 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=19 , nb = -1085168666 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=22 , nb = 1099968211 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=15 , nb = -1104011280 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=15 , nb = 1076262616 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1071636422 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 15, 23, 40, 61 after analyzing : 15, 34, 40, 40 RIGHT_CER before analyzing : 19, 27, 40, 64 after analyzing : 19, 35, 40, 42 LEFT_CER before analyzing : 22, 20, 18, 60 after analyzing : 20, 23, 25, 32 RIGHT_BRAIN before analyzing : 15, 24, 41, 59 after analyzing : 15, 35, 41, 41 LEFT_BRAIN before analyzing : 15, 23, 40, 62 after analyzing : 15, 34, 40, 41 OTHER before analyzing : 24, 68, 86, 95 after analyzing : 24, 80, 86, 83 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...60 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 69.281, std = 7.689 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.13, sigma = 5.76 after rotation: sse = 4.13, sigma = 5.76 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.57, its var is 6.11 before Erosion-Dilatation 1.69% of inacurate vertices after Erosion-Dilatation 1.66% 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...36 iterations mri_strip_skull: done peeling brain Brain Size = 1572747 voxels, voxel volume = 1.000 mm3 = 1572747 mmm3 = 1572.747 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Jun 9 13:57:11 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/brainmind-engineer/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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 '/home/brainmind-engineer/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 = (61, 73, 23) --> (189, 190, 198) using (104, 112, 111) as brain centroid... mean wm in atlas = 107, using box (88,98,89) --> (119, 126,132) to find MRI wm before smoothing, mri peak at 103 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.220981 @ (-9.091, -9.091, 9.091) max log p = -3.983684 @ (4.545, -4.545, -13.636) max log p = -3.915291 @ (2.273, -6.818, 2.273) max log p = -3.905760 @ (1.136, -1.136, 1.136) max log p = -3.905760 @ (0.000, 0.000, 0.000) max log p = -3.905760 @ (0.000, 0.000, 0.000) Found translation: (-1.1, -21.6, -1.1): log p = -3.906 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.9 (thresh=-3.9) 1.064 0.000 0.000 -9.293; 0.000 1.150 0.000 -35.159; 0.000 0.000 1.000 -1.136; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.064 0.000 0.000 -9.293; 0.000 1.150 0.000 -35.159; 0.000 0.000 1.000 -1.136; 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=-3.5, old_max_log_p =-3.6 (thresh=-3.6) 1.103 0.039 -0.005 -18.975; -0.037 1.213 -0.065 -30.094; -0.002 0.071 1.017 -14.073; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.080 0.077 -0.007 -20.947; -0.073 1.211 -0.064 -25.244; -0.003 0.073 1.036 -16.312; 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=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.078 0.055 -0.022 -16.069; -0.055 1.208 -0.091 -24.783; 0.014 0.105 1.038 -21.854; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.075 0.055 -0.022 -15.735; -0.055 1.208 -0.091 -24.783; 0.014 0.105 1.038 -21.854; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.075 0.055 -0.022 -15.735; -0.055 1.208 -0.091 -24.783; 0.014 0.105 1.038 -21.854; 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 1.07508 0.05535 -0.02218 -15.73462; -0.05513 1.20809 -0.09072 -24.78301; 0.01374 0.10473 1.03753 -21.85367; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.07508 0.05535 -0.02218 -15.73462; -0.05513 1.20809 -0.09072 -24.78301; 0.01374 0.10473 1.03753 -21.85367; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.075 0.055 -0.022 -15.735; -0.055 1.208 -0.091 -24.783; 0.014 0.105 1.038 -21.854; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.4 (old=-4.2) transform before final EM align: 1.075 0.055 -0.022 -15.735; -0.055 1.208 -0.091 -24.783; 0.014 0.105 1.038 -21.854; 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 1.07508 0.05535 -0.02218 -15.73462; -0.05513 1.20809 -0.09072 -24.78301; 0.01374 0.10473 1.03753 -21.85367; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.07508 0.05535 -0.02218 -15.73462; -0.05513 1.20809 -0.09072 -24.78301; 0.01374 0.10473 1.03753 -21.85367; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.06, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 011: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 012: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 013: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 014: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 015: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 016: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) dfp_em_step_func: 017: -log(p) = 3.9 after pass:transform: ( 1.08, 0.06, -0.02, -15.73) ( -0.05, 1.21, -0.09, -24.78) ( 0.01, 0.10, 1.04, -21.85) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 019: -log(p) = 3.9 tol 0.000000 final transform: 1.076 0.056 -0.022 -15.735; -0.055 1.208 -0.090 -24.783; 0.014 0.105 1.037 -21.854; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 15 minutes and 28 seconds. #-------------------------------------- #@# CA Normalize Fri Jun 9 14:12:39 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/brainmind-engineer/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 '/home/brainmind-engineer/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 = (61, 73, 23) --> (189, 190, 198) using (104, 112, 111) as brain centroid... mean wm in atlas = 107, using box (88,98,89) --> (119, 126,132) to find MRI wm before smoothing, mri peak at 103 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 244171 sample points... INFO: compute sample coordinates transform 1.076 0.056 -0.022 -15.735; -0.055 1.208 -0.090 -24.783; 0.014 0.105 1.037 -21.854; 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 (123, 77, 30) --> (188, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 106.0 --> 255.0 1 of 15 (6.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 76, 31) --> (128, 175, 193) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 255.0 0 of 13 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 143, 48) --> (171, 181, 101) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 255.0 0 of 19 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 143, 47) --> (126, 179, 102) Right_Cerebellum_White_Matter: limiting intensities to 116.0 --> 255.0 1 of 10 (10.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 79) --> (141, 196, 113) Brain_Stem: limiting intensities to 111.0 --> 255.0 1 of 8 (12.5%) samples deleted using 65 total control points for intensity normalization... bias field = 0.858 +- 0.112 0 of 62 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 77, 30) --> (188, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 218.0 26 of 78 (33.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 76, 31) --> (128, 175, 193) Right_Cerebral_White_Matter: limiting intensities to 85.0 --> 218.0 0 of 95 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 143, 48) --> (171, 181, 101) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 218.0 0 of 21 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 143, 47) --> (126, 179, 102) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 218.0 0 of 54 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 79) --> (141, 196, 113) Brain_Stem: limiting intensities to 89.0 --> 218.0 7 of 49 (14.3%) samples deleted using 297 total control points for intensity normalization... bias field = 0.982 +- 0.089 0 of 264 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 77, 30) --> (188, 178, 192) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 212.0 0 of 176 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 76, 31) --> (128, 175, 193) Right_Cerebral_White_Matter: limiting intensities to 87.0 --> 212.0 0 of 179 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (127, 143, 48) --> (171, 181, 101) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 212.0 0 of 26 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 143, 47) --> (126, 179, 102) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 212.0 0 of 57 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 141, 79) --> (141, 196, 113) Brain_Stem: limiting intensities to 96.0 --> 212.0 30 of 67 (44.8%) samples deleted using 505 total control points for intensity normalization... bias field = 0.997 +- 0.060 0 of 475 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 10 seconds. #-------------------------------------- #@# CA Reg Fri Jun 9 14:13:49 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/brainmind-engineer/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 ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/home/brainmind-engineer/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.36 (predicted orig area = 5.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.764, neg=0, invalid=96777 0001: dt=129.472000, rms=0.716 (6.292%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.701 (2.038%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.692 (1.361%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.689 (0.416%), neg=0, invalid=96777 0005: dt=295.936000, rms=0.682 (1.020%), neg=0, invalid=96777 0006: dt=73.984000, rms=0.679 (0.478%), neg=0, invalid=96777 0007: dt=517.888000, rms=0.672 (1.041%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.670 (0.201%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.670 (0.076%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.670 (0.046%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.669 (0.018%), neg=0, invalid=96777 0012: dt=221.952000, rms=0.667 (0.330%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.667 (0.059%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.667 (0.043%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.666 (0.049%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.666 (0.066%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.665 (0.104%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.664 (0.144%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.663 (0.184%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.662 (0.193%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.660 (0.179%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.659 (0.167%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.658 (0.168%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.657 (0.159%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.656 (0.153%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.655 (0.142%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.654 (0.137%), neg=0, invalid=96777 0028: dt=32.368000, rms=0.653 (0.137%), neg=0, invalid=96777 0029: dt=32.368000, rms=0.653 (0.127%), neg=0, invalid=96777 0030: dt=32.368000, rms=0.652 (0.114%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.651 (0.107%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.651 (0.016%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.651 (0.056%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.650 (0.063%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.650 (0.071%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.649 (0.123%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.648 (0.141%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.647 (0.151%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.646 (0.114%), neg=0, invalid=96777 0040: dt=129.472000, rms=0.645 (0.212%), neg=0, invalid=96777 0041: dt=129.472000, rms=0.644 (0.145%), neg=0, invalid=96777 0042: dt=129.472000, rms=0.643 (0.127%), neg=0, invalid=96777 0043: dt=129.472000, rms=0.643 (0.079%), neg=0, invalid=96777 0044: dt=129.472000, rms=0.642 (0.174%), neg=0, invalid=96777 0045: dt=129.472000, rms=0.641 (0.128%), neg=0, invalid=96777 0046: dt=129.472000, rms=0.640 (0.098%), neg=0, invalid=96777 0047: dt=129.472000, rms=0.639 (0.119%), neg=0, invalid=96777 0048: dt=129.472000, rms=0.639 (0.141%), neg=0, invalid=96777 0049: dt=129.472000, rms=0.638 (0.087%), neg=0, invalid=96777 0050: dt=129.472000, rms=0.637 (0.081%), neg=0, invalid=96777 0051: dt=129.472000, rms=0.637 (0.059%), neg=0, invalid=96777 0052: dt=129.472000, rms=0.637 (0.002%), neg=0, invalid=96777 0053: dt=129.472000, rms=0.637 (0.018%), neg=0, invalid=96777 0054: dt=129.472000, rms=0.637 (0.033%), neg=0, invalid=96777 0055: dt=129.472000, rms=0.637 (0.012%), neg=0, invalid=96777 0056: dt=129.472000, rms=0.637 (0.023%), neg=0, invalid=96777 0057: dt=129.472000, rms=0.636 (0.049%), neg=0, invalid=96777 0058: dt=129.472000, rms=0.636 (0.050%), neg=0, invalid=96777 0059: dt=129.472000, rms=0.636 (0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.636, neg=0, invalid=96777 0060: dt=129.472000, rms=0.635 (0.067%), neg=0, invalid=96777 0061: dt=73.984000, rms=0.635 (0.007%), neg=0, invalid=96777 0062: dt=73.984000, rms=0.635 (0.028%), neg=0, invalid=96777 0063: dt=73.984000, rms=0.635 (0.027%), neg=0, invalid=96777 0064: dt=73.984000, rms=0.635 (0.028%), neg=0, invalid=96777 0065: dt=73.984000, rms=0.634 (0.026%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.639, neg=0, invalid=96777 0066: dt=145.152000, rms=0.632 (1.043%), neg=0, invalid=96777 0067: dt=82.944000, rms=0.625 (1.145%), neg=0, invalid=96777 0068: dt=31.104000, rms=0.624 (0.241%), neg=0, invalid=96777 0069: dt=31.104000, rms=0.622 (0.312%), neg=0, invalid=96777 0070: dt=31.104000, rms=0.619 (0.410%), neg=0, invalid=96777 0071: dt=31.104000, rms=0.616 (0.482%), neg=0, invalid=96777 0072: dt=31.104000, rms=0.613 (0.528%), neg=0, invalid=96777 0073: dt=31.104000, rms=0.610 (0.554%), neg=0, invalid=96777 0074: dt=31.104000, rms=0.606 (0.601%), neg=0, invalid=96777 0075: dt=31.104000, rms=0.603 (0.548%), neg=0, invalid=96777 0076: dt=31.104000, rms=0.600 (0.474%), neg=0, invalid=96777 0077: dt=31.104000, rms=0.597 (0.407%), neg=0, invalid=96777 0078: dt=31.104000, rms=0.595 (0.386%), neg=0, invalid=96777 0079: dt=31.104000, rms=0.593 (0.375%), neg=0, invalid=96777 0080: dt=31.104000, rms=0.591 (0.286%), neg=0, invalid=96777 0081: dt=31.104000, rms=0.590 (0.259%), neg=0, invalid=96777 0082: dt=31.104000, rms=0.588 (0.256%), neg=0, invalid=96777 0083: dt=31.104000, rms=0.587 (0.209%), neg=0, invalid=96777 0084: dt=31.104000, rms=0.586 (0.173%), neg=0, invalid=96777 0085: dt=31.104000, rms=0.585 (0.127%), neg=0, invalid=96777 0086: dt=31.104000, rms=0.584 (0.110%), neg=0, invalid=96777 0087: dt=31.104000, rms=0.584 (0.116%), neg=0, invalid=96777 0088: dt=31.104000, rms=0.583 (0.131%), neg=0, invalid=96777 0089: dt=31.104000, rms=0.582 (0.087%), neg=0, invalid=96777 0090: dt=31.104000, rms=0.582 (0.084%), neg=0, invalid=96777 0091: dt=36.288000, rms=0.582 (0.067%), neg=0, invalid=96777 0092: dt=36.288000, rms=0.581 (0.040%), neg=0, invalid=96777 0093: dt=36.288000, rms=0.581 (0.046%), neg=0, invalid=96777 0094: dt=36.288000, rms=0.581 (0.056%), neg=0, invalid=96777 0095: dt=36.288000, rms=0.581 (0.045%), neg=0, invalid=96777 0096: dt=36.288000, rms=0.580 (0.072%), neg=0, invalid=96777 0097: dt=36.288000, rms=0.580 (0.054%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.580, neg=0, invalid=96777 0098: dt=82.944000, rms=0.579 (0.119%), neg=0, invalid=96777 0099: dt=62.208000, rms=0.579 (0.082%), neg=0, invalid=96777 0100: dt=62.208000, rms=0.579 (-0.012%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=96777 0101: dt=5.849462, rms=0.600 (0.071%), neg=0, invalid=96777 0102: dt=2.400000, rms=0.600 (0.007%), neg=0, invalid=96777 0103: dt=2.400000, rms=0.600 (0.001%), neg=0, invalid=96777 0104: dt=2.400000, rms=0.600 (-0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0105: dt=0.500000, rms=0.600 (0.000%), neg=0, invalid=96777 0106: dt=0.175000, rms=0.600 (0.001%), neg=0, invalid=96777 0107: dt=0.001953, rms=0.600 (-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=0.657, neg=0, invalid=96777 0108: dt=5.234646, rms=0.640 (2.544%), neg=0, invalid=96777 0109: dt=2.880000, rms=0.640 (0.124%), neg=0, invalid=96777 0110: dt=2.880000, rms=0.640 (-0.036%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0111: dt=0.000000, rms=0.640 (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=0.693, neg=0, invalid=96777 0112: dt=1.024000, rms=0.690 (0.458%), neg=0, invalid=96777 0113: dt=2.167785, rms=0.684 (0.782%), neg=0, invalid=96777 0114: dt=0.448000, rms=0.684 (0.060%), neg=0, invalid=96777 0115: dt=0.448000, rms=0.684 (0.041%), neg=0, invalid=96777 0116: dt=0.448000, rms=0.683 (0.058%), neg=0, invalid=96777 0117: dt=0.448000, rms=0.683 (0.037%), neg=0, invalid=96777 0118: dt=0.448000, rms=0.683 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=96777 0119: dt=1.792000, rms=0.681 (0.334%), neg=0, invalid=96777 0120: dt=0.000000, rms=0.681 (0.002%), neg=0, invalid=96777 0121: dt=0.100000, rms=0.681 (-0.003%), 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=0.648, neg=0, invalid=96777 0122: dt=0.146619, rms=0.642 (0.938%), neg=0, invalid=96777 0123: dt=0.016000, rms=0.642 (0.002%), neg=0, invalid=96777 0124: dt=0.016000, rms=0.642 (0.003%), neg=0, invalid=96777 0125: dt=0.016000, rms=0.642 (0.009%), neg=0, invalid=96777 0126: dt=0.016000, rms=0.642 (0.012%), neg=0, invalid=96777 0127: dt=0.016000, rms=0.642 (0.026%), neg=0, invalid=96777 0128: dt=0.016000, rms=0.642 (0.040%), neg=0, invalid=96777 0129: dt=0.016000, rms=0.641 (0.059%), neg=0, invalid=96777 0130: dt=0.016000, rms=0.641 (0.079%), neg=0, invalid=96777 0131: dt=0.016000, rms=0.640 (0.094%), neg=0, invalid=96777 0132: dt=0.016000, rms=0.640 (0.106%), neg=0, invalid=96777 0133: dt=0.016000, rms=0.639 (0.107%), neg=0, invalid=96777 0134: dt=0.016000, rms=0.638 (0.102%), neg=0, invalid=96777 0135: dt=0.016000, rms=0.638 (0.092%), neg=0, invalid=96777 0136: dt=0.000000, rms=0.638 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=96777 0137: dt=0.320000, rms=0.634 (0.644%), neg=0, invalid=96777 0138: dt=0.000000, rms=0.634 (-0.001%), neg=0, invalid=96777 0139: dt=0.012500, rms=0.634 (-0.038%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09780 (26) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (1145 voxels, overlap=0.701) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (1145 voxels, peak = 21), gca=21.0 gca peak = 0.14022 (22) mri peak = 0.11546 (24) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (540 voxels, overlap=0.879) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (540 voxels, peak = 23), gca=22.5 gca peak = 0.24234 (100) mri peak = 0.08929 (102) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (277 voxels, overlap=0.819) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (277 voxels, peak = 104), gca=103.5 gca peak = 0.19192 (97) mri peak = 0.06682 (89) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (223 voxels, overlap=0.255) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (223 voxels, peak = 88), gca=87.8 gca peak = 0.24007 (63) mri peak = 0.07084 (76) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (604 voxels, overlap=0.072) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (604 voxels, peak = 75), gca=74.7 gca peak = 0.29892 (64) mri peak = 0.08651 (75) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (484 voxels, overlap=0.445) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (484 voxels, peak = 71), gca=71.4 gca peak = 0.12541 (104) mri peak = 0.05915 (111) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (52901 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (52901 voxels, peak = 111), gca=110.8 gca peak = 0.13686 (104) mri peak = 0.06491 (106) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (52128 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (52128 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.04606 (63) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17126 voxels, overlap=0.993) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17126 voxels, peak = 63), gca=63.0 gca peak = 0.13270 (63) mri peak = 0.04186 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (18284 voxels, overlap=0.994) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (18284 voxels, peak = 65), gca=64.6 gca peak = 0.15182 (70) mri peak = 0.08197 (84) Right_Caudate (50): linear fit = 1.12 x + 0.0 (511 voxels, overlap=0.320) Right_Caudate (50): linear fit = 1.12 x + 0.0 (511 voxels, peak = 79), gca=78.8 gca peak = 0.14251 (76) mri peak = 0.07452 (86) Left_Caudate (11): linear fit = 1.09 x + 0.0 (700 voxels, overlap=0.678) Left_Caudate (11): linear fit = 1.09 x + 0.0 (700 voxels, peak = 82), gca=82.5 gca peak = 0.12116 (60) mri peak = 0.03964 (68) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (11196 voxels, overlap=0.712) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (11196 voxels, peak = 66), gca=66.3 gca peak = 0.12723 (61) mri peak = 0.05282 (65) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (14856 voxels, overlap=0.810) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (14856 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.06522 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6978 voxels, overlap=0.477) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6978 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.07881 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6952 voxels, overlap=0.508) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6952 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.08362 (70) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (283 voxels, overlap=0.205) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (283 voxels, peak = 69), gca=68.5 gca peak = 0.39668 (62) mri peak = 0.11930 (73) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (280 voxels, overlap=0.232) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (280 voxels, peak = 72), gca=71.6 gca peak = 0.10129 (93) mri peak = 0.04986 (104) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (3926 voxels, overlap=0.415) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (3926 voxels, peak = 105), gca=104.6 gca peak = 0.12071 (89) mri peak = 0.05493 (98) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3199 voxels, overlap=0.557) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3199 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.05740 (90) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1681 voxels, overlap=0.877) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1681 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.05349 (87) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1618 voxels, overlap=0.793) Right_Putamen (51): linear fit = 1.07 x + 0.0 (1618 voxels, peak = 89), gca=89.5 gca peak = 0.08983 (85) mri peak = 0.05538 (88) Brain_Stem (16): linear fit = 1.09 x + 0.0 (9374 voxels, overlap=0.667) Brain_Stem (16): linear fit = 1.09 x + 0.0 (9374 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.08689 (103) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (820 voxels, overlap=0.021) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (820 voxels, peak = 103), gca=102.6 gca peak = 0.12914 (94) mri peak = 0.08874 (106) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (901 voxels, overlap=0.243) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (901 voxels, peak = 105), gca=104.8 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.10903 (26) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (259 voxels, overlap=0.864) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (259 voxels, peak = 25), gca=25.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) 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 1.10 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.94 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=0.663, neg=0, invalid=96777 0140: dt=92.480000, rms=0.657 (0.891%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.656 (0.112%), neg=0, invalid=96777 0142: dt=8.092000, rms=0.656 (0.025%), neg=0, invalid=96777 0143: dt=4.046000, rms=0.656 (0.012%), neg=0, invalid=96777 0144: dt=0.505750, rms=0.656 (0.002%), neg=0, invalid=96777 0145: dt=0.126438, rms=0.656 (0.000%), neg=0, invalid=96777 0146: dt=0.031609, rms=0.656 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0147: dt=0.031609, rms=0.656 (0.000%), neg=0, invalid=96777 0148: dt=0.017340, rms=0.656 (0.000%), neg=0, invalid=96777 0149: dt=0.002168, rms=0.656 (0.000%), neg=0, invalid=96777 0150: dt=0.000034, rms=0.656 (0.000%), neg=0, invalid=96777 0151: dt=0.000017, rms=0.656 (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=0.656, neg=0, invalid=96777 0152: dt=0.000000, rms=0.656 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0153: dt=0.000000, rms=0.656 (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=0.656, neg=0, invalid=96777 0154: dt=0.000000, rms=0.656 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0155: dt=0.000000, rms=0.656 (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=0.656, neg=0, invalid=96777 0156: dt=1.008000, rms=0.649 (1.120%), neg=0, invalid=96777 0157: dt=1.008000, rms=0.642 (1.046%), neg=0, invalid=96777 0158: dt=1.008000, rms=0.636 (0.978%), neg=0, invalid=96777 0159: dt=1.008000, rms=0.630 (0.915%), neg=0, invalid=96777 0160: dt=1.008000, rms=0.625 (0.854%), neg=0, invalid=96777 0161: dt=1.008000, rms=0.620 (0.796%), neg=0, invalid=96777 0162: dt=4.032000, rms=0.602 (2.874%), neg=0, invalid=96777 0163: dt=4.032000, rms=0.589 (2.138%), neg=0, invalid=96777 0164: dt=4.032000, rms=0.579 (1.633%), neg=0, invalid=96777 0165: dt=4.032000, rms=0.572 (1.280%), neg=0, invalid=96777 0166: dt=11.520000, rms=0.556 (2.799%), neg=0, invalid=96777 0167: dt=4.032000, rms=0.553 (0.439%), neg=0, invalid=96777 0168: dt=4.032000, rms=0.551 (0.377%), neg=0, invalid=96777 0169: dt=13.824000, rms=0.545 (1.094%), neg=0, invalid=96777 0170: dt=4.032000, rms=0.544 (0.167%), neg=0, invalid=96777 0171: dt=4.032000, rms=0.544 (0.158%), neg=0, invalid=96777 0172: dt=13.824000, rms=0.541 (0.469%), neg=0, invalid=96777 0173: dt=4.032000, rms=0.541 (0.097%), neg=0, invalid=96777 0174: dt=4.032000, rms=0.540 (0.087%), neg=0, invalid=96777 0175: dt=4.032000, rms=0.540 (0.088%), neg=0, invalid=96777 0176: dt=4.032000, rms=0.539 (0.072%), neg=0, invalid=96777 0177: dt=16.128000, rms=0.538 (0.269%), neg=0, invalid=96777 0178: dt=1.008000, rms=0.538 (0.008%), neg=0, invalid=96777 0179: dt=1.008000, rms=0.538 (0.021%), neg=0, invalid=96777 0180: dt=1.008000, rms=0.537 (0.028%), neg=0, invalid=96777 0181: dt=1.008000, rms=0.537 (0.036%), neg=0, invalid=96777 0182: dt=1.008000, rms=0.537 (0.043%), neg=0, invalid=96777 0183: dt=1.008000, rms=0.537 (0.049%), neg=0, invalid=96777 0184: dt=1.008000, rms=0.536 (0.058%), neg=0, invalid=96777 0185: dt=1.008000, rms=0.536 (0.060%), neg=0, invalid=96777 0186: dt=1.008000, rms=0.536 (0.060%), neg=0, invalid=96777 0187: dt=1.008000, rms=0.535 (0.064%), neg=0, invalid=96777 0188: dt=0.252000, rms=0.535 (-0.002%), neg=0, invalid=96777 0189: dt=0.252000, rms=0.535 (0.002%), neg=0, invalid=96777 0190: dt=0.252000, rms=0.535 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=96777 0191: dt=6.153846, rms=0.535 (0.110%), neg=0, invalid=96777 0192: dt=4.032000, rms=0.535 (0.032%), neg=0, invalid=96777 0193: dt=2.016000, rms=0.535 (0.012%), neg=0, invalid=96777 0194: dt=2.016000, rms=0.535 (0.021%), neg=0, invalid=96777 0195: dt=2.016000, rms=0.534 (0.014%), neg=0, invalid=96777 0196: dt=2.016000, rms=0.534 (0.015%), neg=0, invalid=96777 0197: dt=2.016000, rms=0.534 (0.000%), neg=0, invalid=96777 0198: dt=4.032000, rms=0.534 (0.043%), neg=0, invalid=96777 0199: dt=16.128000, rms=0.533 (0.142%), neg=0, invalid=96777 0200: dt=4.032000, rms=0.533 (0.036%), neg=0, invalid=96777 0201: dt=4.032000, rms=0.533 (0.043%), neg=0, invalid=96777 0202: dt=4.032000, rms=0.533 (0.061%), neg=0, invalid=96777 0203: dt=4.032000, rms=0.532 (0.085%), neg=0, invalid=96777 0204: dt=4.032000, rms=0.532 (0.039%), neg=0, invalid=96777 0205: dt=4.032000, rms=0.532 (0.050%), neg=0, invalid=96777 0206: dt=2.016000, rms=0.532 (0.014%), neg=0, invalid=96777 0207: dt=2.016000, rms=0.532 (0.017%), neg=0, invalid=96777 0208: dt=2.016000, rms=0.531 (0.024%), neg=0, invalid=96777 0209: dt=2.016000, rms=0.531 (0.036%), neg=0, invalid=96777 0210: dt=2.016000, rms=0.531 (0.038%), neg=0, invalid=96777 0211: dt=2.016000, rms=0.531 (0.044%), neg=0, invalid=96777 0212: dt=2.016000, rms=0.531 (0.010%), neg=0, invalid=96777 0213: dt=2.016000, rms=0.531 (0.019%), neg=0, invalid=96777 0214: dt=2.016000, rms=0.530 (0.027%), neg=0, invalid=96777 0215: dt=2.016000, rms=0.530 (0.033%), neg=0, invalid=96777 0216: dt=2.016000, rms=0.530 (0.042%), neg=0, invalid=96777 0217: dt=2.016000, rms=0.530 (0.043%), neg=0, invalid=96777 0218: dt=2.016000, rms=0.530 (0.048%), neg=0, invalid=96777 0219: dt=2.016000, rms=0.529 (0.048%), neg=0, invalid=96777 0220: dt=2.016000, rms=0.529 (0.054%), neg=0, invalid=96777 0221: dt=2.016000, rms=0.529 (0.008%), neg=0, invalid=96777 0222: dt=2.016000, rms=0.529 (0.017%), neg=0, invalid=96777 0223: dt=2.016000, rms=0.529 (0.004%), neg=0, invalid=96777 0224: dt=16.128000, rms=0.529 (0.048%), neg=0, invalid=96777 0225: dt=4.032000, rms=0.529 (0.010%), neg=0, invalid=96777 0226: dt=4.032000, rms=0.529 (0.018%), neg=0, invalid=96777 0227: dt=4.032000, rms=0.528 (0.026%), neg=0, invalid=96777 0228: dt=4.032000, rms=0.528 (0.011%), neg=0, invalid=96777 0229: dt=4.032000, rms=0.528 (0.020%), neg=0, invalid=96777 0230: dt=4.032000, rms=0.528 (0.028%), neg=0, invalid=96777 0231: dt=4.032000, rms=0.528 (0.044%), neg=0, invalid=96777 0232: dt=2.016000, rms=0.528 (0.004%), neg=0, invalid=96777 0233: dt=2.016000, rms=0.528 (0.006%), neg=0, invalid=96777 0234: dt=2.016000, rms=0.528 (0.013%), neg=0, invalid=96777 0235: dt=2.016000, rms=0.528 (0.012%), neg=0, invalid=96777 0236: dt=4.032000, rms=0.528 (0.010%), neg=0, invalid=96777 0237: dt=4.032000, rms=0.528 (0.009%), neg=0, invalid=96777 0238: dt=4.032000, rms=0.527 (0.019%), neg=0, invalid=96777 0239: dt=4.032000, rms=0.527 (0.027%), neg=0, invalid=96777 0240: dt=4.032000, rms=0.527 (0.032%), neg=0, invalid=96777 0241: dt=4.032000, rms=0.527 (0.038%), neg=0, invalid=96777 0242: dt=4.032000, rms=0.527 (0.041%), neg=0, invalid=96777 0243: dt=4.032000, rms=0.526 (0.044%), neg=0, invalid=96777 0244: dt=4.032000, rms=0.526 (0.056%), neg=0, invalid=96777 0245: dt=4.032000, rms=0.526 (0.053%), neg=0, invalid=96777 0246: dt=4.032000, rms=0.526 (0.053%), neg=0, invalid=96777 0247: dt=4.032000, rms=0.526 (0.003%), neg=0, invalid=96777 0248: dt=4.032000, rms=0.526 (0.016%), neg=0, invalid=96777 0249: dt=4.032000, rms=0.525 (0.014%), neg=0, invalid=96777 0250: dt=16.128000, rms=0.525 (0.023%), neg=0, invalid=96777 0251: dt=3.456000, rms=0.525 (0.002%), neg=0, invalid=96777 0252: dt=3.456000, rms=0.525 (0.010%), neg=0, invalid=96777 0253: dt=3.456000, rms=0.525 (0.003%), neg=0, invalid=96777 0254: dt=3.456000, rms=0.525 (0.010%), neg=0, invalid=96777 0255: dt=3.456000, rms=0.525 (0.013%), neg=0, invalid=96777 0256: dt=1.728000, rms=0.525 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.539, neg=0, invalid=96777 0257: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=96777 0258: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=96777 0259: dt=0.000000, rms=0.539 (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=0.516, neg=0, invalid=96777 0260: dt=0.080000, rms=0.513 (0.541%), neg=0, invalid=96777 0261: dt=0.007000, rms=0.513 (0.043%), neg=0, invalid=96777 0262: dt=0.007000, rms=0.513 (0.039%), neg=0, invalid=96777 0263: dt=0.007000, rms=0.512 (0.073%), neg=0, invalid=96777 0264: dt=0.007000, rms=0.512 (0.105%), neg=0, invalid=96777 0265: dt=0.007000, rms=0.511 (0.131%), neg=0, invalid=96777 0266: dt=0.007000, rms=0.510 (0.153%), neg=0, invalid=96777 0267: dt=0.007000, rms=0.509 (0.170%), neg=0, invalid=96777 0268: dt=0.007000, rms=0.508 (0.184%), neg=0, invalid=96777 0269: dt=0.007000, rms=0.508 (0.029%), neg=0, invalid=96777 0270: dt=0.007000, rms=0.508 (0.054%), neg=0, invalid=96777 0271: dt=0.007000, rms=0.508 (0.076%), neg=0, invalid=96777 0272: dt=0.007000, rms=0.507 (0.094%), neg=0, invalid=96777 0273: dt=0.007000, rms=0.507 (0.108%), neg=0, invalid=96777 0274: dt=0.007000, rms=0.506 (0.122%), neg=0, invalid=96777 0275: dt=0.007000, rms=0.505 (0.132%), neg=0, invalid=96777 0276: dt=0.007000, rms=0.505 (0.139%), neg=0, invalid=96777 0277: dt=0.007000, rms=0.504 (0.143%), neg=0, invalid=96777 0278: dt=0.007000, rms=0.503 (0.146%), neg=0, invalid=96777 0279: dt=0.007000, rms=0.502 (0.144%), neg=0, invalid=96777 0280: dt=0.007000, rms=0.502 (0.145%), neg=0, invalid=96777 0281: dt=0.007000, rms=0.501 (0.143%), neg=0, invalid=96777 0282: dt=0.007000, rms=0.500 (0.136%), neg=0, invalid=96777 0283: dt=0.007000, rms=0.500 (0.132%), neg=0, invalid=96777 0284: dt=0.007000, rms=0.499 (0.126%), neg=0, invalid=96777 0285: dt=0.007000, rms=0.498 (0.119%), neg=0, invalid=96777 0286: dt=0.007000, rms=0.498 (0.112%), neg=0, invalid=96777 0287: dt=0.007000, rms=0.497 (0.102%), neg=0, invalid=96777 0288: dt=0.007000, rms=0.497 (0.096%), neg=0, invalid=96777 0289: dt=0.007000, rms=0.496 (0.088%), neg=0, invalid=96777 0290: dt=0.007000, rms=0.496 (0.080%), neg=0, invalid=96777 0291: dt=0.007000, rms=0.496 (0.071%), neg=0, invalid=96777 0292: dt=0.007000, rms=0.495 (0.065%), neg=0, invalid=96777 0293: dt=0.007000, rms=0.495 (0.056%), neg=0, invalid=96777 0294: dt=0.007000, rms=0.495 (0.050%), neg=0, invalid=96777 0295: dt=0.007000, rms=0.495 (0.043%), neg=0, invalid=96777 0296: dt=0.007000, rms=0.494 (0.038%), neg=0, invalid=96777 0297: dt=0.007000, rms=0.494 (0.032%), neg=0, invalid=96777 0298: dt=0.007000, rms=0.494 (0.027%), neg=0, invalid=96777 0299: dt=0.007000, rms=0.494 (0.021%), neg=0, invalid=96777 0300: dt=0.007000, rms=0.494 (-0.001%), neg=0, invalid=96777 0301: dt=0.000000, rms=0.494 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.494, neg=0, invalid=96777 0302: dt=0.320000, rms=0.490 (0.897%), neg=0, invalid=96777 0303: dt=0.112000, rms=0.489 (0.106%), neg=0, invalid=96777 0304: dt=0.006000, rms=0.489 (0.005%), neg=0, invalid=96777 0305: dt=0.006000, rms=0.489 (0.006%), neg=0, invalid=96777 0306: dt=0.006000, rms=0.489 (0.007%), neg=0, invalid=96777 0307: dt=0.006000, rms=0.489 (0.012%), neg=0, invalid=96777 0308: dt=0.006000, rms=0.489 (0.017%), neg=0, invalid=96777 0309: dt=0.006000, rms=0.489 (0.018%), neg=0, invalid=96777 0310: dt=0.006000, rms=0.489 (0.021%), neg=0, invalid=96777 0311: dt=0.006000, rms=0.489 (0.021%), neg=0, invalid=96777 0312: dt=0.006000, rms=0.488 (0.020%), neg=0, invalid=96777 0313: dt=0.006000, rms=0.488 (0.023%), neg=0, invalid=96777 0314: dt=0.006000, rms=0.488 (0.004%), neg=0, invalid=96777 0315: dt=0.096000, rms=0.488 (0.047%), neg=0, invalid=96777 0316: dt=0.007000, rms=0.488 (0.007%), 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=0.486, neg=0, invalid=96777 0317: dt=0.000000, rms=0.486 (0.000%), neg=0, invalid=96777 0318: dt=0.000000, rms=0.486 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0319: dt=73.984000, rms=0.486 (0.013%), neg=0, invalid=96777 0320: dt=129.472000, rms=0.486 (0.021%), neg=0, invalid=96777 0321: dt=92.480000, rms=0.486 (0.018%), neg=0, invalid=96777 0322: dt=92.480000, rms=0.486 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0323: dt=20.736000, rms=0.486 (0.055%), neg=0, invalid=96777 0324: dt=9.072000, rms=0.486 (0.017%), neg=0, invalid=96777 0325: dt=9.072000, rms=0.486 (0.009%), neg=0, invalid=96777 0326: dt=9.072000, rms=0.486 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0327: dt=103.680000, rms=0.483 (0.539%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0328: dt=31.104000, rms=0.482 (0.117%), neg=0, invalid=96777 0329: dt=31.104000, rms=0.482 (0.052%), neg=0, invalid=96777 0330: dt=31.104000, rms=0.482 (0.087%), neg=0, invalid=96777 0331: dt=31.104000, rms=0.481 (0.102%), neg=0, invalid=96777 0332: dt=31.104000, rms=0.481 (0.123%), neg=0, invalid=96777 0333: dt=31.104000, rms=0.480 (0.117%), neg=0, invalid=96777 0334: dt=31.104000, rms=0.480 (0.108%), neg=0, invalid=96777 0335: dt=103.680000, rms=0.479 (0.040%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0336: dt=19.200000, rms=0.478 (0.323%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, 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=0.001 (70.956%) 0337: dt=11.200000, rms=0.478 (0.108%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0338: dt=11.200000, rms=0.477 (0.153%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0339: dt=11.200000, rms=0.476 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000625: new neg 0, old_neg 1, delta 1, rms=0.002 (51.722%) 0340: dt=11.200000, rms=0.476 (0.110%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0341: dt=11.200000, rms=0.475 (0.122%), neg=0, invalid=96777 0342: dt=11.200000, rms=0.474 (0.149%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000621: new neg 0, old_neg 1, delta 1, rms=0.002 (46.465%) 0343: dt=11.200000, rms=0.473 (0.168%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0344: dt=11.200000, rms=0.473 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 22 iterations, nbhd size=3, neg = 0 0345: dt=11.200000, rms=0.473 (0.089%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0346: dt=11.200000, rms=0.472 (0.103%), neg=0, invalid=96777 0347: dt=11.200000, rms=0.472 (0.124%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0348: dt=11.200000, rms=0.471 (0.129%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000625: new neg 0, old_neg 1, delta 1, rms=0.004 (27.936%) 0349: dt=11.200000, rms=0.471 (0.116%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000500: new neg 0, old_neg 1, delta 1, rms=0.003 (35.129%) 0350: dt=11.200000, rms=0.470 (0.029%), neg=0, invalid=96777 0351: dt=32.000000, rms=0.470 (0.071%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000500: new neg 0, old_neg 1, delta 1, rms=0.003 (38.939%) 0352: dt=4.800000, rms=0.470 (0.027%), neg=0, invalid=96777 0353: dt=4.800000, rms=0.470 (0.024%), neg=0, invalid=96777 0354: dt=4.800000, rms=0.470 (0.021%), neg=0, invalid=96777 0355: dt=4.800000, rms=0.470 (0.031%), neg=0, invalid=96777 0356: dt=4.800000, rms=0.469 (0.038%), neg=0, invalid=96777 0357: dt=4.800000, rms=0.469 (0.046%), neg=0, invalid=96777 0358: dt=4.800000, rms=0.469 (0.043%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... iter 1, dt=0.000500: new neg 0, old_neg 2, delta 2, rms=0.002 (62.632%) 0359: dt=44.800000, rms=0.464 (1.069%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.463 (0.244%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.462 (0.103%), neg=0, invalid=96777 0362: dt=11.200000, rms=0.462 (0.180%), neg=0, invalid=96777 0363: dt=11.200000, rms=0.460 (0.234%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.459 (0.228%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, 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=0.002 (53.328%) 0365: dt=11.200000, rms=0.459 (0.183%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0366: dt=11.200000, rms=0.458 (0.069%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.458 (0.067%), neg=0, invalid=96777 0368: dt=9.600000, rms=0.458 (0.021%), neg=0, invalid=96777 0369: dt=9.600000, rms=0.458 (0.043%), neg=0, invalid=96777 0370: dt=9.600000, rms=0.457 (0.051%), neg=0, invalid=96777 0371: dt=9.600000, rms=0.457 (0.058%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, 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=0.002 (55.482%) 0372: dt=9.600000, rms=0.457 (0.078%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0373: dt=9.600000, rms=0.457 (0.031%), neg=0, invalid=96777 0374: dt=9.600000, rms=0.456 (0.037%), neg=0, invalid=96777 iter 0, gcam->neg = 2 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=0.002 (57.418%) 0375: dt=9.600000, rms=0.456 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0376: dt=9.600000, rms=0.456 (0.026%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0377: dt=2.000000, rms=0.461 (0.013%), neg=0, invalid=96777 0378: dt=0.252000, rms=0.461 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000606: new neg 0, old_neg 1, delta 1, rms=0.001 (69.808%) 0379: dt=9.357143, rms=0.460 (0.245%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.000625: new neg 0, old_neg 1, delta 1, rms=0.001 (45.746%) 0380: dt=13.824000, rms=0.459 (0.204%), neg=0, invalid=96777 iter 0, gcam->neg = 74 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000750: new neg 0, old_neg 1, delta 1, rms=0.002 (54.817%) 0381: dt=13.824000, rms=0.459 (0.172%), neg=0, invalid=96777 iter 0, gcam->neg = 414 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.004 (15.671%) 0382: dt=13.824000, rms=0.459 (-0.745%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0383: dt=3.058824, rms=0.458 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.000625: new neg 0, old_neg 1, delta 1, rms=0.001 (54.715%) 0384: dt=11.520000, rms=0.457 (0.241%), neg=0, invalid=96777 0385: dt=4.363636, rms=0.457 (0.094%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0386: dt=0.000000, rms=0.462 (0.014%), neg=0, invalid=96777 0387: dt=0.000000, rms=0.462 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0388: dt=0.000000, rms=0.462 (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=0.453, neg=0, invalid=96777 iter 0, gcam->neg = 469 after 10 iterations, nbhd size=1, neg = 0 0389: dt=1.760037, rms=0.423 (6.619%), neg=0, invalid=96777 0390: dt=0.000109, rms=0.423 (0.007%), neg=0, invalid=96777 0391: dt=0.000109, rms=0.423 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=96777 0392: dt=0.001750, rms=0.423 (0.002%), neg=0, invalid=96777 0393: dt=0.001750, rms=0.423 (0.000%), neg=0, invalid=96777 0394: dt=0.001750, rms=0.423 (0.001%), neg=0, invalid=96777 0395: dt=0.001750, rms=0.423 (-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=0.409, neg=0, invalid=96777 0396: dt=0.000000, rms=0.410 (-0.246%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 0397: dt=23.120000, rms=0.410 (0.001%), neg=0, invalid=96777 0398: dt=0.361250, rms=0.410 (0.000%), neg=0, invalid=96777 0399: dt=0.361250, rms=0.410 (-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=0.411, neg=0, invalid=96777 0400: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0401: dt=36.288000, rms=0.411 (0.019%), neg=0, invalid=96777 0402: dt=31.104000, rms=0.411 (0.004%), neg=0, invalid=96777 0403: dt=31.104000, rms=0.411 (0.003%), neg=0, invalid=96777 0404: dt=31.104000, rms=0.411 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0405: dt=2.800000, rms=0.411 (0.018%), neg=0, invalid=96777 0406: dt=2.800000, rms=0.411 (0.007%), neg=0, invalid=96777 0407: dt=2.800000, rms=0.411 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0408: dt=44.800000, rms=0.409 (0.501%), neg=0, invalid=96777 0409: dt=11.200000, rms=0.409 (0.061%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.408 (0.074%), neg=0, invalid=96777 0411: dt=11.200000, rms=0.408 (0.112%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.407 (0.125%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0413: dt=11.200000, rms=0.407 (0.124%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0414: dt=11.200000, rms=0.407 (0.096%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0415: dt=44.800000, rms=0.406 (0.125%), neg=0, invalid=96777 0416: dt=6.400000, rms=0.406 (0.010%), neg=0, invalid=96777 0417: dt=6.400000, rms=0.406 (0.020%), neg=0, invalid=96777 0418: dt=6.400000, rms=0.406 (0.033%), neg=0, invalid=96777 0419: dt=6.400000, rms=0.406 (0.039%), neg=0, invalid=96777 0420: dt=6.400000, rms=0.405 (0.044%), neg=0, invalid=96777 0421: dt=6.400000, rms=0.405 (0.051%), neg=0, invalid=96777 0422: dt=6.400000, rms=0.405 (0.037%), neg=0, invalid=96777 0423: dt=6.400000, rms=0.405 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 0424: dt=1.008000, rms=0.408 (0.009%), neg=0, invalid=96777 0425: dt=1.008000, rms=0.408 (0.006%), neg=0, invalid=96777 0426: dt=1.008000, rms=0.408 (0.002%), neg=0, invalid=96777 0427: dt=1.008000, rms=0.408 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=96777 iter 0, gcam->neg = 79 after 27 iterations, nbhd size=2, neg = 0 0428: dt=14.976744, rms=0.406 (0.476%), neg=0, invalid=96777 0429: dt=0.015750, rms=0.406 (0.000%), neg=0, invalid=96777 0430: dt=0.015750, rms=0.406 (0.000%), neg=0, invalid=96777 0431: dt=0.015750, rms=0.406 (0.000%), neg=0, invalid=96777 0432: dt=0.015750, rms=0.406 (0.000%), neg=0, invalid=96777 0433: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0434: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0435: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0436: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0437: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0438: dt=0.015750, rms=0.406 (0.001%), neg=0, invalid=96777 0439: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0440: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0441: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0442: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0443: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0444: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0445: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0446: dt=0.015750, rms=0.406 (0.002%), neg=0, invalid=96777 0447: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0448: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0449: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0450: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0451: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0452: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0453: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0454: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0455: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0456: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0457: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0458: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0459: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 0460: dt=0.015750, rms=0.406 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 79 after 28 iterations, nbhd size=3, neg = 0 0461: dt=13.824000, rms=0.405 (0.121%), neg=0, invalid=96777 0462: dt=0.027000, rms=0.405 (0.001%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0463: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0464: dt=0.000000, rms=0.411 (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=0.401, neg=0, invalid=96777 iter 0, gcam->neg = 337 after 21 iterations, nbhd size=2, neg = 0 0465: dt=0.768000, rms=0.391 (2.529%), neg=0, invalid=96777 0466: dt=0.000047, rms=0.391 (0.001%), neg=0, invalid=96777 0467: dt=0.000047, rms=0.391 (0.000%), neg=0, invalid=96777 0468: dt=0.000047, rms=0.391 (0.000%), neg=0, invalid=96777 0469: dt=0.000047, rms=0.391 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0470: dt=0.000438, rms=0.391 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0471: dt=0.028000, rms=0.391 (0.020%), neg=0, invalid=96777 0472: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0473: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0474: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0475: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0476: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0477: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0478: dt=0.000094, rms=0.391 (0.000%), neg=0, invalid=96777 0479: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0480: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0481: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0482: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0483: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0484: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0485: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0486: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0487: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0488: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0489: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0490: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0491: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0492: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0493: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0494: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0495: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0496: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0497: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0498: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0499: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0500: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0501: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0502: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0503: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0504: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0505: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0506: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0507: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0508: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0509: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0510: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 0511: dt=0.000094, rms=0.391 (0.001%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 45 minutes and 36 seconds. #-------------------------------------- #@# CA Reg Inv Fri Jun 9 15:59:25 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Jun 9 16:00:11 AEST 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/brainmind-engineer/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/brainmind-engineer/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... 11438787 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 45 seconds. #-------------------------------------- #@# SkullLTA Fri Jun 9 16:00:56 AEST 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/brainmind-engineer/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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 '/home/brainmind-engineer/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=10.0 skull bounding box = (47, 52, 11) --> (206, 213, 217) using (100, 106, 114) as brain centroid... mean wm in atlas = 126, using box (80,86,89) --> (119, 125,139) to find MRI wm before smoothing, mri peak at 101 after smoothing, mri peak at 101, scaling input intensities by 1.248 scaling channel 0 by 1.24752 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.0 (thresh=-4.0) 1.076 0.056 -0.022 -15.735; -0.058 1.285 -0.096 -34.084; 0.014 0.105 1.037 -21.854; 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=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.076 0.014 -0.050 -7.000; -0.022 1.337 -0.067 -48.844; 0.048 0.056 1.000 -15.645; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.076 0.014 -0.050 -7.000; -0.022 1.337 -0.067 -48.844; 0.048 0.056 1.000 -15.645; 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=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.078 0.014 -0.042 -7.679; -0.022 1.336 -0.067 -48.644; 0.039 0.056 1.002 -14.697; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.079 0.014 -0.042 -7.835; -0.022 1.337 -0.067 -48.842; 0.039 0.056 1.003 -14.838; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.079 0.014 -0.042 -7.835; -0.022 1.336 -0.067 -48.643; 0.039 0.056 1.003 -14.838; 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 1.07877 0.01401 -0.04230 -7.83544; -0.02213 1.33581 -0.06662 -48.64330; 0.03944 0.05620 1.00304 -14.83774; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.07877 0.01401 -0.04230 -7.83544; -0.02213 1.33581 -0.06662 -48.64330; 0.03944 0.05620 1.00304 -14.83774; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.079 0.014 -0.042 -7.835; -0.022 1.336 -0.067 -48.643; 0.039 0.056 1.003 -14.838; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.0) transform before final EM align: 1.079 0.014 -0.042 -7.835; -0.022 1.336 -0.067 -48.643; 0.039 0.056 1.003 -14.838; 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 1.07877 0.01401 -0.04230 -7.83544; -0.02213 1.33581 -0.06662 -48.64330; 0.03944 0.05620 1.00304 -14.83774; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.07877 0.01401 -0.04230 -7.83544; -0.02213 1.33581 -0.06662 -48.64330; 0.03944 0.05620 1.00304 -14.83774; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.5 tol 0.000000 final transform: 1.079 0.014 -0.042 -7.835; -0.022 1.336 -0.067 -48.643; 0.039 0.056 1.003 -14.838; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 17 minutes and 29 seconds. #-------------------------------------- #@# SubCort Seg Fri Jun 9 16:18:25 AEST 2017 mri_ca_label -align norm.mgz transforms/talairach.m3z /home/brainmind-engineer/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname brainmindengineer-Precision-Tower-7910 machine x86_64 setenv SUBJECTS_DIR /home/brainmind-engineer/freesurfer/subjects cd /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/brainmind-engineer/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 /home/brainmind-engineer/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 /home/brainmind-engineer/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 = 0.10488 (25) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (390 voxels, overlap=0.850) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (390 voxels, peak = 24), gca=23.6 gca peak = 0.14982 (20) mri peak = 0.10281 (24) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (216 voxels, overlap=0.669) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (216 voxels, peak = 22), gca=22.5 gca peak = 0.28003 (97) mri peak = 0.09583 (108) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (240 voxels, overlap=0.827) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (240 voxels, peak = 101), gca=101.4 gca peak = 0.18160 (96) mri peak = 0.09559 (102) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (132 voxels, overlap=0.619) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (132 voxels, peak = 101), gca=101.3 gca peak = 0.27536 (62) mri peak = 0.07813 (74) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (509 voxels, overlap=0.474) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (509 voxels, peak = 69), gca=68.5 gca peak = 0.32745 (63) mri peak = 0.09716 (75) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (462 voxels, overlap=0.247) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (462 voxels, peak = 72), gca=71.5 gca peak = 0.08597 (105) mri peak = 0.06744 (113) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (26719 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (26719 voxels, peak = 112), gca=111.8 gca peak = 0.09209 (106) mri peak = 0.06295 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (27849 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (27849 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.05171 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (16578 voxels, overlap=0.928) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (16578 voxels, peak = 65), gca=64.6 gca peak = 0.08598 (64) mri peak = 0.04741 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (16207 voxels, overlap=0.954) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (16207 voxels, peak = 66), gca=65.6 gca peak = 0.24164 (71) mri peak = 0.09798 (83) Right_Caudate (50): linear fit = 1.13 x + 0.0 (517 voxels, overlap=0.227) Right_Caudate (50): linear fit = 1.13 x + 0.0 (517 voxels, peak = 81), gca=80.6 gca peak = 0.18227 (75) mri peak = 0.09655 (83) Left_Caudate (11): linear fit = 1.03 x + 0.0 (647 voxels, overlap=0.697) Left_Caudate (11): linear fit = 1.03 x + 0.0 (647 voxels, peak = 78), gca=77.6 gca peak = 0.10629 (62) mri peak = 0.05799 (68) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (10983 voxels, overlap=0.717) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (10983 voxels, peak = 69), gca=68.5 gca peak = 0.11668 (59) mri peak = 0.05820 (67) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (13143 voxels, overlap=0.739) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (13143 voxels, peak = 66), gca=65.8 gca peak = 0.17849 (88) mri peak = 0.09756 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4374 voxels, overlap=0.603) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4374 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.09927 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4521 voxels, overlap=0.592) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4521 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.09524 (75) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (227 voxels, overlap=0.078) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (227 voxels, peak = 75), gca=74.6 gca peak = 0.42394 (62) mri peak = 0.09502 (72) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (222 voxels, overlap=0.078) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (222 voxels, peak = 73), gca=73.5 gca peak = 0.10041 (96) mri peak = 0.05992 (104) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (2892 voxels, overlap=0.593) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (2892 voxels, peak = 105), gca=105.1 gca peak = 0.13978 (88) mri peak = 0.07064 (98) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2617 voxels, overlap=0.520) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2617 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.05899 (89) Left_Putamen (12): linear fit = 1.08 x + 0.0 (1071 voxels, overlap=0.832) Left_Putamen (12): linear fit = 1.08 x + 0.0 (1071 voxels, peak = 87), gca=87.1 gca peak = 0.09624 (82) mri peak = 0.06359 (89) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1150 voxels, overlap=0.636) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1150 voxels, peak = 89), gca=89.0 gca peak = 0.07543 (88) mri peak = 0.05480 (88) Brain_Stem (16): linear fit = 1.09 x + 0.0 (8065 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.09 x + 0.0 (8065 voxels, peak = 95), gca=95.5 gca peak = 0.12757 (95) mri peak = 0.09054 (103) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (831 voxels, overlap=0.066) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (831 voxels, peak = 106), gca=105.9 gca peak = 0.17004 (92) mri peak = 0.09497 (107) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (806 voxels, overlap=0.180) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (806 voxels, peak = 102), gca=101.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.12739 (26) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (157 voxels, overlap=0.835) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (157 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 1.11 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.18019 (24) mri peak = 0.10488 (25) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (390 voxels, overlap=0.956) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (390 voxels, peak = 25), gca=24.6 gca peak = 0.18352 (23) mri peak = 0.10281 (24) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (216 voxels, overlap=0.664) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (216 voxels, peak = 23), gca=23.3 gca peak = 0.29928 (102) mri peak = 0.09583 (108) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (240 voxels, overlap=1.016) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (240 voxels, peak = 104), gca=103.5 gca peak = 0.18247 (101) mri peak = 0.09559 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (132 voxels, overlap=0.882) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (132 voxels, peak = 101), gca=101.0 gca peak = 0.23406 (68) mri peak = 0.07813 (74) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (509 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (509 voxels, peak = 70), gca=69.7 gca peak = 0.22973 (71) mri peak = 0.09716 (75) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (462 voxels, overlap=1.002) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (462 voxels, peak = 69), gca=69.2 gca peak = 0.08154 (112) mri peak = 0.06744 (113) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26719 voxels, overlap=0.818) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (26719 voxels, peak = 112), gca=112.0 gca peak = 0.08574 (111) mri peak = 0.06295 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27849 voxels, overlap=0.843) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27849 voxels, peak = 111), gca=111.0 gca peak = 0.07462 (65) mri peak = 0.05171 (62) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (16578 voxels, overlap=0.887) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (16578 voxels, peak = 65), gca=65.0 gca peak = 0.08729 (65) mri peak = 0.04741 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16207 voxels, overlap=0.938) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (16207 voxels, peak = 64), gca=64.0 gca peak = 0.22403 (80) mri peak = 0.09798 (83) Right_Caudate (50): linear fit = 0.99 x + 0.0 (517 voxels, overlap=1.004) Right_Caudate (50): linear fit = 0.99 x + 0.0 (517 voxels, peak = 79), gca=78.8 gca peak = 0.16210 (77) mri peak = 0.09655 (83) Left_Caudate (11): linear fit = 1.04 x + 0.0 (647 voxels, overlap=0.999) Left_Caudate (11): linear fit = 1.04 x + 0.0 (647 voxels, peak = 80), gca=80.5 gca peak = 0.09420 (69) mri peak = 0.05799 (68) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10983 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10983 voxels, peak = 69), gca=69.0 gca peak = 0.10767 (66) mri peak = 0.05820 (67) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (13143 voxels, overlap=0.995) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (13143 voxels, peak = 65), gca=65.0 gca peak = 0.17137 (94) mri peak = 0.09756 (94) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4374 voxels, overlap=0.979) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4374 voxels, peak = 93), gca=92.6 gca peak = 0.15715 (93) mri peak = 0.09927 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4521 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4521 voxels, peak = 93), gca=92.5 gca peak = 0.30533 (74) mri peak = 0.09524 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (227 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (227 voxels, peak = 74), gca=74.0 gca peak = 0.30698 (74) mri peak = 0.09502 (72) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (222 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (222 voxels, peak = 73), gca=72.9 gca peak = 0.09356 (103) mri peak = 0.05992 (104) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2892 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2892 voxels, peak = 103), gca=103.0 gca peak = 0.11462 (95) mri peak = 0.07064 (98) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2617 voxels, overlap=0.964) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2617 voxels, peak = 95), gca=95.5 gca peak = 0.08410 (87) mri peak = 0.05899 (89) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1071 voxels, overlap=0.997) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1071 voxels, peak = 85), gca=84.8 gca peak = 0.09859 (82) mri peak = 0.06359 (89) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1150 voxels, overlap=0.997) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1150 voxels, peak = 81), gca=80.8 gca peak = 0.07238 (93) mri peak = 0.05480 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8065 voxels, overlap=0.871) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8065 voxels, peak = 93), gca=93.5 gca peak = 0.10777 (106) mri peak = 0.09054 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (831 voxels, overlap=0.790) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (831 voxels, peak = 105), gca=105.5 gca peak = 0.15580 (102) mri peak = 0.09497 (107) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (806 voxels, overlap=0.864) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (806 voxels, peak = 102), gca=102.0 gca peak = 0.19676 (37) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20195 (25) mri peak = 0.12739 (26) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (157 voxels, overlap=0.787) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (157 voxels, peak = 24), gca=24.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26012 (40) gca peak Third_Ventricle = 0.19676 (37) gca peak CSF = 0.17152 (39) gca peak Left_Accumbens_area = 0.44011 (72) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65116 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.28428 (35) gca peak Right_Accumbens_area = 0.30029 (82) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.96811 (42) gca peak WM_hypointensities = 0.17746 (86) gca peak non_WM_hypointensities = 0.10275 (56) gca peak Optic_Chiasm = 0.34475 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 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 17716 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 422 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 90491 changed. image ll: -2.195, PF=1.000 pass 2: 14097 changed. image ll: -2.191, PF=1.000 pass 3: 4132 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 9 minutes and 36 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/cc_up.lta fsMM.nii.mgz will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/transforms/cc_up.lta reading aseg from /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/aseg.auto_noCCseg.mgz reading norm from /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/norm.mgz 40647 voxels in left wm, 56700 in right wm, xrange [121, 132] searching rotation angles z=[-9 5], y=[-9 5] searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 global minimum found at slice 126.9, rotations (-2.18, -2.23) final transformation (x=126.9, yr=-2.175, zr=-2.230): 0.999 0.039 -0.038 0.949; -0.039 0.999 0.001 14.859; 0.038 -0.000 0.999 11.264; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 155 143 eigenvectors: -0.001 -0.011 1.000; 0.146 -0.989 -0.011; 0.989 0.146 0.002; writing aseg with callosum to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Fri Jun 9 16:28:42 AEST 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Jun 9 16:28:42 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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... 4330 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 105 gm peak at 69 (69), valley at 35 (35) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 34 (34) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 15 seconds. #-------------------------------------------- #@# Mask BFS Fri Jun 9 16:30:58 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1512738 voxels in mask (pct= 9.02) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Jun 9 16:30:59 AEST 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 (104.0): 104.2 +- 6.3 [80.0 --> 125.0] GM (72.0) : 70.5 +- 9.9 [30.0 --> 96.0] setting bottom of white matter range to 80.4 setting top of gray matter range to 90.3 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... 17142 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4595 filled 573 bright non-wm voxels segmented. 6745 diagonally connected voxels added... white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.49 minutes reading wm segmentation from wm.seg.mgz... 955 voxels added to wm to prevent paths from MTL structures to cortex 2236 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35739 voxels turned on, 36994 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 96 new 96 115,126,128 old 96 new 96 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 35 found - 35 modified | TOTAL: 35 pass 2 (xy+): 0 found - 35 modified | TOTAL: 35 pass 1 (xy-): 31 found - 31 modified | TOTAL: 66 pass 2 (xy-): 0 found - 31 modified | TOTAL: 66 pass 1 (yz+): 41 found - 41 modified | TOTAL: 107 pass 2 (yz+): 0 found - 41 modified | TOTAL: 107 pass 1 (yz-): 51 found - 51 modified | TOTAL: 158 pass 2 (yz-): 0 found - 51 modified | TOTAL: 158 pass 1 (xz+): 45 found - 45 modified | TOTAL: 203 pass 2 (xz+): 0 found - 45 modified | TOTAL: 203 pass 1 (xz-): 42 found - 42 modified | TOTAL: 245 pass 2 (xz-): 0 found - 42 modified | TOTAL: 245 Iteration Number : 1 pass 1 (+++): 39 found - 39 modified | TOTAL: 39 pass 2 (+++): 0 found - 39 modified | TOTAL: 39 pass 1 (+++): 24 found - 24 modified | TOTAL: 63 pass 2 (+++): 0 found - 24 modified | TOTAL: 63 pass 1 (+++): 22 found - 22 modified | TOTAL: 85 pass 2 (+++): 0 found - 22 modified | TOTAL: 85 pass 1 (+++): 34 found - 34 modified | TOTAL: 119 pass 2 (+++): 0 found - 34 modified | TOTAL: 119 Iteration Number : 1 pass 1 (++): 221 found - 221 modified | TOTAL: 221 pass 2 (++): 0 found - 221 modified | TOTAL: 221 pass 1 (+-): 201 found - 201 modified | TOTAL: 422 pass 2 (+-): 0 found - 201 modified | TOTAL: 422 pass 1 (--): 213 found - 213 modified | TOTAL: 635 pass 2 (--): 0 found - 213 modified | TOTAL: 635 pass 1 (-+): 202 found - 202 modified | TOTAL: 837 pass 2 (-+): 0 found - 202 modified | TOTAL: 837 Iteration Number : 2 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 7 found - 7 modified | TOTAL: 24 pass 2 (xy-): 0 found - 7 modified | TOTAL: 24 pass 1 (yz+): 8 found - 8 modified | TOTAL: 32 pass 2 (yz+): 0 found - 8 modified | TOTAL: 32 pass 1 (yz-): 5 found - 5 modified | TOTAL: 37 pass 2 (yz-): 0 found - 5 modified | TOTAL: 37 pass 1 (xz+): 12 found - 12 modified | TOTAL: 49 pass 2 (xz+): 0 found - 12 modified | TOTAL: 49 pass 1 (xz-): 9 found - 9 modified | TOTAL: 58 pass 2 (xz-): 0 found - 9 modified | TOTAL: 58 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 5 found - 5 modified | TOTAL: 9 pass 2 (--): 0 found - 5 modified | TOTAL: 9 pass 1 (-+): 5 found - 5 modified | TOTAL: 14 pass 2 (-+): 0 found - 5 modified | TOTAL: 14 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 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 = 1279 (out of 507618: 0.251961) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Jun 9 16:32:43 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 1.076 0.056 -0.022 -15.735; -0.055 1.208 -0.090 -24.783; 0.014 0.105 1.037 -21.854; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.076 0.056 -0.022 -15.735; -0.055 1.208 -0.090 -24.783; 0.014 0.105 1.037 -21.854; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2683 (min = 350, max = 1400), aspect = 1.35 (min = 0.10, max = 0.75) need search nearby using seed (127, 119, 149), TAL = (1.0, 21.0, 9.0) talairach voxel to voxel transform 0.927 -0.044 0.016 13.837; 0.041 0.819 0.072 22.529; -0.017 -0.082 0.956 18.604; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 119, 149) --> (1.0, 21.0, 9.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (1.00, 21.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 21.00, 9.00) SRC: (111.98, 135.26, 149.52) search lh wm seed point around talairach space (-17.00, 21.00, 9.00), SRC: (145.37, 136.73, 148.93) 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 Fri Jun 9 16:33:09 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 2 found - 2 modified | TOTAL: 7 pass 2 (xz-): 0 found - 2 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 245640: 0.003664) 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: 906 vertices, 1015 faces slice 40: 6084 vertices, 6286 faces slice 50: 13488 vertices, 13750 faces slice 60: 22135 vertices, 22507 faces slice 70: 33419 vertices, 33845 faces slice 80: 43653 vertices, 44004 faces slice 90: 54474 vertices, 54889 faces slice 100: 66569 vertices, 67060 faces slice 110: 78912 vertices, 79360 faces slice 120: 90599 vertices, 91054 faces slice 130: 101212 vertices, 101650 faces slice 140: 109726 vertices, 110100 faces slice 150: 117276 vertices, 117670 faces slice 160: 125205 vertices, 125555 faces slice 170: 131704 vertices, 132067 faces slice 180: 137210 vertices, 137517 faces slice 190: 141150 vertices, 141378 faces slice 200: 141970 vertices, 142106 faces slice 210: 141970 vertices, 142106 faces slice 220: 141970 vertices, 142106 faces slice 230: 141970 vertices, 142106 faces slice 240: 141970 vertices, 142106 faces slice 250: 141970 vertices, 142106 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... 141970 voxel in cpt #1: X=-136 [v=141970,e=426318,f=284212] located at (-24.658504, -23.719885, 1.848940) For the whole surface: X=-136 [v=141970,e=426318,f=284212] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Jun 9 16:33:14 AEST 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 Fri Jun 9 16:33:17 AEST 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts avg radius = 46.9 mm, total surface area = 71750 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.083 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.056 (target=0.015) step 020: RMS=0.049 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.035 (target=0.015) step 055: RMS=0.035 (target=0.015) step 060: RMS=0.034 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Jun 9 16:33:40 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 0.95 +- 0.59 (0.00-->6.52) (max @ vno 100952 --> 100962) face area 0.02 +- 0.03 (-0.16-->0.56) scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.550, avgs=0 005/300: dt: 0.9000, rms radial error=177.292, avgs=0 010/300: dt: 0.9000, rms radial error=176.736, avgs=0 015/300: dt: 0.9000, rms radial error=176.005, avgs=0 020/300: dt: 0.9000, rms radial error=175.173, avgs=0 025/300: dt: 0.9000, rms radial error=174.284, avgs=0 030/300: dt: 0.9000, rms radial error=173.361, avgs=0 035/300: dt: 0.9000, rms radial error=172.421, avgs=0 040/300: dt: 0.9000, rms radial error=171.472, avgs=0 045/300: dt: 0.9000, rms radial error=170.521, avgs=0 050/300: dt: 0.9000, rms radial error=169.571, avgs=0 055/300: dt: 0.9000, rms radial error=168.622, avgs=0 060/300: dt: 0.9000, rms radial error=167.676, avgs=0 065/300: dt: 0.9000, rms radial error=166.735, avgs=0 070/300: dt: 0.9000, rms radial error=165.799, avgs=0 075/300: dt: 0.9000, rms radial error=164.867, avgs=0 080/300: dt: 0.9000, rms radial error=163.940, avgs=0 085/300: dt: 0.9000, rms radial error=163.018, avgs=0 090/300: dt: 0.9000, rms radial error=162.101, avgs=0 095/300: dt: 0.9000, rms radial error=161.189, avgs=0 100/300: dt: 0.9000, rms radial error=160.282, avgs=0 105/300: dt: 0.9000, rms radial error=159.379, avgs=0 110/300: dt: 0.9000, rms radial error=158.482, avgs=0 115/300: dt: 0.9000, rms radial error=157.590, avgs=0 120/300: dt: 0.9000, rms radial error=156.702, avgs=0 125/300: dt: 0.9000, rms radial error=155.819, avgs=0 130/300: dt: 0.9000, rms radial error=154.941, avgs=0 135/300: dt: 0.9000, rms radial error=154.068, avgs=0 140/300: dt: 0.9000, rms radial error=153.199, avgs=0 145/300: dt: 0.9000, rms radial error=152.336, avgs=0 150/300: dt: 0.9000, rms radial error=151.477, avgs=0 155/300: dt: 0.9000, rms radial error=150.623, avgs=0 160/300: dt: 0.9000, rms radial error=149.774, avgs=0 165/300: dt: 0.9000, rms radial error=148.930, avgs=0 170/300: dt: 0.9000, rms radial error=148.091, avgs=0 175/300: dt: 0.9000, rms radial error=147.257, avgs=0 180/300: dt: 0.9000, rms radial error=146.427, avgs=0 185/300: dt: 0.9000, rms radial error=145.602, avgs=0 190/300: dt: 0.9000, rms radial error=144.781, avgs=0 195/300: dt: 0.9000, rms radial error=143.965, avgs=0 200/300: dt: 0.9000, rms radial error=143.153, avgs=0 205/300: dt: 0.9000, rms radial error=142.346, avgs=0 210/300: dt: 0.9000, rms radial error=141.544, avgs=0 215/300: dt: 0.9000, rms radial error=140.746, avgs=0 220/300: dt: 0.9000, rms radial error=139.952, avgs=0 225/300: dt: 0.9000, rms radial error=139.163, avgs=0 230/300: dt: 0.9000, rms radial error=138.379, avgs=0 235/300: dt: 0.9000, rms radial error=137.599, avgs=0 240/300: dt: 0.9000, rms radial error=136.823, avgs=0 245/300: dt: 0.9000, rms radial error=136.052, avgs=0 250/300: dt: 0.9000, rms radial error=135.285, avgs=0 255/300: dt: 0.9000, rms radial error=134.522, avgs=0 260/300: dt: 0.9000, rms radial error=133.763, avgs=0 265/300: dt: 0.9000, rms radial error=133.009, avgs=0 270/300: dt: 0.9000, rms radial error=132.259, avgs=0 275/300: dt: 0.9000, rms radial error=131.513, avgs=0 280/300: dt: 0.9000, rms radial error=130.771, avgs=0 285/300: dt: 0.9000, rms radial error=130.034, avgs=0 290/300: dt: 0.9000, rms radial error=129.301, avgs=0 295/300: dt: 0.9000, rms radial error=128.571, avgs=0 300/300: dt: 0.9000, rms radial error=127.846, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17039.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3030.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 356.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00505 epoch 4 (K=640.0), pass 1, starting sse = 27.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00675 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Jun 9 16:36:38 AEST 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 fsMM.nii.mgz 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=-136 (nv=141970, nf=284212, ne=426318, g=69) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 6924 ambiguous faces found in tessellation segmenting defects... 77 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 4 -merging segment 23 into 22 -merging segment 26 into 25 -merging segment 59 into 56 73 defects to be corrected 0 vertices coincident reading input surface /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2911 (-4.6456) -vertex loglikelihood: -6.2591 (-3.1295) -normal dot loglikelihood: -3.5799 (-3.5799) -quad curv loglikelihood: -6.6187 (-3.3093) Total Loglikelihood : -25.7487 CORRECTING DEFECT 0 (vertices=40, convex hull=59) After retessellation of defect 0, euler #=-74 (137557,410462,272831) : difference with theory (-70) = 4 CORRECTING DEFECT 1 (vertices=320, convex hull=307) After retessellation of defect 1, euler #=-73 (137609,410794,273112) : difference with theory (-69) = 4 CORRECTING DEFECT 2 (vertices=36, convex hull=67) After retessellation of defect 2, euler #=-72 (137629,410884,273183) : difference with theory (-68) = 4 CORRECTING DEFECT 3 (vertices=14, convex hull=39) After retessellation of defect 3, euler #=-71 (137631,410901,273199) : difference with theory (-67) = 4 CORRECTING DEFECT 4 (vertices=223, convex hull=178) After retessellation of defect 4, euler #=-69 (137701,411200,273430) : difference with theory (-66) = 3 CORRECTING DEFECT 5 (vertices=32, convex hull=47) After retessellation of defect 5, euler #=-68 (137716,411264,273480) : difference with theory (-65) = 3 CORRECTING DEFECT 6 (vertices=24, convex hull=66) After retessellation of defect 6, euler #=-67 (137725,411322,273530) : difference with theory (-64) = 3 CORRECTING DEFECT 7 (vertices=18, convex hull=53) After retessellation of defect 7, euler #=-66 (137733,411362,273563) : difference with theory (-63) = 3 CORRECTING DEFECT 8 (vertices=21, convex hull=67) After retessellation of defect 8, euler #=-65 (137747,411431,273619) : difference with theory (-62) = 3 CORRECTING DEFECT 9 (vertices=33, convex hull=67) After retessellation of defect 9, euler #=-64 (137755,411483,273664) : difference with theory (-61) = 3 CORRECTING DEFECT 10 (vertices=61, convex hull=112) After retessellation of defect 10, euler #=-63 (137785,411621,273773) : difference with theory (-60) = 3 CORRECTING DEFECT 11 (vertices=24, convex hull=65) After retessellation of defect 11, euler #=-62 (137794,411670,273814) : difference with theory (-59) = 3 CORRECTING DEFECT 12 (vertices=25, convex hull=41) After retessellation of defect 12, euler #=-61 (137803,411713,273849) : difference with theory (-58) = 3 CORRECTING DEFECT 13 (vertices=63, convex hull=85) After retessellation of defect 13, euler #=-60 (137834,411849,273955) : difference with theory (-57) = 3 CORRECTING DEFECT 14 (vertices=30, convex hull=82) After retessellation of defect 14, euler #=-59 (137853,411939,274027) : difference with theory (-56) = 3 CORRECTING DEFECT 15 (vertices=42, convex hull=119) After retessellation of defect 15, euler #=-58 (137881,412072,274133) : difference with theory (-55) = 3 CORRECTING DEFECT 16 (vertices=113, convex hull=143) After retessellation of defect 16, euler #=-57 (137944,412343,274342) : difference with theory (-54) = 3 CORRECTING DEFECT 17 (vertices=118, convex hull=152) After retessellation of defect 17, euler #=-56 (137987,412553,274510) : difference with theory (-53) = 3 CORRECTING DEFECT 18 (vertices=87, convex hull=83) After retessellation of defect 18, euler #=-55 (138020,412690,274615) : difference with theory (-52) = 3 CORRECTING DEFECT 19 (vertices=11, convex hull=20) After retessellation of defect 19, euler #=-54 (138021,412699,274624) : difference with theory (-51) = 3 CORRECTING DEFECT 20 (vertices=8, convex hull=19) After retessellation of defect 20, euler #=-53 (138024,412714,274637) : difference with theory (-50) = 3 CORRECTING DEFECT 21 (vertices=141, convex hull=180) After retessellation of defect 21, euler #=-51 (138113,413074,274910) : difference with theory (-49) = 2 CORRECTING DEFECT 22 (vertices=20, convex hull=49) After retessellation of defect 22, euler #=-50 (138123,413119,274946) : difference with theory (-48) = 2 CORRECTING DEFECT 23 (vertices=25, convex hull=50) After retessellation of defect 23, euler #=-48 (138124,413145,274973) : difference with theory (-47) = 1 CORRECTING DEFECT 24 (vertices=38, convex hull=59) After retessellation of defect 24, euler #=-47 (138145,413232,275040) : difference with theory (-46) = 1 CORRECTING DEFECT 25 (vertices=34, convex hull=58) After retessellation of defect 25, euler #=-46 (138161,413307,275100) : difference with theory (-45) = 1 CORRECTING DEFECT 26 (vertices=20, convex hull=42) After retessellation of defect 26, euler #=-45 (138170,413349,275134) : difference with theory (-44) = 1 CORRECTING DEFECT 27 (vertices=23, convex hull=48) After retessellation of defect 27, euler #=-44 (138177,413384,275163) : difference with theory (-43) = 1 CORRECTING DEFECT 28 (vertices=35, convex hull=43) After retessellation of defect 28, euler #=-43 (138183,413419,275193) : difference with theory (-42) = 1 CORRECTING DEFECT 29 (vertices=19, convex hull=45) After retessellation of defect 29, euler #=-42 (138192,413461,275227) : difference with theory (-41) = 1 CORRECTING DEFECT 30 (vertices=6, convex hull=15) After retessellation of defect 30, euler #=-41 (138193,413467,275233) : difference with theory (-40) = 1 CORRECTING DEFECT 31 (vertices=16, convex hull=19) After retessellation of defect 31, euler #=-40 (138195,413476,275241) : difference with theory (-39) = 1 CORRECTING DEFECT 32 (vertices=27, convex hull=55) After retessellation of defect 32, euler #=-39 (138204,413523,275280) : difference with theory (-38) = 1 CORRECTING DEFECT 33 (vertices=170, convex hull=97) After retessellation of defect 33, euler #=-38 (138224,413617,275355) : difference with theory (-37) = 1 CORRECTING DEFECT 34 (vertices=18, convex hull=25) Warning - incorrect dp selected!!!!(-70.975762 >= -70.975763 ) After retessellation of defect 34, euler #=-37 (138225,413629,275367) : difference with theory (-36) = 1 CORRECTING DEFECT 35 (vertices=705, convex hull=452) After retessellation of defect 35, euler #=-36 (138420,414462,276006) : difference with theory (-35) = 1 CORRECTING DEFECT 36 (vertices=13, convex hull=22) After retessellation of defect 36, euler #=-35 (138421,414473,276017) : difference with theory (-34) = 1 CORRECTING DEFECT 37 (vertices=7, convex hull=18) After retessellation of defect 37, euler #=-34 (138423,414483,276026) : difference with theory (-33) = 1 CORRECTING DEFECT 38 (vertices=58, convex hull=33) After retessellation of defect 38, euler #=-33 (138431,414518,276054) : difference with theory (-32) = 1 CORRECTING DEFECT 39 (vertices=9, convex hull=22) After retessellation of defect 39, euler #=-32 (138434,414533,276067) : difference with theory (-31) = 1 CORRECTING DEFECT 40 (vertices=11, convex hull=24) After retessellation of defect 40, euler #=-31 (138436,414546,276079) : difference with theory (-30) = 1 CORRECTING DEFECT 41 (vertices=130, convex hull=42) After retessellation of defect 41, euler #=-30 (138445,414588,276113) : difference with theory (-29) = 1 CORRECTING DEFECT 42 (vertices=7, convex hull=25) After retessellation of defect 42, euler #=-29 (138449,414608,276130) : difference with theory (-28) = 1 CORRECTING DEFECT 43 (vertices=58, convex hull=61) After retessellation of defect 43, euler #=-28 (138458,414656,276170) : difference with theory (-27) = 1 CORRECTING DEFECT 44 (vertices=17, convex hull=61) After retessellation of defect 44, euler #=-27 (138467,414706,276212) : difference with theory (-26) = 1 CORRECTING DEFECT 45 (vertices=5, convex hull=20) After retessellation of defect 45, euler #=-26 (138469,414717,276222) : difference with theory (-25) = 1 CORRECTING DEFECT 46 (vertices=206, convex hull=51) After retessellation of defect 46, euler #=-25 (138481,414774,276268) : difference with theory (-24) = 1 CORRECTING DEFECT 47 (vertices=27, convex hull=52) After retessellation of defect 47, euler #=-24 (138489,414815,276302) : difference with theory (-23) = 1 CORRECTING DEFECT 48 (vertices=34, convex hull=65) After retessellation of defect 48, euler #=-23 (138510,414903,276370) : difference with theory (-22) = 1 CORRECTING DEFECT 49 (vertices=21, convex hull=27) After retessellation of defect 49, euler #=-22 (138513,414919,276384) : difference with theory (-21) = 1 CORRECTING DEFECT 50 (vertices=460, convex hull=244) After retessellation of defect 50, euler #=-21 (138661,415490,276808) : difference with theory (-20) = 1 CORRECTING DEFECT 51 (vertices=17, convex hull=39) After retessellation of defect 51, euler #=-20 (138671,415531,276840) : difference with theory (-19) = 1 CORRECTING DEFECT 52 (vertices=38, convex hull=28) After retessellation of defect 52, euler #=-19 (138679,415565,276867) : difference with theory (-18) = 1 CORRECTING DEFECT 53 (vertices=32, convex hull=61) After retessellation of defect 53, euler #=-17 (138695,415643,276931) : difference with theory (-17) = 0 CORRECTING DEFECT 54 (vertices=27, convex hull=32) After retessellation of defect 54, euler #=-16 (138703,415675,276956) : difference with theory (-16) = 0 CORRECTING DEFECT 55 (vertices=9, convex hull=23) After retessellation of defect 55, euler #=-15 (138706,415691,276970) : difference with theory (-15) = 0 CORRECTING DEFECT 56 (vertices=5, convex hull=14) After retessellation of defect 56, euler #=-14 (138707,415696,276975) : difference with theory (-14) = 0 CORRECTING DEFECT 57 (vertices=86, convex hull=115) After retessellation of defect 57, euler #=-13 (138737,415842,277092) : difference with theory (-13) = 0 CORRECTING DEFECT 58 (vertices=16, convex hull=51) After retessellation of defect 58, euler #=-12 (138748,415897,277137) : difference with theory (-12) = 0 CORRECTING DEFECT 59 (vertices=19, convex hull=30) After retessellation of defect 59, euler #=-11 (138752,415919,277156) : difference with theory (-11) = 0 CORRECTING DEFECT 60 (vertices=53, convex hull=96) After retessellation of defect 60, euler #=-10 (138764,415993,277219) : difference with theory (-10) = 0 CORRECTING DEFECT 61 (vertices=22, convex hull=54) After retessellation of defect 61, euler #=-9 (138773,416041,277259) : difference with theory (-9) = 0 CORRECTING DEFECT 62 (vertices=20, convex hull=39) After retessellation of defect 62, euler #=-8 (138776,416067,277283) : difference with theory (-8) = 0 CORRECTING DEFECT 63 (vertices=23, convex hull=21) After retessellation of defect 63, euler #=-7 (138777,416075,277291) : difference with theory (-7) = 0 CORRECTING DEFECT 64 (vertices=31, convex hull=62) After retessellation of defect 64, euler #=-6 (138797,416155,277352) : difference with theory (-6) = 0 CORRECTING DEFECT 65 (vertices=48, convex hull=93) After retessellation of defect 65, euler #=-5 (138808,416226,277413) : difference with theory (-5) = 0 CORRECTING DEFECT 66 (vertices=53, convex hull=100) After retessellation of defect 66, euler #=-4 (138842,416368,277522) : difference with theory (-4) = 0 CORRECTING DEFECT 67 (vertices=59, convex hull=72) After retessellation of defect 67, euler #=-3 (138865,416469,277601) : difference with theory (-3) = 0 CORRECTING DEFECT 68 (vertices=7, convex hull=26) After retessellation of defect 68, euler #=-2 (138866,416479,277611) : difference with theory (-2) = 0 CORRECTING DEFECT 69 (vertices=38, convex hull=75) After retessellation of defect 69, euler #=-1 (138888,416576,277687) : difference with theory (-1) = 0 CORRECTING DEFECT 70 (vertices=30, convex hull=68) After retessellation of defect 70, euler #=0 (138897,416630,277733) : difference with theory (0) = 0 CORRECTING DEFECT 71 (vertices=22, convex hull=50) After retessellation of defect 71, euler #=1 (138909,416682,277774) : difference with theory (1) = 0 CORRECTING DEFECT 72 (vertices=61, convex hull=83) After retessellation of defect 72, euler #=2 (138935,416799,277866) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.24 (0.03-->6.08) (max @ vno 1875 --> 3401) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.24 (0.03-->6.08) (max @ vno 1875 --> 3401) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 258 mutations (35.6%), 466 crossovers (64.4%), 264 vertices were eliminated building final representation... 3035 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138935, nf=277866, ne=416799, g=0) writing corrected surface to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 33.8 minutes 0 defective edges removing intersecting faces 000: 406 intersecting 001: 12 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 138935 - 416799 + 277866 = 2 --> 0 holes F =2V-4: 277866 = 277870-4 (0) 2E=3F: 833598 = 833598 (0) total defect index = 0 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 40 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Jun 9 17:10:32 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs fsMM.nii.mgz 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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/filled.mgz... reading volume /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/brain.finalsurfs.mgz... reading volume /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/wm.mgz... 22009 bright wm thresholded. 625 bright non-wm voxels segmented. reading original surface position from /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.orig... computing class statistics... border white: 258685 voxels (1.54%) border gray 289608 voxels (1.73%) WM (93.0): 93.8 +- 8.3 [70.0 --> 110.0] GM (80.0) : 78.8 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.0 (was 70) setting MAX_BORDER_WHITE to 109.3 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 49.0 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->3.23) (max @ vno 131413 --> 133291) face area 0.27 +- 0.13 (0.00-->2.39) mean absolute distance = 0.78 +- 1.00 3522 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=101, GM=71 mean inside = 93.3, mean outside = 76.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=80.1, 123 (123) missing vertices, mean dist 0.2 [0.8 (%34.3)->0.8 (%65.7))] %59 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.05-->3.98) (max @ vno 64669 --> 65993) face area 0.27 +- 0.14 (0.00-->2.04) mean absolute distance = 0.36 +- 0.59 3354 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5126108.0, rms=9.59 001: dt: 0.5000, sse=6761393.5, rms=6.979 (0.000%) 002: dt: 0.5000, sse=7331791.5, rms=5.440 (0.000%) 003: dt: 0.5000, sse=7840863.5, rms=4.542 (0.000%) 004: dt: 0.5000, sse=8178664.5, rms=4.023 (0.000%) 005: dt: 0.5000, sse=8379942.0, rms=3.769 (0.000%) 006: dt: 0.5000, sse=8503006.0, rms=3.605 (0.000%) 007: dt: 0.5000, sse=8572688.0, rms=3.549 (0.000%) 008: dt: 0.5000, sse=8610794.0, rms=3.482 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8631766.0, rms=3.462 (0.000%) 010: dt: 0.2500, sse=5659039.0, rms=2.631 (0.000%) 011: dt: 0.2500, sse=5331558.5, rms=2.395 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=5121389.0, rms=2.352 (0.000%) 013: dt: 0.1250, sse=4995457.5, rms=2.294 (0.000%) rms = 2.29, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4959929.0, rms=2.288 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.8, 142 (36) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.3 (%31.2))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.27 (0.07-->4.34) (max @ vno 64658 --> 65979) face area 0.34 +- 0.17 (0.00-->2.77) mean absolute distance = 0.27 +- 0.38 3608 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5390203.0, rms=4.20 015: dt: 0.5000, sse=5953690.5, rms=2.924 (0.000%) rms = 3.12, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5547639.0, rms=2.376 (0.000%) 017: dt: 0.2500, sse=5414671.0, rms=2.074 (0.000%) 018: dt: 0.2500, sse=5295052.5, rms=1.963 (0.000%) rms = 1.93, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5257602.0, rms=1.926 (0.000%) rms = 1.88, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5181499.0, rms=1.884 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.1, 161 (23) missing vertices, mean dist -0.1 [0.3 (%69.8)->0.2 (%30.2))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=brain, 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 +- 0.26 (0.04-->4.68) (max @ vno 64658 --> 65979) face area 0.33 +- 0.17 (0.00-->2.73) mean absolute distance = 0.23 +- 0.32 3027 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5367326.5, rms=3.34 021: dt: 0.5000, sse=5775807.5, rms=2.803 (0.000%) rms = 3.07, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5421236.0, rms=2.079 (0.000%) 023: dt: 0.2500, sse=5424127.5, rms=1.793 (0.000%) 024: dt: 0.2500, sse=5364189.0, rms=1.713 (0.000%) rms = 1.72, time step reduction 2 of 3 to 0.125... rms = 1.69, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5321669.5, rms=1.690 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.9, 189 (17) missing vertices, mean dist -0.0 [0.2 (%54.2)->0.2 (%45.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=brain, 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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5333651.5, rms=1.87 rms = 1.97, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5489264.0, rms=1.461 (0.000%) 027: dt: 0.2500, sse=5825609.0, rms=1.262 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.26, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5821791.0, rms=1.257 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 31 non-cortical segments detected only using segment with 1867 vertices erasing segment 0 (vno[0] = 52751) erasing segment 1 (vno[0] = 52800) erasing segment 2 (vno[0] = 53994) erasing segment 3 (vno[0] = 54024) erasing segment 4 (vno[0] = 55094) erasing segment 5 (vno[0] = 55152) erasing segment 6 (vno[0] = 55183) erasing segment 7 (vno[0] = 56242) erasing segment 9 (vno[0] = 63544) erasing segment 10 (vno[0] = 78934) erasing segment 11 (vno[0] = 81166) erasing segment 12 (vno[0] = 81452) erasing segment 13 (vno[0] = 87825) erasing segment 14 (vno[0] = 88005) erasing segment 15 (vno[0] = 90762) erasing segment 16 (vno[0] = 90944) erasing segment 17 (vno[0] = 90959) erasing segment 18 (vno[0] = 91742) erasing segment 19 (vno[0] = 91974) erasing segment 20 (vno[0] = 93007) erasing segment 21 (vno[0] = 94696) erasing segment 22 (vno[0] = 94745) erasing segment 23 (vno[0] = 96798) erasing segment 24 (vno[0] = 97890) erasing segment 25 (vno[0] = 97959) erasing segment 26 (vno[0] = 98865) erasing segment 27 (vno[0] = 100698) erasing segment 28 (vno[0] = 103780) erasing segment 29 (vno[0] = 104490) erasing segment 30 (vno[0] = 104518) writing cortex label to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/label/lh.cortex.label... writing curvature file /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->4.74) (max @ vno 64658 --> 65979) face area 0.33 +- 0.17 (0.00-->2.67) refinement took 3.5 minutes #-------------------------------------------- #@# Smooth2 lh Fri Jun 9 17:14:01 AEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 Fri Jun 9 17:14:04 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.1 mm, total surface area = 82648 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.053 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 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 162 vertices thresholded to be in k1 ~ [-0.33 0.47], k2 ~ [-0.11 0.12] total integrated curvature = 0.566*4pi (7.110) --> 0 handles ICI = 1.4, FI = 9.3, variation=156.017 138 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 123 vertices thresholded to be in [-0.13 0.21] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Fri Jun 9 17:15:24 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm fsMM.nii.mgz 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 [ fsMM.nii.mgz/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 [ 251 ] Gb_filter = 0 WARN: S lookup min: -0.696070 WARN: S explicit min: 0.000000 vertex = 48 #-------------------------------------------- #@# Sphere lh Fri Jun 9 17:15:26 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 0.273... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=brain, 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 %20.43 pass 1: epoch 2 of 3 starting distance error %20.33 unfolding complete - removing small folds... starting distance error %20.23 removing remaining folds... final distance error %20.24 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.45 hours #-------------------------------------------- #@# Surf Reg lh Fri Jun 9 17:42:36 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_register -curv ../surf/lh.sphere /home/brainmind-engineer/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 /home/brainmind-engineer/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=brain, 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=brain, 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 = 0.596 curvature mean = 0.057, std = 0.940 curvature mean = 0.022, std = 0.859 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 345409.5, tmin=0.6212 d=32.00 min @ (8.00, 8.00, 0.00) sse = 246653.5, tmin=1.2454 d=8.00 min @ (2.00, 0.00, 0.00) sse = 244386.2, tmin=2.4986 d=4.00 min @ (-1.00, 0.00, 1.00) sse = 243019.2, tmin=3.1241 d=2.00 min @ (0.00, -0.50, -0.50) sse = 242798.8, tmin=3.7553 d=0.50 min @ (0.12, 0.00, -0.25) sse = 242790.6, tmin=5.0274 tol=1.0e+00, sigma=0.5, host=brain, 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 5.03 min curvature mean = 0.025, std = 0.961 curvature mean = 0.010, std = 0.940 curvature mean = 0.024, std = 0.973 curvature mean = 0.005, std = 0.973 curvature mean = 0.022, std = 0.975 curvature mean = 0.002, std = 0.989 2 Reading smoothwm curvature mean = -0.024, std = 0.328 curvature mean = 0.004, std = 0.066 curvature mean = 0.065, std = 0.300 curvature mean = 0.003, std = 0.078 curvature mean = 0.031, std = 0.474 curvature mean = 0.003, std = 0.085 curvature mean = 0.019, std = 0.604 curvature mean = 0.003, std = 0.088 curvature mean = 0.007, std = 0.712 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Jun 9 17:58:09 AEST 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 Jun 9 17:58:11 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mrisp_paint -a 5 /home/brainmind-engineer/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 /home/brainmind-engineer/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Jun 9 17:58:12 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsMM.nii.mgz lh ../surf/lh.sphere.reg /home/brainmind-engineer/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 /home/brainmind-engineer/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... 1130 labels changed using aseg relabeling using gibbs priors... 000: 3091 changed, 138935 examined... 001: 704 changed, 13237 examined... 002: 179 changed, 3845 examined... 003: 45 changed, 1031 examined... 004: 22 changed, 295 examined... 005: 7 changed, 130 examined... 006: 2 changed, 45 examined... 007: 2 changed, 14 examined... 008: 1 changed, 14 examined... 009: 0 changed, 7 examined... 217 labels changed using aseg 000: 120 total segments, 78 labels (233 vertices) changed 001: 43 total segments, 1 labels (1 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1402 vertices marked for relabeling... 1402 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 32 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Jun 9 17:58:45 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs fsMM.nii.mgz 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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/filled.mgz... reading volume /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/brain.finalsurfs.mgz... reading volume /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/wm.mgz... 22009 bright wm thresholded. 625 bright non-wm voxels segmented. reading original surface position from /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.orig... computing class statistics... border white: 258685 voxels (1.54%) border gray 289608 voxels (1.73%) WM (93.0): 93.8 +- 8.3 [70.0 --> 110.0] GM (80.0) : 78.8 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.0 (was 70) setting MAX_BORDER_WHITE to 109.3 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 49.0 (was 40) setting MAX_GRAY to 92.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=71 mean inside = 93.3, mean outside = 76.2 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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->3.23) (max @ vno 131413 --> 133291) face area 0.27 +- 0.13 (0.00-->2.39) mean absolute distance = 0.78 +- 1.01 3626 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 38 points - only 0.00% unknown deleting segment 1 with 12 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 5 with 716 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 42 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown mean border=80.1, 123 (123) missing vertices, mean dist 0.2 [0.8 (%34.4)->0.8 (%65.6))] %60 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.05-->3.98) (max @ vno 64669 --> 65993) face area 0.27 +- 0.14 (0.00-->2.04) mean absolute distance = 0.36 +- 0.60 3101 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5142605.5, rms=9.58 001: dt: 0.5000, sse=6804581.5, rms=6.966 (0.000%) 002: dt: 0.5000, sse=7378620.0, rms=5.431 (0.000%) 003: dt: 0.5000, sse=7889385.5, rms=4.534 (0.000%) 004: dt: 0.5000, sse=8228843.5, rms=4.017 (0.000%) 005: dt: 0.5000, sse=8433801.0, rms=3.765 (0.000%) 006: dt: 0.5000, sse=8555804.0, rms=3.602 (0.000%) 007: dt: 0.5000, sse=8631274.0, rms=3.546 (0.000%) 008: dt: 0.5000, sse=8667919.0, rms=3.480 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8689489.0, rms=3.459 (0.000%) 010: dt: 0.2500, sse=5698027.0, rms=2.630 (0.000%) 011: dt: 0.2500, sse=5368278.0, rms=2.396 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=5156520.0, rms=2.352 (0.000%) 013: dt: 0.1250, sse=5030958.0, rms=2.294 (0.000%) rms = 2.29, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4995592.0, rms=2.289 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 59 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 688 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown deleting segment 19 with 32 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 22 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 24 with 2 points - only 0.00% unknown deleting segment 25 with 5 points - only 0.00% unknown mean border=82.8, 151 (36) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.3 (%31.2))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.26 (0.07-->4.34) (max @ vno 64658 --> 65979) face area 0.34 +- 0.17 (0.00-->2.77) mean absolute distance = 0.27 +- 0.38 3696 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5429550.5, rms=4.20 015: dt: 0.5000, sse=5998558.5, rms=2.924 (0.000%) rms = 3.11, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5590630.5, rms=2.377 (0.000%) 017: dt: 0.2500, sse=5458599.5, rms=2.077 (0.000%) 018: dt: 0.2500, sse=5337817.5, rms=1.967 (0.000%) rms = 1.93, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5300507.5, rms=1.930 (0.000%) rms = 1.89, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=5223869.5, rms=1.888 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 63 points - only 0.00% unknown deleting segment 1 with 20 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 687 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown mean border=85.1, 162 (22) missing vertices, mean dist -0.1 [0.3 (%69.7)->0.2 (%30.3))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=brain, 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 +- 0.26 (0.04-->4.68) (max @ vno 64658 --> 65979) face area 0.33 +- 0.17 (0.00-->2.73) mean absolute distance = 0.23 +- 0.33 3117 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5410494.5, rms=3.34 021: dt: 0.5000, sse=5822091.5, rms=2.802 (0.000%) rms = 3.07, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=5466345.0, rms=2.082 (0.000%) 023: dt: 0.2500, sse=5472027.0, rms=1.798 (0.000%) 024: dt: 0.2500, sse=5412404.5, rms=1.718 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... rms = 1.69, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5369331.5, rms=1.694 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 62 points - only 0.00% unknown deleting segment 1 with 20 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 7 with 699 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 5 points - only 0.00% unknown deleting segment 12 with 40 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown mean border=85.8, 188 (17) missing vertices, mean dist -0.0 [0.2 (%54.2)->0.2 (%45.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=brain, 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=5381862.5, rms=1.87 rms = 1.97, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5540800.0, rms=1.467 (0.000%) 027: dt: 0.2500, sse=5882118.5, rms=1.266 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.26, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5879339.0, rms=1.260 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=61.0, 157 (157) missing vertices, mean dist 1.8 [0.6 (%0.0)->2.4 (%100.0))] %24 local maxima, %49 large gradients and %23 min vals, 1213 gradients ignored tol=1.0e-04, sigma=2.0, host=brain, 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=19355798.0, rms=24.83 001: dt: 0.5000, sse=14937735.0, rms=21.196 (0.000%) 002: dt: 0.5000, sse=11712862.0, rms=18.097 (0.000%) 003: dt: 0.5000, sse=9564984.0, rms=15.543 (0.000%) 004: dt: 0.5000, sse=8398387.0, rms=13.498 (0.000%) 005: dt: 0.5000, sse=7798173.5, rms=11.888 (0.000%) 006: dt: 0.5000, sse=7517151.0, rms=10.663 (0.000%) 007: dt: 0.5000, sse=7307317.0, rms=9.665 (0.000%) 008: dt: 0.5000, sse=7298145.5, rms=8.835 (0.000%) 009: dt: 0.5000, sse=7216418.0, rms=8.066 (0.000%) 010: dt: 0.5000, sse=7327809.5, rms=7.356 (0.000%) 011: dt: 0.5000, sse=7311933.5, rms=6.627 (0.000%) 012: dt: 0.5000, sse=7413197.0, rms=5.954 (0.000%) 013: dt: 0.5000, sse=7490053.5, rms=5.396 (0.000%) 014: dt: 0.5000, sse=7639648.5, rms=5.040 (0.000%) 015: dt: 0.5000, sse=7690613.0, rms=4.805 (0.000%) 016: dt: 0.5000, sse=7803920.0, rms=4.660 (0.000%) 017: dt: 0.5000, sse=7820952.5, rms=4.552 (0.000%) 018: dt: 0.5000, sse=7878073.5, rms=4.497 (0.000%) 019: dt: 0.5000, sse=7881436.5, rms=4.434 (0.000%) rms = 4.42, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=7915293.5, rms=4.420 (0.000%) 021: dt: 0.2500, sse=5743353.5, rms=3.717 (0.000%) 022: dt: 0.2500, sse=5568093.0, rms=3.492 (0.000%) rms = 3.48, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5426366.0, rms=3.482 (0.000%) 024: dt: 0.1250, sse=5159601.0, rms=3.301 (0.000%) rms = 3.27, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5116098.5, rms=3.268 (0.000%) positioning took 1.8 minutes mean border=57.8, 1004 (31) missing vertices, mean dist 0.2 [0.2 (%39.4)->0.6 (%60.6))] %47 local maxima, %31 large gradients and %18 min vals, 467 gradients ignored tol=1.0e-04, sigma=1.0, host=brain, 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=6013420.5, rms=5.92 026: dt: 0.5000, sse=6221777.0, rms=4.964 (0.000%) 027: dt: 0.5000, sse=7901958.5, rms=4.759 (0.000%) rms = 4.79, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6512488.0, rms=3.900 (0.000%) 029: dt: 0.2500, sse=5924498.5, rms=3.598 (0.000%) rms = 3.55, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5909453.5, rms=3.549 (0.000%) 031: dt: 0.1250, sse=5556369.5, rms=3.227 (0.000%) 032: dt: 0.1250, sse=5508003.5, rms=3.155 (0.000%) rms = 3.14, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5485187.5, rms=3.143 (0.000%) positioning took 0.6 minutes mean border=55.4, 1204 (23) missing vertices, mean dist 0.1 [0.2 (%32.3)->0.3 (%67.7))] %60 local maxima, %17 large gradients and %18 min vals, 598 gradients ignored tol=1.0e-04, sigma=0.5, host=brain, 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=5788852.0, rms=4.52 rms = 4.64, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5532148.0, rms=3.828 (0.000%) 035: dt: 0.2500, sse=5451095.0, rms=3.435 (0.000%) 036: dt: 0.2500, sse=5782623.0, rms=3.334 (0.000%) rms = 3.34, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=5660569.0, rms=3.205 (0.000%) 038: dt: 0.1250, sse=5540409.0, rms=3.011 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5515475.5, rms=2.962 (0.000%) positioning took 0.5 minutes mean border=54.4, 2294 (17) missing vertices, mean dist 0.0 [0.2 (%40.5)->0.2 (%59.5))] %62 local maxima, %15 large gradients and %18 min vals, 459 gradients ignored tol=1.0e-04, sigma=0.2, host=brain, 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 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5558821.5, rms=3.23 rms = 4.38, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5456384.0, rms=2.967 (0.000%) rms = 2.96, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5765197.0, rms=2.956 (0.000%) 042: dt: 0.1250, sse=5603003.0, rms=2.829 (0.000%) rms = 2.78, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=5641116.0, rms=2.783 (0.000%) positioning took 0.3 minutes writing curvature file /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.area.pial vertex spacing 1.01 +- 0.44 (0.03-->7.20) (max @ vno 87793 --> 88799) face area 0.40 +- 0.32 (0.00-->6.02) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138935 vertices processed 25000 of 138935 vertices processed 50000 of 138935 vertices processed 75000 of 138935 vertices processed 100000 of 138935 vertices processed 125000 of 138935 vertices processed 0 of 138935 vertices processed 25000 of 138935 vertices processed 50000 of 138935 vertices processed 75000 of 138935 vertices processed 100000 of 138935 vertices processed 125000 of 138935 vertices processed thickness calculation complete, 516:851 truncations. 27675 vertices at 0 distance 89129 vertices at 1 distance 90967 vertices at 2 distance 41351 vertices at 3 distance 12251 vertices at 4 distance 3492 vertices at 5 distance 1193 vertices at 6 distance 469 vertices at 7 distance 231 vertices at 8 distance 117 vertices at 9 distance 60 vertices at 10 distance 33 vertices at 11 distance 28 vertices at 12 distance 26 vertices at 13 distance 18 vertices at 14 distance 15 vertices at 15 distance 15 vertices at 16 distance 14 vertices at 17 distance 18 vertices at 18 distance 14 vertices at 19 distance 14 vertices at 20 distance writing curvature file /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.thickness positioning took 7.3 minutes #-------------------------------------------- #@# Surf Volume lh Fri Jun 9 18:06:06 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 Jun 9 18:06:06 AEST 2017 /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts pctsurfcon --s fsMM.nii.mgz --lh-only Log file is /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts/pctsurfcon.log Fri Jun 9 18:06:06 AEST 2017 setenv SUBJECTS_DIR /home/brainmind-engineer/freesurfer/subjects cd /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/scripts /home/brainmind-engineer/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/brainmind-engineer/freesurfer mri_vol2surf --mov /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/tmp.pctsurfcon.14807/lh.wm.mgh --regheader fsMM.nii.mgz --cortex srcvol = /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz as target reference. Loading label /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/label/lh.cortex.label Reading surface /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/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 = 117392 Masking with /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/label/lh.cortex.label Writing to /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/tmp.pctsurfcon.14807/lh.wm.mgh Dim: 138935 1 1 mri_vol2surf --mov /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/tmp.pctsurfcon.14807/lh.gm.mgh --projfrac 0.3 --regheader fsMM.nii.mgz --cortex srcvol = /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/mri/orig.mgz as target reference. Loading label /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/label/lh.cortex.label Reading surface /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.white Done reading source surface Reading thickness /home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.thickness mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.thickness, -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsMM.nii.mgz exited with ERRORS at Fri Jun 9 18:06:13 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting