Thu Sep 18 08:56:46 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2 /usr/local/freesurfer/bin/recon-all -i /usr/local/freesurfer/subjects/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all subjid case018_tp2 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 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 63657 maxlocks unlimited maxsignal 63657 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8169760 3407624 4762136 21732 79824 2421296 -/+ buffers/cache: 906504 7263256 Swap: 8385532 0 8385532 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 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: 2014/09/18-12:56:46-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-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: 2014/09/18-12:56:46-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-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: 2014/09/18-12:56:46-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:46-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:46-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:47-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:48-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-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: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-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: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/09/18-12:56:49-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: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2014/09/18-12:56:49-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: mahmoud Machine: ubuntu Platform: Linux PlatformVersion: 3.13.0-35-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/case018_tp2 mri_convert /usr/local/freesurfer/subjects/Case018/case018_tp2/22-1.dcm /usr/local/freesurfer/subjects/case018_tp2/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/Case018/case018_tp2/22-1.dcm /usr/local/freesurfer/subjects/case018_tp2/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/Case018/case018_tp2/22-1.dcm... Getting Series No INFO: Found 178 files in /usr/local/freesurfer/subjects/Case018/case018_tp2 INFO: Scanning for Series Number 22 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 21 INFO: sorting. INFO: (512 512 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /usr/local/freesurfer/subjects/Case018/case018_tp2/22-1.dcm Identification NumarisVer syngo MR B17 ScannerModel Verio PatientName HANKS-CONTROL-MD-04082011 Date and time StudyDate 20110408 StudyTime 132916.390000 SeriesTime 141301.390000 AcqTime 140816.752500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol T1 MPRAGE SAG NON-SEL. PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.26 InversionTime 900 RepetitionTime 1950 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 21 SeriesNo 22 ImageNo 1 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 92.3999 129.0694 111.9054 VolRes 0.5000 0.5000 1.0000 VolDim 512 512 176 Vc -0.0206 -0.9998 -0.0000 Vr -0.0038 0.0001 -1.0000 Vs -0.9998 0.0206 0.0038 VolCenter 1.2900 2.9230 -15.7586 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=1950.00, TE=2.26, TI=900.00, flip angle=9.00 i_ras = (-0.0206399, -0.999787, -7.45047e-09) j_ras = (-0.00380732, 7.86068e-05, -0.999993) k_ras = (-0.99978, 0.0206397, 0.00380815) writing to /usr/local/freesurfer/subjects/case018_tp2/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Sep 18 08:57:26 EDT 2014 Found 1 runs /usr/local/freesurfer/subjects/case018_tp2/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/case018_tp2/mri/orig/001.mgz /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz /usr/local/freesurfer/subjects/case018_tp2 mri_convert /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz -rt cubic --conform mri_convert /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz -rt cubic --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz... TR=1950.00, TE=2.26, TI=900.00, flip angle=9.00 i_ras = (-0.0206399, -0.999787, -7.45047e-09) j_ras = (-0.00380732, 7.86068e-05, -0.999993) k_ras = (-0.99978, 0.0206397, 0.00380815) Original Data has (0.5, 0.5, 1) mm size and (512, 512, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using MRItoBSpline degree 3 writing to /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Sep 18 08:58:03 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 18 09:00:09 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7878, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/talairach_avi.log TalAviQA: 0.97905 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 18 09:00:09 EDT 2014 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/case018_tp2/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 18 09:00:10 EDT 2014 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.17196 /usr/local/freesurfer/subjects/case018_tp2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17196/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17196/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=1950.00, TE=2.26, TI=900.00, flip angle=9.00 i_ras = (-1, -1.11759e-08, 2.77068e-08) j_ras = (-4.72646e-08, 9.60426e-10, -1) k_ras = (-2.23517e-08, 1, -1.74623e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17196/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 18 09:00:13 EDT 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.17196/nu0.mnc ./tmp.mri_nu_correct.mni.17196/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17196/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mahmoud@ubuntu:/usr/local/freesurfer/subjects/case018_tp2/mri/] [2014-09-18 09:00:13] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17196/0/ ./tmp.mri_nu_correct.mni.17196/nu0.mnc ./tmp.mri_nu_correct.mni.17196/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 47 CV of field change: 0.00096718 [mahmoud@ubuntu:/usr/local/freesurfer/subjects/case018_tp2/mri/] [2014-09-18 09:00:48] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17196/nu0.mnc ./tmp.mri_nu_correct.mni.17196/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Sep 18 09:00:51 EDT 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.17196/nu1.mnc ./tmp.mri_nu_correct.mni.17196/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17196/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mahmoud@ubuntu:/usr/local/freesurfer/subjects/case018_tp2/mri/] [2014-09-18 09:00:51] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17196/1/ ./tmp.mri_nu_correct.mni.17196/nu1.mnc ./tmp.mri_nu_correct.mni.17196/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000979496 [mahmoud@ubuntu:/usr/local/freesurfer/subjects/case018_tp2/mri/] [2014-09-18 09:01:25] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17196/nu1.mnc ./tmp.mri_nu_correct.mni.17196/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17196/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17196/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/case018_tp2/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17196/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17196/ones.mgz sysname Linux hostname ubuntu machine x86_64 user mahmoud input ./tmp.mri_nu_correct.mni.17196/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.17196/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.17196/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17196/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17196/input.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17196/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17196/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17196/input.mean.dat sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17196/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.17196/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17196/ones.mgz --i ./tmp.mri_nu_correct.mni.17196/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17196/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17196/output.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17196/ones.mgz --i ./tmp.mri_nu_correct.mni.17196/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17196/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17196/output.mean.dat sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17196/ones.mgz Loading ./tmp.mri_nu_correct.mni.17196/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.17196/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.17196/nu2.mnc ./tmp.mri_nu_correct.mni.17196/nu2.mnc mul .96394854119390984420 Saving result to './tmp.mri_nu_correct.mni.17196/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.17196/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.17196/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.17196/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.11759e-08, 2.77068e-08) j_ras = (-4.72646e-08, 9.60426e-10, -1) k_ras = (-2.23517e-08, 1, -1.74623e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 2, 104) to ( 3, 110) Thu Sep 18 09:02:15 EDT 2014 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Sep 18 09:02:18 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.124 -0.013 -0.039 -3.009; 0.022 1.016 0.143 -15.614; 0.014 -0.064 1.115 1.650; 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 109 gm peak at 84 (84), valley at 65 (65) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 63 (63) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 28 seconds. #-------------------------------------------- #@# Skull Stripping Thu Sep 18 09:04:47 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_em_register -skull nu.mgz /usr/local/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 '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (45, 24, 25) --> (204, 255, 226) using (98, 101, 126) as brain centroid... mean wm in atlas = 126, using box (78,72,101) --> (117, 129,150) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.561486 @ (9.091, 9.091, -9.091) max log p = -4.458162 @ (-4.545, 4.545, -4.545) max log p = -4.428743 @ (-2.273, -2.273, 2.273) max log p = -4.428743 @ (0.000, 0.000, 0.000) max log p = -4.410796 @ (0.568, -2.841, -2.841) max log p = -4.410796 @ (0.000, 0.000, 0.000) Found translation: (2.8, 8.5, -14.2): log p = -4.411 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.4 (thresh=-4.4) 1.236 0.000 0.000 -33.699; 0.000 1.140 0.150 -25.307; 0.000 -0.150 1.140 -14.158; 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) 1.226 -0.149 -0.020 -13.223; 0.161 1.130 0.149 -44.868; 0.000 -0.161 1.226 -30.672; 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=-4.1) 1.226 -0.149 -0.020 -13.223; 0.161 1.130 0.149 -44.868; 0.000 -0.161 1.226 -30.672; 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=-4.1) 1.166 -0.044 0.041 -23.007; 0.040 1.154 0.196 -37.811; -0.049 -0.189 1.174 -9.197; 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) 1.144 -0.043 0.041 -20.217; 0.040 1.154 0.196 -37.811; -0.049 -0.189 1.174 -9.197; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.142 -0.034 0.042 -20.694; 0.031 1.158 0.186 -35.850; -0.049 -0.180 1.175 -10.493; 0.000 0.000 0.000 1.000; **************************************** 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) 1.142 -0.034 0.042 -20.694; 0.031 1.158 0.186 -35.850; -0.049 -0.180 1.175 -10.493; 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 1.14171 -0.03369 0.04205 -20.69384; 0.03071 1.15766 0.18630 -35.84992; -0.04876 -0.17953 1.17530 -10.49343; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.14171 -0.03369 0.04205 -20.69384; 0.03071 1.15766 0.18630 -35.84992; -0.04876 -0.17953 1.17530 -10.49343; 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: 1.142 -0.034 0.042 -20.694; 0.031 1.158 0.186 -35.850; -0.049 -0.180 1.175 -10.493; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.6) transform before final EM align: 1.142 -0.034 0.042 -20.694; 0.031 1.158 0.186 -35.850; -0.049 -0.180 1.175 -10.493; 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 1.14171 -0.03369 0.04205 -20.69384; 0.03071 1.15766 0.18630 -35.84992; -0.04876 -0.17953 1.17530 -10.49343; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.14171 -0.03369 0.04205 -20.69384; 0.03071 1.15766 0.18630 -35.84992; -0.04876 -0.17953 1.17530 -10.49343; 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: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.142 -0.034 0.042 -20.694; 0.031 1.158 0.186 -35.850; -0.049 -0.180 1.175 -10.493; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 33 minutes and 44 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=105 z=128 r=91 first estimation of the main basin volume: 3231453 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=109, y=93, z=93, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=17807529681 voxels, voxel volume =1.000 = 17807529681 mmm3 = 17807529.984 cm3 done. PostAnalyze...Basin Prior 64 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=109, z=116, r=9760 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=7, CSF_MAX=26 , nb = 44234 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=25 , nb = -1032734051 LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=33 , nb = -1054485599 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=7, CSF_MAX=31 , nb = 1077451187 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=30 , nb = 1051336198 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=47 , nb = 1079675142 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 26, 35, 50, 77 after analyzing : 26, 45, 50, 53 RIGHT_CER before analyzing : 25, 30, 45, 92 after analyzing : 25, 40, 45, 53 LEFT_CER before analyzing : 33, 41, 54, 90 after analyzing : 33, 49, 54, 59 RIGHT_BRAIN before analyzing : 31, 42, 53, 77 after analyzing : 31, 49, 53, 56 LEFT_BRAIN before analyzing : 30, 38, 49, 77 after analyzing : 30, 45, 49, 53 OTHER before analyzing : 47, 34, 25, 56 after analyzing : 25, 34, 34, 39 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.648, std = 6.690 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.11, sigma = 4.72 after rotation: sse = 3.11, sigma = 4.72 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.25, its var is 4.10 before Erosion-Dilatation 0.36% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1600725 voxels, voxel volume = 1.000 mm3 = 1600725 mmm3 = 1600.725 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Sep 18 09:39:00 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/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 '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 44, 39) --> (190, 174, 208) using (106, 87, 124) as brain centroid... mean wm in atlas = 107, using box (91,71,103) --> (121, 102,144) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.999782 @ (-9.091, 9.091, -9.091) max log p = -3.909609 @ (4.545, -4.545, -4.545) max log p = -3.838058 @ (2.273, 2.273, 2.273) max log p = -3.814901 @ (1.136, 1.136, -1.136) max log p = -3.809174 @ (1.705, 0.568, -0.568) max log p = -3.809174 @ (0.000, 0.000, 0.000) Found translation: (0.6, 8.5, -13.1): log p = -3.809 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-3.8 (thresh=-3.8) 1.064 0.000 0.000 -7.480; 0.000 1.075 0.000 7.747; 0.000 0.000 1.000 -13.068; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.064 0.000 0.000 -7.480; 0.000 1.075 0.000 7.747; 0.000 0.000 1.000 -13.068; 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 =-3.7 (thresh=-3.7) 1.123 0.034 0.034 -24.269; -0.035 1.089 0.100 -4.645; -0.034 -0.109 0.994 5.099; 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) 1.124 0.038 0.002 -21.043; -0.036 1.064 0.130 -5.482; 0.004 -0.141 0.973 6.196; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.123 0.035 0.034 -24.338; -0.036 1.068 0.098 -2.172; -0.034 -0.109 0.994 5.232; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.125 0.019 0.016 -20.359; -0.018 1.066 0.106 -5.788; -0.015 -0.118 0.995 3.199; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.123 0.019 0.016 -20.014; -0.018 1.065 0.106 -5.642; -0.015 -0.118 0.994 3.319; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 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 1.12235 0.02693 0.02466 -21.85567; -0.02718 1.06510 0.11444 -4.93665; -0.02436 -0.12637 0.99139 6.13101; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.12235 0.02693 0.02466 -21.85567; -0.02718 1.06510 0.11444 -4.93665; -0.02436 -0.12637 0.99139 6.13101; 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: 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.5 (old=-4.2) transform before final EM align: 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 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 1.12235 0.02693 0.02466 -21.85567; -0.02718 1.06510 0.11444 -4.93665; -0.02436 -0.12637 0.99139 6.13101; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.12235 0.02693 0.02466 -21.85567; -0.02718 1.06510 0.11444 -4.93665; -0.02436 -0.12637 0.99139 6.13101; 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) = 3.9 tol 0.000000 final transform: 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 31 minutes and 9 seconds. #-------------------------------------- #@# CA Normalize Thu Sep 18 10:10:09 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 44, 39) --> (190, 174, 209) using (106, 87, 124) as brain centroid... mean wm in atlas = 107, using box (91,71,103) --> (121, 102,144) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 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 (126, 45, 39) --> (185, 153, 206) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 247.0 0 of 798 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 46, 38) --> (127, 152, 206) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 247.0 0 of 1342 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 124, 65) --> (170, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 101.0 --> 247.0 0 of 13 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 124, 62) --> (127, 165, 119) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 247.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 99) --> (140, 182, 130) Brain_Stem: limiting intensities to 98.0 --> 247.0 4 of 5 (80.0%) samples deleted using 2170 total control points for intensity normalization... bias field = 1.035 +- 0.049 5 of 2166 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 45, 39) --> (185, 153, 206) Left_Cerebral_White_Matter: limiting intensities to 103.0 --> 241.0 237 of 807 (29.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 46, 38) --> (127, 152, 206) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 241.0 0 of 1243 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 124, 65) --> (170, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 241.0 29 of 50 (58.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 124, 62) --> (127, 165, 119) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 241.0 0 of 55 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 99) --> (140, 182, 130) Brain_Stem: limiting intensities to 89.0 --> 241.0 33 of 70 (47.1%) samples deleted using 2225 total control points for intensity normalization... bias field = 1.006 +- 0.039 12 of 1926 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 45, 39) --> (185, 153, 206) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 238.0 0 of 875 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 46, 38) --> (127, 152, 206) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 238.0 0 of 1271 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 124, 65) --> (170, 167, 119) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 238.0 0 of 61 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 124, 62) --> (127, 165, 119) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 238.0 0 of 62 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 99) --> (140, 182, 130) Brain_Stem: limiting intensities to 85.0 --> 238.0 54 of 151 (35.8%) samples deleted using 2420 total control points for intensity normalization... bias field = 1.011 +- 0.039 6 of 2366 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 47 seconds. #-------------------------------------- #@# CA Reg Thu Sep 18 10:11:56 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.20 (predicted orig area = 6.7) 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=0.814, neg=0, invalid=96777 0001: dt=221.952000, rms=0.734 (9.841%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.720 (1.877%), neg=0, invalid=96777 0003: dt=221.952000, rms=0.709 (1.563%), neg=0, invalid=96777 0004: dt=73.984000, rms=0.706 (0.405%), neg=0, invalid=96777 0005: dt=517.888000, rms=0.699 (1.040%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.695 (0.555%), neg=0, invalid=96777 0007: dt=110.976000, rms=0.694 (0.111%), neg=0, invalid=96777 0008: dt=110.976000, rms=0.693 (0.186%), neg=0, invalid=96777 0009: dt=110.976000, rms=0.691 (0.281%), neg=0, invalid=96777 0010: dt=110.976000, rms=0.689 (0.347%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.686 (0.389%), neg=0, invalid=96777 0012: dt=110.976000, rms=0.683 (0.353%), neg=0, invalid=96777 0013: dt=110.976000, rms=0.681 (0.375%), neg=0, invalid=96777 0014: dt=110.976000, rms=0.679 (0.320%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.677 (0.214%), neg=0, invalid=96777 0016: dt=110.976000, rms=0.677 (0.116%), neg=0, invalid=96777 0017: dt=110.976000, rms=0.676 (0.067%), neg=0, invalid=96777 0018: dt=295.936000, rms=0.675 (0.153%), neg=0, invalid=96777 0019: dt=55.488000, rms=0.675 (0.037%), neg=0, invalid=96777 0020: dt=55.488000, rms=0.675 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=96777 0021: dt=295.936000, rms=0.670 (0.783%), neg=0, invalid=96777 0022: dt=110.976000, rms=0.669 (0.109%), neg=0, invalid=96777 0023: dt=110.976000, rms=0.668 (0.049%), neg=0, invalid=96777 0024: dt=110.976000, rms=0.668 (0.076%), neg=0, invalid=96777 0025: dt=110.976000, rms=0.667 (0.119%), neg=0, invalid=96777 0026: dt=110.976000, rms=0.666 (0.211%), neg=0, invalid=96777 0027: dt=110.976000, rms=0.664 (0.244%), neg=0, invalid=96777 0028: dt=110.976000, rms=0.663 (0.208%), neg=0, invalid=96777 0029: dt=110.976000, rms=0.662 (0.166%), neg=0, invalid=96777 0030: dt=110.976000, rms=0.661 (0.113%), neg=0, invalid=96777 0031: dt=110.976000, rms=0.660 (0.099%), neg=0, invalid=96777 0032: dt=295.936000, rms=0.660 (0.098%), neg=0, invalid=96777 0033: dt=295.936000, rms=0.660 (-0.414%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=96777 0034: dt=31.104000, rms=0.663 (0.204%), neg=0, invalid=96777 0035: dt=62.208000, rms=0.661 (0.322%), neg=0, invalid=96777 0036: dt=248.832000, rms=0.651 (1.476%), neg=0, invalid=96777 0037: dt=31.104000, rms=0.647 (0.707%), neg=0, invalid=96777 0038: dt=25.920000, rms=0.646 (0.164%), neg=0, invalid=96777 0039: dt=25.920000, rms=0.644 (0.194%), neg=0, invalid=96777 0040: dt=25.920000, rms=0.643 (0.294%), neg=0, invalid=96777 0041: dt=25.920000, rms=0.640 (0.342%), neg=0, invalid=96777 0042: dt=25.920000, rms=0.638 (0.347%), neg=0, invalid=96777 0043: dt=25.920000, rms=0.635 (0.470%), neg=0, invalid=96777 0044: dt=25.920000, rms=0.632 (0.466%), neg=0, invalid=96777 0045: dt=25.920000, rms=0.630 (0.374%), neg=0, invalid=96777 0046: dt=25.920000, rms=0.628 (0.292%), neg=0, invalid=96777 0047: dt=25.920000, rms=0.626 (0.279%), neg=0, invalid=96777 0048: dt=25.920000, rms=0.624 (0.336%), neg=0, invalid=96777 0049: dt=25.920000, rms=0.622 (0.339%), neg=0, invalid=96777 0050: dt=25.920000, rms=0.620 (0.294%), neg=0, invalid=96777 0051: dt=25.920000, rms=0.619 (0.209%), neg=0, invalid=96777 0052: dt=25.920000, rms=0.618 (0.179%), neg=0, invalid=96777 0053: dt=25.920000, rms=0.617 (0.185%), neg=0, invalid=96777 0054: dt=25.920000, rms=0.615 (0.184%), neg=0, invalid=96777 0055: dt=25.920000, rms=0.615 (0.133%), neg=0, invalid=96777 0056: dt=25.920000, rms=0.614 (0.156%), neg=0, invalid=96777 0057: dt=25.920000, rms=0.613 (0.155%), neg=0, invalid=96777 0058: dt=25.920000, rms=0.612 (0.132%), neg=0, invalid=96777 0059: dt=25.920000, rms=0.611 (0.113%), neg=0, invalid=96777 0060: dt=25.920000, rms=0.611 (0.117%), neg=0, invalid=96777 0061: dt=25.920000, rms=0.610 (0.149%), neg=0, invalid=96777 0062: dt=25.920000, rms=0.609 (0.135%), neg=0, invalid=96777 0063: dt=25.920000, rms=0.608 (0.104%), neg=0, invalid=96777 0064: dt=25.920000, rms=0.608 (0.036%), neg=0, invalid=96777 0065: dt=82.944000, rms=0.607 (0.076%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.607 (0.015%), neg=0, invalid=96777 0067: dt=20.736000, rms=0.607 (0.017%), neg=0, invalid=96777 0068: dt=20.736000, rms=0.607 (0.009%), neg=0, invalid=96777 0069: dt=20.736000, rms=0.607 (0.025%), neg=0, invalid=96777 0070: dt=20.736000, rms=0.607 (0.032%), neg=0, invalid=96777 0071: dt=20.736000, rms=0.607 (0.038%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.607 (0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=96777 0073: dt=103.680000, rms=0.603 (0.530%), neg=0, invalid=96777 0074: dt=9.072000, rms=0.603 (0.017%), neg=0, invalid=96777 0075: dt=9.072000, rms=0.603 (0.012%), neg=0, invalid=96777 0076: dt=9.072000, rms=0.603 (-0.036%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=96777 0077: dt=8.000000, rms=0.635 (0.210%), neg=0, invalid=96777 0078: dt=11.200000, rms=0.634 (0.145%), neg=0, invalid=96777 0079: dt=11.200000, rms=0.633 (0.144%), neg=0, invalid=96777 0080: dt=11.200000, rms=0.632 (0.063%), neg=0, invalid=96777 0081: dt=11.200000, rms=0.632 (-0.068%), neg=0, invalid=96777 0082: dt=44.800000, rms=0.629 (0.543%), neg=0, invalid=96777 0083: dt=11.200000, rms=0.628 (0.089%), neg=0, invalid=96777 0084: dt=11.200000, rms=0.628 (0.109%), neg=0, invalid=96777 0085: dt=11.200000, rms=0.627 (0.149%), neg=0, invalid=96777 0086: dt=11.200000, rms=0.625 (0.249%), neg=0, invalid=96777 0087: dt=11.200000, rms=0.624 (0.278%), neg=0, invalid=96777 0088: dt=11.200000, rms=0.622 (0.273%), neg=0, invalid=96777 0089: dt=11.200000, rms=0.620 (0.237%), neg=0, invalid=96777 0090: dt=11.200000, rms=0.619 (0.215%), neg=0, invalid=96777 0091: dt=11.200000, rms=0.618 (0.222%), neg=0, invalid=96777 0092: dt=11.200000, rms=0.617 (0.103%), neg=0, invalid=96777 0093: dt=11.200000, rms=0.616 (0.138%), neg=0, invalid=96777 0094: dt=11.200000, rms=0.616 (0.102%), neg=0, invalid=96777 0095: dt=11.200000, rms=0.615 (0.083%), neg=0, invalid=96777 0096: dt=6.400000, rms=0.615 (0.046%), neg=0, invalid=96777 0097: dt=6.400000, rms=0.615 (0.023%), neg=0, invalid=96777 0098: dt=6.400000, rms=0.615 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0099: dt=2.800000, rms=0.615 (0.010%), neg=0, invalid=96777 0100: dt=1.600000, rms=0.615 (0.004%), neg=0, invalid=96777 0101: dt=1.600000, rms=0.615 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.661, neg=0, invalid=96777 0102: dt=0.144000, rms=0.661 (0.002%), neg=0, invalid=96777 0103: dt=0.000000, rms=0.661 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=96777 0104: dt=0.252000, rms=0.661 (0.018%), neg=0, invalid=96777 0105: dt=0.216000, rms=0.661 (0.007%), neg=0, invalid=96777 0106: dt=0.216000, rms=0.661 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.744, neg=0, invalid=96777 0107: dt=0.869055, rms=0.724 (2.637%), neg=0, invalid=96777 0108: dt=1.024609, rms=0.720 (0.499%), neg=0, invalid=96777 0109: dt=1.114094, rms=0.719 (0.203%), neg=0, invalid=96777 0110: dt=1.114094, rms=0.718 (0.099%), neg=0, invalid=96777 0111: dt=1.114094, rms=0.718 (-0.083%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.718, neg=0, invalid=96777 0112: dt=1.330882, rms=0.716 (0.257%), neg=0, invalid=96777 0113: dt=0.256000, rms=0.716 (0.007%), neg=0, invalid=96777 0114: dt=0.256000, rms=0.716 (0.002%), neg=0, invalid=96777 0115: dt=0.256000, rms=0.716 (-0.006%), 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=0.676, neg=0, invalid=96777 0116: dt=0.137653, rms=0.671 (0.762%), neg=0, invalid=96777 0117: dt=0.306250, rms=0.670 (0.131%), neg=0, invalid=96777 0118: dt=0.153125, rms=0.667 (0.465%), neg=0, invalid=96777 0119: dt=0.153125, rms=0.666 (0.197%), neg=0, invalid=96777 0120: dt=0.153125, rms=0.666 (-0.091%), neg=0, invalid=96777 0121: dt=0.000000, rms=0.666 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.666, neg=0, invalid=96777 0122: dt=0.080000, rms=0.666 (0.063%), neg=0, invalid=96777 0123: dt=0.384000, rms=0.665 (0.079%), neg=0, invalid=96777 0124: dt=0.096000, rms=0.665 (0.039%), neg=0, invalid=96777 0125: dt=0.096000, rms=0.665 (0.013%), neg=0, invalid=96777 0126: dt=0.096000, rms=0.665 (0.020%), neg=0, invalid=96777 0127: dt=0.096000, rms=0.664 (0.034%), neg=0, invalid=96777 0128: dt=0.096000, rms=0.664 (0.045%), neg=0, invalid=96777 0129: dt=0.096000, rms=0.664 (0.064%), neg=0, invalid=96777 0130: dt=0.096000, rms=0.663 (0.066%), neg=0, invalid=96777 0131: dt=0.096000, rms=0.663 (0.059%), neg=0, invalid=96777 0132: dt=0.096000, rms=0.662 (0.054%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.12720 (34) Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (1292 voxels, overlap=0.392) Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (1292 voxels, peak = 33), gca=32.8 gca peak = 0.14022 (22) mri peak = 0.10403 (37) Right_Lateral_Ventricle (43): linear fit = 1.49 x + 0.0 (1525 voxels, overlap=0.150) Right_Lateral_Ventricle (43): linear fit = 1.49 x + 0.0 (1525 voxels, peak = 33), gca=32.7 gca peak = 0.24234 (100) mri peak = 0.17285 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (515 voxels, overlap=0.024) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (515 voxels, peak = 108), gca=107.5 gca peak = 0.19192 (97) mri peak = 0.08511 (110) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (437 voxels, overlap=0.032) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (437 voxels, peak = 109), gca=109.1 gca peak = 0.24007 (63) mri peak = 0.10954 (83) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (983 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (983 voxels, peak = 82), gca=81.6 gca peak = 0.29892 (64) mri peak = 0.09916 (82) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (941 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (941 voxels, peak = 82), gca=81.6 gca peak = 0.12541 (104) mri peak = 0.12223 (110) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (83002 voxels, overlap=0.474) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (83002 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.07660 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (86912 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (86912 voxels, peak = 110), gca=109.7 gca peak = 0.11691 (63) mri peak = 0.03930 (80) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (36511 voxels, overlap=0.022) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (36511 voxels, peak = 78), gca=78.4 gca peak = 0.13270 (63) mri peak = 0.04270 (78) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (39648 voxels, overlap=0.004) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (39648 voxels, peak = 78), gca=78.4 gca peak = 0.15182 (70) mri peak = 0.13470 (91) Right_Caudate (50): linear fit = 1.24 x + 0.0 (351 voxels, overlap=0.010) Right_Caudate (50): linear fit = 1.24 x + 0.0 (351 voxels, peak = 86), gca=86.5 gca peak = 0.14251 (76) mri peak = 0.10636 (91) Left_Caudate (11): linear fit = 1.18 x + 0.0 (918 voxels, overlap=0.023) Left_Caudate (11): linear fit = 1.18 x + 0.0 (918 voxels, peak = 90), gca=90.1 gca peak = 0.12116 (60) mri peak = 0.04109 (83) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (16621 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (16621 voxels, peak = 84), gca=84.3 gca peak = 0.12723 (61) mri peak = 0.04484 (84) Right_Cerebellum_Cortex (47): linear fit = 1.36 x + 0.0 (20629 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.36 x + 0.0 (20629 voxels, peak = 83), gca=82.7 gca peak = 0.22684 (88) mri peak = 0.04637 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9194 voxels, overlap=0.977) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9194 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.05221 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8587 voxels, overlap=0.994) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (8587 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.11081 (85) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (422 voxels, overlap=0.068) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (422 voxels, peak = 82), gca=81.5 gca peak = 0.39668 (62) mri peak = 0.09824 (81) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (413 voxels, overlap=0.068) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (413 voxels, peak = 82), gca=81.5 gca peak = 0.10129 (93) mri peak = 0.09436 (107) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5630 voxels, overlap=0.053) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5630 voxels, peak = 106), gca=105.6 gca peak = 0.12071 (89) mri peak = 0.08756 (106) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4437 voxels, overlap=0.115) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4437 voxels, peak = 103), gca=102.8 gca peak = 0.13716 (82) mri peak = 0.08096 (96) Left_Putamen (12): linear fit = 1.16 x + 0.0 (2810 voxels, overlap=0.019) Left_Putamen (12): linear fit = 1.16 x + 0.0 (2810 voxels, peak = 96), gca=95.5 gca peak = 0.15214 (84) mri peak = 0.07424 (99) Right_Putamen (51): linear fit = 1.18 x + 0.0 (2742 voxels, overlap=0.156) Right_Putamen (51): linear fit = 1.18 x + 0.0 (2742 voxels, peak = 100), gca=99.5 gca peak = 0.08983 (85) mri peak = 0.05964 (88) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11759 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11759 voxels, peak = 91), gca=90.5 gca peak = 0.11809 (92) mri peak = 0.11367 (105) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (1068 voxels, overlap=0.011) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (1068 voxels, peak = 104), gca=104.4 gca peak = 0.12914 (94) mri peak = 0.09413 (109) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1147 voxels, overlap=0.028) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1147 voxels, peak = 106), gca=105.8 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.13989 (33) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (507 voxels, overlap=0.630) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (507 voxels, peak = 30), gca=29.8 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 1.28 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.32 x + 0.0 Left_Pallidum too bright - rescaling by 0.971 (from 1.125) to 105.9 (was 109.1) Right_Putamen too bright - rescaling by 0.987 (from 1.185) to 98.3 (was 99.5) Right_Pallidum too bright - rescaling by 0.985 (from 1.075) to 105.9 (was 107.5) 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=0.676, neg=0, invalid=96777 0133: dt=110.976000, rms=0.635 (6.086%), neg=0, invalid=96777 0134: dt=129.472000, rms=0.629 (1.028%), neg=0, invalid=96777 0135: dt=129.472000, rms=0.626 (0.433%), neg=0, invalid=96777 0136: dt=129.472000, rms=0.624 (0.346%), neg=0, invalid=96777 0137: dt=92.480000, rms=0.622 (0.274%), neg=0, invalid=96777 0138: dt=129.472000, rms=0.620 (0.256%), neg=0, invalid=96777 0139: dt=129.472000, rms=0.619 (0.169%), neg=0, invalid=96777 0140: dt=129.472000, rms=0.618 (0.215%), neg=0, invalid=96777 0141: dt=129.472000, rms=0.617 (0.139%), neg=0, invalid=96777 0142: dt=221.952000, rms=0.616 (0.192%), neg=0, invalid=96777 0143: dt=92.480000, rms=0.615 (0.110%), neg=0, invalid=96777 0144: dt=129.472000, rms=0.614 (0.127%), neg=0, invalid=96777 0145: dt=129.472000, rms=0.614 (0.076%), neg=0, invalid=96777 0146: dt=221.952000, rms=0.613 (0.135%), neg=0, invalid=96777 0147: dt=129.472000, rms=0.613 (0.099%), neg=0, invalid=96777 0148: dt=295.936000, rms=0.612 (0.109%), neg=0, invalid=96777 0149: dt=92.480000, rms=0.611 (0.132%), neg=0, invalid=96777 0150: dt=129.472000, rms=0.611 (0.035%), neg=0, invalid=96777 0151: dt=129.472000, rms=0.610 (0.082%), neg=0, invalid=96777 0152: dt=129.472000, rms=0.610 (0.100%), neg=0, invalid=96777 0153: dt=129.472000, rms=0.609 (0.147%), neg=0, invalid=96777 0154: dt=129.472000, rms=0.608 (0.161%), neg=0, invalid=96777 0155: dt=129.472000, rms=0.607 (0.151%), neg=0, invalid=96777 0156: dt=129.472000, rms=0.606 (0.188%), neg=0, invalid=96777 0157: dt=129.472000, rms=0.605 (0.172%), neg=0, invalid=96777 0158: dt=129.472000, rms=0.604 (0.129%), neg=0, invalid=96777 0159: dt=129.472000, rms=0.603 (0.157%), neg=0, invalid=96777 0160: dt=129.472000, rms=0.602 (0.138%), neg=0, invalid=96777 0161: dt=129.472000, rms=0.602 (0.092%), neg=0, invalid=96777 0162: dt=129.472000, rms=0.601 (0.146%), neg=0, invalid=96777 0163: dt=129.472000, rms=0.601 (0.031%), neg=0, invalid=96777 0164: dt=129.472000, rms=0.600 (0.146%), neg=0, invalid=96777 0165: dt=129.472000, rms=0.599 (0.110%), neg=0, invalid=96777 0166: dt=129.472000, rms=0.598 (0.098%), neg=0, invalid=96777 0167: dt=129.472000, rms=0.598 (0.080%), neg=0, invalid=96777 0168: dt=129.472000, rms=0.597 (0.129%), neg=0, invalid=96777 0169: dt=129.472000, rms=0.597 (0.056%), neg=0, invalid=96777 0170: dt=129.472000, rms=0.596 (0.139%), neg=0, invalid=96777 0171: dt=129.472000, rms=0.595 (0.107%), neg=0, invalid=96777 0172: dt=129.472000, rms=0.595 (0.116%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.594 (0.086%), neg=0, invalid=96777 0174: dt=129.472000, rms=0.594 (0.040%), neg=0, invalid=96777 0175: dt=129.472000, rms=0.594 (0.057%), neg=0, invalid=96777 0176: dt=129.472000, rms=0.593 (0.044%), neg=0, invalid=96777 0177: dt=129.472000, rms=0.593 (0.069%), neg=0, invalid=96777 0178: dt=129.472000, rms=0.593 (0.071%), neg=0, invalid=96777 0179: dt=129.472000, rms=0.592 (0.096%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.592 (0.008%), neg=0, invalid=96777 0181: dt=129.472000, rms=0.592 (0.017%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.592 (0.016%), neg=0, invalid=96777 0183: dt=92.480000, rms=0.591 (0.056%), neg=0, invalid=96777 0184: dt=92.480000, rms=0.591 (0.009%), neg=0, invalid=96777 0185: dt=92.480000, rms=0.591 (0.013%), neg=0, invalid=96777 0186: dt=92.480000, rms=0.591 (0.009%), neg=0, invalid=96777 0187: dt=92.480000, rms=0.591 (0.013%), neg=0, invalid=96777 0188: dt=92.480000, rms=0.591 (0.007%), neg=0, invalid=96777 0189: dt=73.984000, rms=0.591 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.591, neg=0, invalid=96777 0190: dt=369.920000, rms=0.590 (0.207%), neg=0, invalid=96777 0191: dt=73.984000, rms=0.590 (0.056%), neg=0, invalid=96777 0192: dt=295.936000, rms=0.589 (0.071%), neg=0, invalid=96777 0193: dt=129.472000, rms=0.589 (0.035%), neg=0, invalid=96777 0194: dt=129.472000, rms=0.589 (0.015%), neg=0, invalid=96777 0195: dt=129.472000, rms=0.589 (0.042%), neg=0, invalid=96777 0196: dt=129.472000, rms=0.588 (0.047%), neg=0, invalid=96777 0197: dt=129.472000, rms=0.588 (0.066%), neg=0, invalid=96777 0198: dt=129.472000, rms=0.588 (0.054%), neg=0, invalid=96777 0199: dt=129.472000, rms=0.587 (0.063%), neg=0, invalid=96777 0200: dt=129.472000, rms=0.587 (0.055%), neg=0, invalid=96777 0201: dt=129.472000, rms=0.587 (0.050%), neg=0, invalid=96777 0202: dt=129.472000, rms=0.586 (0.040%), neg=0, invalid=96777 0203: dt=129.472000, rms=0.586 (0.059%), neg=0, invalid=96777 0204: dt=129.472000, rms=0.586 (0.052%), neg=0, invalid=96777 0205: dt=129.472000, rms=0.585 (0.049%), neg=0, invalid=96777 0206: dt=129.472000, rms=0.585 (0.052%), neg=0, invalid=96777 0207: dt=129.472000, rms=0.585 (0.044%), neg=0, invalid=96777 0208: dt=129.472000, rms=0.585 (0.049%), neg=0, invalid=96777 0209: dt=129.472000, rms=0.584 (0.044%), neg=0, invalid=96777 0210: dt=129.472000, rms=0.584 (0.044%), neg=0, invalid=96777 0211: dt=129.472000, rms=0.584 (0.048%), neg=0, invalid=96777 0212: dt=129.472000, rms=0.584 (0.041%), neg=0, invalid=96777 0213: dt=129.472000, rms=0.583 (0.035%), neg=0, invalid=96777 0214: dt=129.472000, rms=0.583 (0.039%), neg=0, invalid=96777 0215: dt=129.472000, rms=0.583 (0.040%), neg=0, invalid=96777 0216: dt=129.472000, rms=0.583 (0.035%), neg=0, invalid=96777 0217: dt=129.472000, rms=0.583 (0.029%), neg=0, invalid=96777 0218: dt=129.472000, rms=0.582 (0.025%), neg=0, invalid=96777 0219: dt=129.472000, rms=0.582 (0.026%), neg=0, invalid=96777 0220: dt=129.472000, rms=0.582 (0.029%), neg=0, invalid=96777 0221: dt=129.472000, rms=0.582 (0.027%), neg=0, invalid=96777 0222: dt=129.472000, rms=0.582 (0.059%), neg=0, invalid=96777 0223: dt=129.472000, rms=0.581 (0.041%), neg=0, invalid=96777 0224: dt=129.472000, rms=0.581 (0.017%), neg=0, invalid=96777 0225: dt=129.472000, rms=0.581 (0.030%), neg=0, invalid=96777 0226: dt=129.472000, rms=0.581 (0.027%), neg=0, invalid=96777 0227: dt=129.472000, rms=0.581 (0.032%), neg=0, invalid=96777 0228: dt=129.472000, rms=0.580 (0.035%), neg=0, invalid=96777 0229: dt=129.472000, rms=0.580 (0.023%), neg=0, invalid=96777 0230: dt=129.472000, rms=0.580 (0.023%), neg=0, invalid=96777 0231: dt=73.984000, rms=0.580 (0.002%), neg=0, invalid=96777 0232: dt=73.984000, rms=0.580 (0.004%), neg=0, invalid=96777 0233: dt=73.984000, rms=0.580 (0.003%), neg=0, invalid=96777 0234: dt=73.984000, rms=0.580 (0.007%), neg=0, invalid=96777 0235: dt=73.984000, rms=0.580 (0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.582, neg=0, invalid=96777 0236: dt=82.944000, rms=0.580 (0.217%), neg=0, invalid=96777 0237: dt=248.832000, rms=0.576 (0.830%), neg=0, invalid=96777 0238: dt=20.736000, rms=0.574 (0.256%), neg=0, invalid=96777 0239: dt=82.944000, rms=0.573 (0.216%), neg=0, invalid=96777 0240: dt=31.104000, rms=0.572 (0.155%), neg=0, invalid=96777 0241: dt=36.288000, rms=0.571 (0.137%), neg=0, invalid=96777 0242: dt=103.680000, rms=0.570 (0.220%), neg=0, invalid=96777 0243: dt=25.920000, rms=0.569 (0.159%), neg=0, invalid=96777 0244: dt=145.152000, rms=0.567 (0.360%), neg=0, invalid=96777 0245: dt=25.920000, rms=0.566 (0.092%), neg=0, invalid=96777 0246: dt=103.680000, rms=0.566 (0.145%), neg=0, invalid=96777 0247: dt=31.104000, rms=0.565 (0.124%), neg=0, invalid=96777 0248: dt=145.152000, rms=0.564 (0.207%), neg=0, invalid=96777 0249: dt=20.736000, rms=0.563 (0.100%), neg=0, invalid=96777 0250: dt=145.152000, rms=0.562 (0.166%), neg=0, invalid=96777 0251: dt=31.104000, rms=0.562 (0.115%), neg=0, invalid=96777 0252: dt=82.944000, rms=0.561 (0.104%), neg=0, invalid=96777 0253: dt=25.920000, rms=0.561 (0.078%), neg=0, invalid=96777 0254: dt=82.944000, rms=0.560 (0.076%), neg=0, invalid=96777 0255: dt=25.920000, rms=0.560 (0.070%), neg=0, invalid=96777 0256: dt=82.944000, rms=0.559 (0.073%), neg=0, invalid=96777 0257: dt=20.736000, rms=0.559 (0.071%), neg=0, invalid=96777 0258: dt=145.152000, rms=0.558 (0.110%), neg=0, invalid=96777 0259: dt=36.288000, rms=0.558 (0.113%), neg=0, invalid=96777 0260: dt=36.288000, rms=0.557 (0.049%), neg=0, invalid=96777 0261: dt=36.288000, rms=0.557 (0.048%), neg=0, invalid=96777 0262: dt=36.288000, rms=0.557 (0.074%), neg=0, invalid=96777 0263: dt=36.288000, rms=0.556 (0.105%), neg=0, invalid=96777 0264: dt=36.288000, rms=0.555 (0.132%), neg=0, invalid=96777 0265: dt=36.288000, rms=0.554 (0.178%), neg=0, invalid=96777 0266: dt=36.288000, rms=0.554 (0.156%), neg=0, invalid=96777 0267: dt=36.288000, rms=0.552 (0.197%), neg=0, invalid=96777 0268: dt=36.288000, rms=0.551 (0.183%), neg=0, invalid=96777 0269: dt=36.288000, rms=0.550 (0.168%), neg=0, invalid=96777 0270: dt=36.288000, rms=0.550 (0.170%), neg=0, invalid=96777 0271: dt=36.288000, rms=0.549 (0.164%), neg=0, invalid=96777 0272: dt=36.288000, rms=0.548 (0.168%), neg=0, invalid=96777 0273: dt=36.288000, rms=0.547 (0.178%), neg=0, invalid=96777 0274: dt=36.288000, rms=0.546 (0.177%), neg=0, invalid=96777 0275: dt=36.288000, rms=0.545 (0.153%), neg=0, invalid=96777 0276: dt=36.288000, rms=0.544 (0.129%), neg=0, invalid=96777 0277: dt=36.288000, rms=0.544 (0.135%), neg=0, invalid=96777 0278: dt=36.288000, rms=0.543 (0.135%), neg=0, invalid=96777 0279: dt=36.288000, rms=0.542 (0.150%), neg=0, invalid=96777 0280: dt=36.288000, rms=0.541 (0.141%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.541 (0.126%), neg=0, invalid=96777 0282: dt=36.288000, rms=0.540 (0.117%), neg=0, invalid=96777 0283: dt=36.288000, rms=0.539 (0.102%), neg=0, invalid=96777 0284: dt=36.288000, rms=0.539 (0.113%), neg=0, invalid=96777 0285: dt=36.288000, rms=0.538 (0.105%), neg=0, invalid=96777 0286: dt=36.288000, rms=0.538 (0.077%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.537 (0.069%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.537 (0.101%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.536 (0.122%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.536 (0.096%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.535 (0.083%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.535 (0.056%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.534 (0.085%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.534 (0.074%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.534 (0.061%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.533 (0.058%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.533 (0.074%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.533 (0.071%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.532 (0.067%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.532 (0.054%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.532 (0.056%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.531 (0.059%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.531 (0.042%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.531 (0.035%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.531 (0.054%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.530 (0.079%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.530 (0.055%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.530 (0.040%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.530 (0.017%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.530 (0.037%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.529 (0.058%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.529 (0.046%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.529 (0.027%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.529 (0.026%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.528 (0.041%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.528 (0.032%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.528 (0.019%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.528 (0.037%), neg=0, invalid=96777 0319: dt=36.288000, rms=0.528 (0.039%), neg=0, invalid=96777 0320: dt=36.288000, rms=0.528 (0.038%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.527 (0.027%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.527 (0.004%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.527 (0.020%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.527 (0.054%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.527 (0.044%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.527 (0.009%), neg=0, invalid=96777 0327: dt=36.288000, rms=0.527 (0.010%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.527 (0.029%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.526 (0.013%), neg=0, invalid=96777 0330: dt=36.288000, rms=0.526 (0.018%), neg=0, invalid=96777 0331: dt=36.288000, rms=0.526 (0.012%), neg=0, invalid=96777 0332: dt=62.208000, rms=0.526 (0.041%), neg=0, invalid=96777 0333: dt=7.776000, rms=0.526 (0.001%), neg=0, invalid=96777 0334: dt=7.776000, rms=0.526 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=96777 0335: dt=124.416000, rms=0.525 (0.300%), neg=0, invalid=96777 0336: dt=25.920000, rms=0.524 (0.115%), neg=0, invalid=96777 0337: dt=103.680000, rms=0.524 (0.073%), neg=0, invalid=96777 0338: dt=36.288000, rms=0.523 (0.052%), neg=0, invalid=96777 0339: dt=103.680000, rms=0.523 (0.056%), neg=0, invalid=96777 0340: dt=31.104000, rms=0.523 (0.031%), neg=0, invalid=96777 0341: dt=31.104000, rms=0.523 (0.020%), neg=0, invalid=96777 0342: dt=31.104000, rms=0.523 (0.027%), neg=0, invalid=96777 0343: dt=31.104000, rms=0.522 (0.043%), neg=0, invalid=96777 0344: dt=31.104000, rms=0.522 (0.047%), neg=0, invalid=96777 0345: dt=31.104000, rms=0.522 (0.046%), neg=0, invalid=96777 0346: dt=31.104000, rms=0.522 (0.046%), neg=0, invalid=96777 0347: dt=31.104000, rms=0.521 (0.034%), neg=0, invalid=96777 0348: dt=31.104000, rms=0.521 (0.056%), neg=0, invalid=96777 0349: dt=31.104000, rms=0.521 (0.055%), neg=0, invalid=96777 0350: dt=31.104000, rms=0.521 (0.045%), neg=0, invalid=96777 0351: dt=31.104000, rms=0.521 (0.022%), neg=0, invalid=96777 0352: dt=31.104000, rms=0.520 (0.036%), neg=0, invalid=96777 0353: dt=31.104000, rms=0.520 (0.053%), neg=0, invalid=96777 0354: dt=31.104000, rms=0.520 (0.037%), neg=0, invalid=96777 0355: dt=31.104000, rms=0.520 (0.045%), neg=0, invalid=96777 0356: dt=31.104000, rms=0.519 (0.038%), neg=0, invalid=96777 0357: dt=31.104000, rms=0.519 (0.037%), neg=0, invalid=96777 0358: dt=31.104000, rms=0.519 (0.049%), neg=0, invalid=96777 0359: dt=31.104000, rms=0.519 (0.036%), neg=0, invalid=96777 0360: dt=31.104000, rms=0.519 (0.034%), neg=0, invalid=96777 0361: dt=31.104000, rms=0.518 (0.038%), neg=0, invalid=96777 0362: dt=31.104000, rms=0.518 (0.046%), neg=0, invalid=96777 0363: dt=31.104000, rms=0.518 (0.040%), neg=0, invalid=96777 0364: dt=31.104000, rms=0.518 (0.039%), neg=0, invalid=96777 0365: dt=31.104000, rms=0.518 (0.048%), neg=0, invalid=96777 0366: dt=31.104000, rms=0.517 (0.032%), neg=0, invalid=96777 0367: dt=31.104000, rms=0.517 (0.032%), neg=0, invalid=96777 0368: dt=31.104000, rms=0.517 (0.025%), neg=0, invalid=96777 0369: dt=31.104000, rms=0.517 (0.033%), neg=0, invalid=96777 0370: dt=31.104000, rms=0.517 (0.019%), neg=0, invalid=96777 0371: dt=31.104000, rms=0.517 (0.034%), neg=0, invalid=96777 0372: dt=31.104000, rms=0.517 (0.020%), neg=0, invalid=96777 0373: dt=31.104000, rms=0.516 (0.030%), neg=0, invalid=96777 0374: dt=31.104000, rms=0.516 (0.032%), neg=0, invalid=96777 0375: dt=31.104000, rms=0.516 (0.017%), neg=0, invalid=96777 0376: dt=31.104000, rms=0.516 (0.025%), neg=0, invalid=96777 0377: dt=31.104000, rms=0.516 (0.021%), neg=0, invalid=96777 0378: dt=31.104000, rms=0.516 (0.022%), neg=0, invalid=96777 0379: dt=31.104000, rms=0.516 (0.013%), neg=0, invalid=96777 0380: dt=36.288000, rms=0.516 (0.013%), neg=0, invalid=96777 0381: dt=9.072000, rms=0.516 (0.002%), neg=0, invalid=96777 0382: dt=9.072000, rms=0.516 (-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=0.526, neg=0, invalid=96777 0383: dt=11.200000, rms=0.526 (0.095%), neg=0, invalid=96777 0384: dt=25.600000, rms=0.525 (0.110%), neg=0, invalid=96777 0385: dt=11.200000, rms=0.525 (0.072%), neg=0, invalid=96777 0386: dt=38.400000, rms=0.524 (0.188%), neg=0, invalid=96777 0387: dt=6.769231, rms=0.523 (0.086%), neg=0, invalid=96777 0388: dt=102.400000, rms=0.521 (0.461%), neg=0, invalid=96777 0389: dt=11.234043, rms=0.520 (0.204%), neg=0, invalid=96777 0390: dt=11.200000, rms=0.519 (0.179%), neg=0, invalid=96777 0391: dt=25.600000, rms=0.518 (0.132%), neg=0, invalid=96777 0392: dt=9.600000, rms=0.518 (0.103%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.517 (0.081%), neg=0, invalid=96777 0394: dt=44.800000, rms=0.517 (0.165%), neg=0, invalid=96777 0395: dt=6.037736, rms=0.516 (0.081%), neg=0, invalid=96777 0396: dt=44.800000, rms=0.515 (0.249%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.515 (0.072%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.514 (0.051%), neg=0, invalid=96777 0399: dt=44.800000, rms=0.514 (0.137%), neg=0, invalid=96777 0400: dt=6.095238, rms=0.513 (0.039%), neg=0, invalid=96777 0401: dt=6.095238, rms=0.513 (0.064%), neg=0, invalid=96777 0402: dt=6.095238, rms=0.513 (0.048%), neg=0, invalid=96777 0403: dt=6.095238, rms=0.512 (0.063%), neg=0, invalid=96777 0404: dt=6.095238, rms=0.512 (0.077%), neg=0, invalid=96777 0405: dt=6.095238, rms=0.512 (0.081%), neg=0, invalid=96777 0406: dt=6.095238, rms=0.511 (0.094%), neg=0, invalid=96777 0407: dt=6.095238, rms=0.511 (0.102%), neg=0, invalid=96777 0408: dt=6.095238, rms=0.510 (0.109%), neg=0, invalid=96777 0409: dt=6.095238, rms=0.509 (0.116%), neg=0, invalid=96777 0410: dt=6.095238, rms=0.509 (0.116%), neg=0, invalid=96777 0411: dt=6.095238, rms=0.508 (0.118%), neg=0, invalid=96777 0412: dt=6.095238, rms=0.508 (0.113%), neg=0, invalid=96777 0413: dt=6.095238, rms=0.507 (0.105%), neg=0, invalid=96777 0414: dt=6.095238, rms=0.507 (0.099%), neg=0, invalid=96777 0415: dt=6.095238, rms=0.506 (0.102%), neg=0, invalid=96777 0416: dt=6.095238, rms=0.506 (0.105%), neg=0, invalid=96777 0417: dt=6.095238, rms=0.505 (0.106%), neg=0, invalid=96777 0418: dt=6.095238, rms=0.505 (0.102%), neg=0, invalid=96777 0419: dt=6.095238, rms=0.504 (0.097%), neg=0, invalid=96777 0420: dt=6.095238, rms=0.504 (0.093%), neg=0, invalid=96777 0421: dt=6.095238, rms=0.503 (0.084%), neg=0, invalid=96777 0422: dt=6.095238, rms=0.503 (0.083%), neg=0, invalid=96777 0423: dt=6.095238, rms=0.502 (0.082%), neg=0, invalid=96777 0424: dt=6.095238, rms=0.502 (0.073%), neg=0, invalid=96777 0425: dt=6.095238, rms=0.502 (0.073%), neg=0, invalid=96777 0426: dt=6.095238, rms=0.501 (0.066%), neg=0, invalid=96777 0427: dt=6.095238, rms=0.501 (0.064%), neg=0, invalid=96777 0428: dt=6.095238, rms=0.501 (0.065%), neg=0, invalid=96777 0429: dt=6.095238, rms=0.500 (0.069%), neg=0, invalid=96777 0430: dt=6.095238, rms=0.500 (0.062%), neg=0, invalid=96777 0431: dt=6.095238, rms=0.500 (0.053%), neg=0, invalid=96777 0432: dt=6.095238, rms=0.500 (0.046%), neg=0, invalid=96777 0433: dt=6.095238, rms=0.499 (0.044%), neg=0, invalid=96777 0434: dt=6.095238, rms=0.499 (0.045%), neg=0, invalid=96777 0435: dt=6.095238, rms=0.499 (0.039%), neg=0, invalid=96777 0436: dt=6.095238, rms=0.499 (0.035%), neg=0, invalid=96777 0437: dt=6.095238, rms=0.499 (0.031%), neg=0, invalid=96777 0438: dt=6.095238, rms=0.498 (0.034%), neg=0, invalid=96777 0439: dt=6.095238, rms=0.498 (0.033%), neg=0, invalid=96777 0440: dt=6.095238, rms=0.498 (0.034%), neg=0, invalid=96777 0441: dt=6.095238, rms=0.498 (0.031%), neg=0, invalid=96777 0442: dt=6.095238, rms=0.498 (0.026%), neg=0, invalid=96777 0443: dt=6.095238, rms=0.498 (0.022%), neg=0, invalid=96777 0444: dt=6.095238, rms=0.498 (0.028%), neg=0, invalid=96777 0445: dt=6.095238, rms=0.497 (0.029%), neg=0, invalid=96777 0446: dt=6.095238, rms=0.497 (0.026%), neg=0, invalid=96777 0447: dt=6.095238, rms=0.497 (0.023%), neg=0, invalid=96777 0448: dt=6.095238, rms=0.497 (0.021%), neg=0, invalid=96777 0449: dt=4.800000, rms=0.497 (0.003%), neg=0, invalid=96777 0450: dt=4.800000, rms=0.497 (0.001%), neg=0, invalid=96777 0451: dt=4.800000, rms=0.497 (0.003%), neg=0, invalid=96777 0452: dt=4.800000, rms=0.497 (0.005%), neg=0, invalid=96777 0453: dt=4.800000, rms=0.497 (0.004%), neg=0, invalid=96777 0454: dt=4.800000, rms=0.497 (0.005%), neg=0, invalid=96777 0455: dt=4.800000, rms=0.497 (0.006%), neg=0, invalid=96777 0456: dt=4.800000, rms=0.497 (0.008%), neg=0, invalid=96777 0457: dt=4.800000, rms=0.497 (0.008%), neg=0, invalid=96777 0458: dt=4.800000, rms=0.497 (0.010%), neg=0, invalid=96777 0459: dt=4.800000, rms=0.497 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0460: dt=44.800000, rms=0.494 (0.587%), neg=0, invalid=96777 0461: dt=11.200000, rms=0.494 (0.044%), neg=0, invalid=96777 0462: dt=11.200000, rms=0.493 (0.036%), neg=0, invalid=96777 0463: dt=11.200000, rms=0.493 (0.043%), neg=0, invalid=96777 0464: dt=11.200000, rms=0.493 (0.045%), neg=0, invalid=96777 0465: dt=11.200000, rms=0.493 (0.046%), neg=0, invalid=96777 0466: dt=11.200000, rms=0.492 (0.055%), neg=0, invalid=96777 0467: dt=11.200000, rms=0.492 (0.057%), neg=0, invalid=96777 0468: dt=11.200000, rms=0.492 (0.040%), neg=0, invalid=96777 0469: dt=11.200000, rms=0.492 (0.018%), neg=0, invalid=96777 0470: dt=11.200000, rms=0.492 (0.015%), neg=0, invalid=96777 0471: dt=44.800000, rms=0.492 (0.056%), neg=0, invalid=96777 0472: dt=11.200000, rms=0.491 (0.034%), neg=0, invalid=96777 0473: dt=11.200000, rms=0.491 (0.019%), neg=0, invalid=96777 0474: dt=11.200000, rms=0.491 (0.025%), neg=0, invalid=96777 0475: dt=11.200000, rms=0.491 (0.044%), neg=0, invalid=96777 0476: dt=11.200000, rms=0.491 (0.046%), neg=0, invalid=96777 0477: dt=11.200000, rms=0.491 (0.041%), neg=0, invalid=96777 0478: dt=11.200000, rms=0.490 (0.031%), neg=0, invalid=96777 0479: dt=11.200000, rms=0.490 (0.028%), neg=0, invalid=96777 0480: dt=11.200000, rms=0.490 (0.042%), neg=0, invalid=96777 0481: dt=11.200000, rms=0.490 (0.040%), neg=0, invalid=96777 0482: dt=11.200000, rms=0.490 (0.051%), neg=0, invalid=96777 0483: dt=11.200000, rms=0.489 (0.045%), neg=0, invalid=96777 0484: dt=11.200000, rms=0.489 (0.045%), neg=0, invalid=96777 0485: dt=11.200000, rms=0.489 (0.041%), neg=0, invalid=96777 0486: dt=11.200000, rms=0.489 (0.038%), neg=0, invalid=96777 0487: dt=11.200000, rms=0.489 (0.029%), neg=0, invalid=96777 0488: dt=11.200000, rms=0.488 (0.036%), neg=0, invalid=96777 0489: dt=11.200000, rms=0.488 (0.030%), neg=0, invalid=96777 0490: dt=11.200000, rms=0.488 (0.031%), neg=0, invalid=96777 0491: dt=11.200000, rms=0.488 (0.022%), neg=0, invalid=96777 0492: dt=11.200000, rms=0.488 (0.035%), neg=0, invalid=96777 0493: dt=11.200000, rms=0.488 (0.033%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.488 (0.031%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.487 (0.028%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.487 (0.031%), neg=0, invalid=96777 0497: dt=11.200000, rms=0.487 (0.038%), neg=0, invalid=96777 0498: dt=11.200000, rms=0.487 (0.034%), neg=0, invalid=96777 0499: dt=11.200000, rms=0.487 (0.039%), neg=0, invalid=96777 0500: dt=11.200000, rms=0.487 (0.044%), neg=0, invalid=96777 0501: dt=11.200000, rms=0.486 (0.029%), neg=0, invalid=96777 0502: dt=11.200000, rms=0.486 (0.018%), neg=0, invalid=96777 0503: dt=11.200000, rms=0.486 (0.023%), neg=0, invalid=96777 0504: dt=11.200000, rms=0.486 (0.037%), neg=0, invalid=96777 0505: dt=11.200000, rms=0.486 (0.037%), neg=0, invalid=96777 0506: dt=11.200000, rms=0.486 (0.030%), neg=0, invalid=96777 0507: dt=11.200000, rms=0.486 (0.035%), neg=0, invalid=96777 0508: dt=11.200000, rms=0.485 (0.030%), neg=0, invalid=96777 0509: dt=11.200000, rms=0.485 (0.029%), neg=0, invalid=96777 0510: dt=11.200000, rms=0.485 (0.028%), neg=0, invalid=96777 0511: dt=11.200000, rms=0.485 (0.030%), neg=0, invalid=96777 0512: dt=11.200000, rms=0.485 (0.032%), neg=0, invalid=96777 0513: dt=11.200000, rms=0.485 (0.018%), neg=0, invalid=96777 0514: dt=11.200000, rms=0.485 (0.033%), neg=0, invalid=96777 0515: dt=11.200000, rms=0.484 (0.035%), neg=0, invalid=96777 0516: dt=11.200000, rms=0.484 (0.026%), neg=0, invalid=96777 0517: dt=11.200000, rms=0.484 (0.023%), neg=0, invalid=96777 0518: dt=11.200000, rms=0.484 (0.017%), neg=0, invalid=96777 0519: dt=11.200000, rms=0.484 (0.011%), neg=0, invalid=96777 0520: dt=11.200000, rms=0.484 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=96777 0521: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=96777 0522: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=96777 0523: dt=1.384314, rms=0.541 (0.705%), neg=0, invalid=96777 0524: dt=0.384000, rms=0.541 (0.021%), neg=0, invalid=96777 0525: dt=0.384000, rms=0.541 (-0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0526: dt=1.117021, rms=0.540 (0.178%), neg=0, invalid=96777 0527: dt=0.448000, rms=0.540 (0.014%), neg=0, invalid=96777 0528: dt=0.448000, rms=0.540 (-0.006%), 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=0.499, neg=0, invalid=96777 0529: dt=0.145197, rms=0.494 (0.855%), neg=0, invalid=96777 0530: dt=0.127212, rms=0.492 (0.541%), neg=0, invalid=96777 0531: dt=0.116667, rms=0.490 (0.380%), neg=0, invalid=96777 0532: dt=0.320000, rms=0.486 (0.822%), neg=0, invalid=96777 0533: dt=0.007000, rms=0.486 (0.008%), neg=0, invalid=96777 0534: dt=0.007000, rms=0.486 (0.009%), neg=0, invalid=96777 0535: dt=0.007000, rms=0.486 (0.015%), neg=0, invalid=96777 0536: dt=0.007000, rms=0.485 (0.025%), neg=0, invalid=96777 0537: dt=0.007000, rms=0.485 (0.029%), neg=0, invalid=96777 0538: dt=0.007000, rms=0.485 (0.034%), neg=0, invalid=96777 0539: dt=0.007000, rms=0.485 (0.037%), neg=0, invalid=96777 0540: dt=0.007000, rms=0.485 (0.042%), neg=0, invalid=96777 0541: dt=0.007000, rms=0.485 (0.046%), neg=0, invalid=96777 0542: dt=0.007000, rms=0.484 (0.047%), neg=0, invalid=96777 0543: dt=0.007000, rms=0.484 (0.048%), neg=0, invalid=96777 0544: dt=0.007000, rms=0.484 (0.050%), neg=0, invalid=96777 0545: dt=0.007000, rms=0.484 (0.050%), neg=0, invalid=96777 0546: dt=0.007000, rms=0.483 (0.050%), neg=0, invalid=96777 0547: dt=0.007000, rms=0.483 (0.049%), neg=0, invalid=96777 0548: dt=0.007000, rms=0.483 (0.048%), neg=0, invalid=96777 0549: dt=0.007000, rms=0.483 (0.049%), neg=0, invalid=96777 0550: dt=0.007000, rms=0.482 (0.046%), neg=0, invalid=96777 0551: dt=0.007000, rms=0.482 (0.045%), neg=0, invalid=96777 0552: dt=0.007000, rms=0.482 (0.043%), neg=0, invalid=96777 0553: dt=0.007000, rms=0.482 (0.041%), neg=0, invalid=96777 0554: dt=0.007000, rms=0.482 (0.041%), neg=0, invalid=96777 0555: dt=0.007000, rms=0.481 (0.036%), neg=0, invalid=96777 0556: dt=0.007000, rms=0.481 (0.037%), neg=0, invalid=96777 0557: dt=0.007000, rms=0.481 (0.032%), neg=0, invalid=96777 0558: dt=0.007000, rms=0.481 (0.032%), neg=0, invalid=96777 0559: dt=0.007000, rms=0.481 (0.031%), neg=0, invalid=96777 0560: dt=0.007000, rms=0.481 (0.028%), neg=0, invalid=96777 0561: dt=0.007000, rms=0.481 (0.026%), neg=0, invalid=96777 0562: dt=0.007000, rms=0.480 (0.024%), neg=0, invalid=96777 0563: dt=0.007000, rms=0.480 (0.023%), neg=0, invalid=96777 0564: dt=0.384000, rms=0.480 (0.048%), neg=0, invalid=96777 0565: dt=0.007000, rms=0.480 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=96777 0566: dt=0.007000, rms=0.480 (0.019%), neg=0, invalid=96777 0567: dt=0.112000, rms=0.479 (0.300%), neg=0, invalid=96777 0568: dt=0.112000, rms=0.477 (0.227%), neg=0, invalid=96777 0569: dt=0.112000, rms=0.477 (0.176%), neg=0, invalid=96777 0570: dt=0.112000, rms=0.476 (0.135%), neg=0, invalid=96777 0571: dt=0.112000, rms=0.475 (0.105%), neg=0, invalid=96777 0572: dt=0.112000, rms=0.475 (0.087%), neg=0, invalid=96777 0573: dt=0.112000, rms=0.475 (0.066%), neg=0, invalid=96777 0574: dt=0.112000, rms=0.474 (0.057%), neg=0, invalid=96777 0575: dt=0.112000, rms=0.474 (0.047%), neg=0, invalid=96777 0576: dt=0.112000, rms=0.474 (0.038%), neg=0, invalid=96777 0577: dt=0.112000, rms=0.474 (0.068%), neg=0, invalid=96777 0578: dt=0.112000, rms=0.473 (0.082%), neg=0, invalid=96777 0579: dt=0.112000, rms=0.473 (0.086%), neg=0, invalid=96777 0580: dt=0.112000, rms=0.473 (0.076%), neg=0, invalid=96777 0581: dt=0.112000, rms=0.472 (0.061%), neg=0, invalid=96777 0582: dt=0.028000, rms=0.472 (-0.001%), neg=0, invalid=96777 0583: dt=0.000000, rms=0.472 (0.000%), 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=0.470, neg=0, invalid=96777 0584: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0585: dt=129.472000, rms=0.470 (0.046%), neg=0, invalid=96777 0586: dt=443.904000, rms=0.470 (0.096%), neg=0, invalid=96777 0587: dt=32.368000, rms=0.470 (0.041%), neg=0, invalid=96777 0588: dt=32.368000, rms=0.470 (0.003%), neg=0, invalid=96777 0589: dt=32.368000, rms=0.470 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0590: dt=9.072000, rms=0.470 (0.010%), neg=0, invalid=96777 0591: dt=7.776000, rms=0.470 (0.004%), neg=0, invalid=96777 0592: dt=7.776000, rms=0.470 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0593: dt=145.152000, rms=0.467 (0.542%), neg=0, invalid=96777 0594: dt=31.104000, rms=0.467 (0.067%), neg=0, invalid=96777 0595: dt=31.104000, rms=0.466 (0.065%), neg=0, invalid=96777 0596: dt=31.104000, rms=0.466 (0.085%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0597: dt=31.104000, rms=0.466 (0.094%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0598: dt=31.104000, rms=0.465 (0.125%), neg=0, invalid=96777 0599: dt=31.104000, rms=0.464 (0.140%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0600: dt=31.104000, rms=0.464 (0.131%), neg=0, invalid=96777 0601: dt=31.104000, rms=0.463 (0.115%), neg=0, invalid=96777 0602: dt=31.104000, rms=0.463 (0.097%), neg=0, invalid=96777 0603: dt=36.288000, rms=0.463 (0.022%), neg=0, invalid=96777 0604: dt=36.288000, rms=0.463 (0.013%), neg=0, invalid=96777 0605: dt=36.288000, rms=0.462 (0.028%), neg=0, invalid=96777 0606: dt=36.288000, rms=0.462 (0.035%), neg=0, invalid=96777 0607: dt=36.288000, rms=0.462 (0.058%), neg=0, invalid=96777 0608: dt=36.288000, rms=0.462 (0.053%), neg=0, invalid=96777 0609: dt=36.288000, rms=0.461 (0.060%), neg=0, invalid=96777 0610: dt=36.288000, rms=0.461 (0.059%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0611: dt=11.200000, rms=0.461 (0.110%), neg=0, invalid=96777 0612: dt=11.200000, rms=0.461 (0.065%), neg=0, invalid=96777 0613: dt=11.200000, rms=0.461 (0.045%), neg=0, invalid=96777 0614: dt=11.200000, rms=0.461 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0615: dt=11.200000, rms=0.461 (-0.052%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 0616: dt=44.800000, rms=0.455 (1.244%), neg=0, invalid=96777 0617: dt=11.200000, rms=0.454 (0.209%), neg=0, invalid=96777 0618: dt=11.200000, rms=0.453 (0.133%), neg=0, invalid=96777 0619: dt=11.200000, rms=0.453 (0.163%), neg=0, invalid=96777 0620: dt=11.200000, rms=0.452 (0.205%), neg=0, invalid=96777 0621: dt=11.200000, rms=0.451 (0.215%), neg=0, invalid=96777 0622: dt=11.200000, rms=0.449 (0.320%), neg=0, invalid=96777 0623: dt=11.200000, rms=0.448 (0.282%), neg=0, invalid=96777 0624: dt=11.200000, rms=0.447 (0.273%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0625: dt=11.200000, rms=0.446 (0.226%), neg=0, invalid=96777 0626: dt=11.200000, rms=0.445 (0.229%), neg=0, invalid=96777 0627: dt=11.200000, rms=0.444 (0.169%), neg=0, invalid=96777 0628: dt=11.200000, rms=0.443 (0.168%), neg=0, invalid=96777 0629: dt=11.200000, rms=0.443 (0.136%), neg=0, invalid=96777 0630: dt=11.200000, rms=0.442 (0.128%), neg=0, invalid=96777 0631: dt=11.200000, rms=0.441 (0.127%), neg=0, invalid=96777 0632: dt=11.200000, rms=0.441 (0.127%), neg=0, invalid=96777 0633: dt=11.200000, rms=0.440 (0.102%), neg=0, invalid=96777 0634: dt=11.200000, rms=0.440 (0.094%), neg=0, invalid=96777 0635: dt=9.600000, rms=0.440 (0.022%), neg=0, invalid=96777 0636: dt=9.600000, rms=0.440 (0.006%), neg=0, invalid=96777 0637: dt=9.600000, rms=0.440 (0.010%), neg=0, invalid=96777 0638: dt=9.600000, rms=0.440 (0.001%), neg=0, invalid=96777 0639: dt=9.600000, rms=0.440 (-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=0.445, neg=0, invalid=96777 0640: dt=0.252000, rms=0.445 (0.001%), neg=0, invalid=96777 0641: dt=0.027000, rms=0.445 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=96777 0642: dt=3.456000, rms=0.445 (0.038%), neg=0, invalid=96777 0643: dt=2.304000, rms=0.445 (0.016%), neg=0, invalid=96777 0644: dt=2.304000, rms=0.445 (0.001%), neg=0, invalid=96777 0645: dt=2.304000, rms=0.445 (-0.025%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=96777 0646: dt=0.256000, rms=0.453 (0.005%), neg=0, invalid=96777 0647: dt=0.005000, rms=0.453 (0.002%), neg=0, invalid=96777 0648: dt=0.005000, rms=0.453 (0.000%), neg=0, invalid=96777 0649: dt=0.005000, rms=0.453 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=96777 0650: dt=1.536000, rms=0.452 (0.175%), neg=0, invalid=96777 0651: dt=0.500000, rms=0.452 (0.018%), neg=0, invalid=96777 0652: dt=0.500000, rms=0.452 (0.007%), neg=0, invalid=96777 0653: dt=0.500000, rms=0.452 (-0.016%), 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=0.443, neg=0, invalid=96777 iter 0, gcam->neg = 342 after 10 iterations, nbhd size=1, neg = 0 0654: dt=1.792000, rms=0.417 (6.019%), neg=0, invalid=96777 0655: dt=0.000375, rms=0.417 (-0.003%), neg=0, invalid=96777 0656: dt=0.000375, rms=0.417 (0.001%), neg=0, invalid=96777 0657: dt=0.000375, rms=0.417 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0658: dt=0.007000, rms=0.417 (0.005%), neg=0, invalid=96777 0659: dt=0.001250, rms=0.417 (0.001%), neg=0, invalid=96777 0660: dt=0.001250, rms=0.417 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0661: dt=0.001250, rms=0.417 (-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=0.404, neg=0, invalid=96777 0662: dt=0.000000, rms=0.404 (-0.107%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0663: dt=32.368000, rms=0.404 (0.003%), neg=0, invalid=96777 0664: dt=27.744000, rms=0.404 (0.001%), neg=0, invalid=96777 0665: dt=27.744000, rms=0.404 (0.000%), neg=0, invalid=96777 0666: dt=27.744000, rms=0.404 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0667: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0668: dt=36.288000, rms=0.404 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0669: dt=124.416000, rms=0.404 (0.037%), neg=0, invalid=96777 0670: dt=145.152000, rms=0.404 (0.049%), neg=0, invalid=96777 0671: dt=31.104000, rms=0.404 (0.005%), neg=0, invalid=96777 0672: dt=31.104000, rms=0.404 (0.005%), neg=0, invalid=96777 0673: dt=31.104000, rms=0.404 (0.007%), neg=0, invalid=96777 0674: dt=31.104000, rms=0.404 (0.010%), neg=0, invalid=96777 0675: dt=31.104000, rms=0.404 (0.013%), neg=0, invalid=96777 0676: dt=31.104000, rms=0.404 (0.013%), neg=0, invalid=96777 0677: dt=31.104000, rms=0.404 (0.011%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0678: dt=2.800000, rms=0.404 (0.009%), neg=0, invalid=96777 0679: dt=0.700000, rms=0.404 (0.000%), neg=0, invalid=96777 0680: dt=0.700000, rms=0.404 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 iter 0, gcam->neg = 31 after 10 iterations, nbhd size=1, neg = 0 0681: dt=102.400000, rms=0.402 (0.655%), neg=0, invalid=96777 0682: dt=11.200000, rms=0.401 (0.123%), neg=0, invalid=96777 0683: dt=11.200000, rms=0.401 (0.074%), neg=0, invalid=96777 0684: dt=11.200000, rms=0.401 (0.076%), neg=0, invalid=96777 0685: dt=11.200000, rms=0.400 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 24 iterations, nbhd size=3, neg = 0 0686: dt=11.200000, rms=0.400 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0687: dt=11.200000, rms=0.400 (0.077%), neg=0, invalid=96777 0688: dt=11.200000, rms=0.400 (0.050%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0689: dt=44.800000, rms=0.399 (0.171%), neg=0, invalid=96777 0690: dt=25.600000, rms=0.399 (0.051%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0691: dt=1.008000, rms=0.402 (0.011%), neg=0, invalid=96777 0692: dt=0.720000, rms=0.402 (0.003%), neg=0, invalid=96777 0693: dt=0.720000, rms=0.402 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 iter 0, gcam->neg = 71 after 11 iterations, nbhd size=1, neg = 0 0694: dt=12.656085, rms=0.400 (0.417%), neg=0, invalid=96777 0695: dt=0.027000, rms=0.400 (0.000%), neg=0, invalid=96777 0696: dt=0.027000, rms=0.400 (0.001%), neg=0, invalid=96777 0697: dt=0.027000, rms=0.400 (0.001%), neg=0, invalid=96777 0698: dt=0.027000, rms=0.400 (0.001%), neg=0, invalid=96777 0699: dt=0.027000, rms=0.400 (0.002%), neg=0, invalid=96777 0700: dt=0.027000, rms=0.400 (0.002%), neg=0, invalid=96777 0701: dt=0.027000, rms=0.400 (0.002%), neg=0, invalid=96777 0702: dt=0.027000, rms=0.400 (0.003%), neg=0, invalid=96777 0703: dt=0.027000, rms=0.400 (0.003%), neg=0, invalid=96777 0704: dt=0.027000, rms=0.400 (0.003%), neg=0, invalid=96777 0705: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0706: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0707: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0708: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0709: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0710: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0711: dt=0.027000, rms=0.400 (0.004%), neg=0, invalid=96777 0712: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0713: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0714: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0715: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0716: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0717: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0718: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0719: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0720: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 0721: dt=0.027000, rms=0.400 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 151 after 21 iterations, nbhd size=2, neg = 0 0722: dt=36.864000, rms=0.398 (0.437%), neg=0, invalid=96777 0723: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0724: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0725: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0726: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0727: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0728: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0729: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0730: dt=0.063000, rms=0.398 (0.001%), neg=0, invalid=96777 0731: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0732: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0733: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0734: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0735: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0736: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0737: dt=0.063000, rms=0.398 (0.002%), neg=0, invalid=96777 0738: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0739: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0740: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0741: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0742: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0743: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0744: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0745: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0746: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0747: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0748: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0749: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0750: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0751: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0752: dt=0.063000, rms=0.397 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 76 after 18 iterations, nbhd size=2, neg = 0 0753: dt=36.864000, rms=0.397 (0.137%), neg=0, invalid=96777 0754: dt=0.054000, rms=0.397 (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=0.402, neg=0, invalid=96777 0755: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0756: dt=0.000000, rms=0.402 (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=0.393, neg=0, invalid=96777 iter 0, gcam->neg = 328 after 13 iterations, nbhd size=1, neg = 0 0757: dt=0.883674, rms=0.384 (2.361%), neg=0, invalid=96777 0758: dt=0.000109, rms=0.384 (0.002%), neg=0, invalid=96777 0759: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0760: dt=0.000109, rms=0.384 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0761: dt=0.003000, rms=0.384 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0762: dt=0.048000, rms=0.384 (0.037%), neg=0, invalid=96777 0763: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0764: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0765: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0766: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0767: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0768: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0769: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0770: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0771: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0772: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777 0773: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0774: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0775: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0776: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0777: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0778: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0779: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0780: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0781: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0782: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0783: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0784: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0785: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0786: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0787: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0788: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0789: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0790: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0791: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0792: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 0793: dt=0.000109, rms=0.384 (0.001%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 46 minutes and 31 seconds. #-------------------------------------- #@# Remove Neck Thu Sep 18 13:58:27 EDT 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11293415 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 0 seconds. #-------------------------------------- #@# SkullLTA Thu Sep 18 13:59:28 EDT 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= 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 '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=5.0 skull bounding box = (46, 24, 22) --> (208, 205, 227) using (100, 84, 125) as brain centroid... mean wm in atlas = 126, using box (80,62,100) --> (119, 106,150) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.122 0.027 0.025 -21.856; -0.029 1.133 0.122 -12.972; -0.026 -0.136 1.066 -1.362; 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) 1.100 -0.046 0.016 -10.075; 0.045 1.132 0.123 -22.340; -0.026 -0.136 1.066 -1.362; 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) 1.100 -0.046 0.016 -10.075; 0.045 1.132 0.123 -22.340; -0.026 -0.136 1.066 -1.362; 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) 1.096 -0.038 0.026 -12.110; 0.036 1.134 0.123 -21.386; -0.035 -0.136 1.069 -0.626; 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) 1.096 -0.038 0.026 -12.110; 0.036 1.134 0.123 -21.386; -0.035 -0.136 1.071 -0.751; 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 1.09623 -0.03801 0.02599 -12.10965; 0.03562 1.13402 0.12302 -21.38585; -0.03531 -0.13610 1.07057 -0.75084; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09623 -0.03801 0.02599 -12.10965; 0.03562 1.13402 0.12302 -21.38585; -0.03531 -0.13610 1.07057 -0.75084; 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: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.096 -0.038 0.026 -12.110; 0.036 1.134 0.123 -21.386; -0.035 -0.136 1.071 -0.751; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.1) transform before final EM align: 1.096 -0.038 0.026 -12.110; 0.036 1.134 0.123 -21.386; -0.035 -0.136 1.071 -0.751; 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 1.09623 -0.03801 0.02599 -12.10965; 0.03562 1.13402 0.12302 -21.38585; -0.03531 -0.13610 1.07057 -0.75084; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09623 -0.03801 0.02599 -12.10965; 0.03562 1.13402 0.12302 -21.38585; -0.03531 -0.13610 1.07057 -0.75084; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.04, 1.13, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 008: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.04, 1.13, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 009: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.04, 1.13, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) 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... dfp_em_step_func: 010: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 011: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 012: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 013: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) dfp_em_step_func: 014: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.04, -0.14, 1.07, -0.75) 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 3 through quasi-newton minimization... dfp_em_step_func: 015: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.03, -0.14, 1.07, -0.75) dfp_em_step_func: 016: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.03, -0.14, 1.07, -0.75) dfp_em_step_func: 017: -log(p) = 4.4 after pass:transform: ( 1.10, -0.04, 0.03, -12.11) ( 0.03, 1.14, 0.12, -21.39) ( -0.03, -0.14, 1.07, -0.75) 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 4 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 019: -log(p) = 4.4 tol 0.000000 final transform: 1.098 -0.038 0.025 -12.110; 0.034 1.138 0.120 -21.386; -0.035 -0.136 1.070 -0.751; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 25 minutes and 3 seconds. #-------------------------------------- #@# SubCort Seg Thu Sep 18 14:24:31 EDT 2014 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname ubuntu machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/case018_tp2/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels more than 0.5 sigmas from label mean, with sigma=0.0mm, wsize=0mm renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.12265 (34) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (1064 voxels, overlap=0.263) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (1064 voxels, peak = 37), gca=36.6 gca peak = 0.14982 (20) mri peak = 0.12931 (35) Right_Lateral_Ventricle (43): linear fit = 1.58 x + 0.0 (1239 voxels, overlap=0.151) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1239 voxels, peak = 32), gca=30.0 gca peak = 0.28003 (97) mri peak = 0.16981 (106) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (370 voxels, overlap=0.032) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (370 voxels, peak = 105), gca=105.2 gca peak = 0.18160 (96) mri peak = 0.10104 (111) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (333 voxels, overlap=0.044) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (333 voxels, peak = 108), gca=108.0 gca peak = 0.27536 (62) mri peak = 0.10882 (83) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (766 voxels, overlap=0.014) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (766 voxels, peak = 82), gca=81.5 gca peak = 0.32745 (63) mri peak = 0.10357 (85) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (555 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (555 voxels, peak = 82), gca=81.6 gca peak = 0.08597 (105) mri peak = 0.16259 (110) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44723 voxels, overlap=0.498) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (44723 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.10547 (112) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43401 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43401 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.04658 (76) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (31800 voxels, overlap=0.252) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (31800 voxels, peak = 77), gca=77.2 gca peak = 0.08598 (64) mri peak = 0.05087 (77) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (27769 voxels, overlap=0.113) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (27769 voxels, peak = 78), gca=78.4 gca peak = 0.24164 (71) mri peak = 0.13566 (92) Right_Caudate (50): linear fit = 1.26 x + 0.0 (518 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.26 x + 0.0 (518 voxels, peak = 90), gca=89.8 gca peak = 0.18227 (75) mri peak = 0.14037 (91) Left_Caudate (11): linear fit = 1.20 x + 0.0 (925 voxels, overlap=0.021) Left_Caudate (11): linear fit = 1.20 x + 0.0 (925 voxels, peak = 90), gca=89.6 gca peak = 0.10629 (62) mri peak = 0.05820 (83) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (19242 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (19242 voxels, peak = 84), gca=84.0 gca peak = 0.11668 (59) mri peak = 0.05582 (79) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (21941 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (21941 voxels, peak = 78), gca=78.2 gca peak = 0.17849 (88) mri peak = 0.10631 (98) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (4838 voxels, overlap=0.022) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (4838 voxels, peak = 98), gca=98.1 gca peak = 0.16819 (86) mri peak = 0.11238 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5096 voxels, overlap=0.725) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5096 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.13546 (85) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (285 voxels, overlap=0.046) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (285 voxels, peak = 84), gca=83.5 gca peak = 0.42394 (62) mri peak = 0.10776 (81) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (242 voxels, overlap=0.064) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (242 voxels, peak = 78), gca=78.4 gca peak = 0.10041 (96) mri peak = 0.10931 (107) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (4107 voxels, overlap=0.292) Left_Thalamus_Proper (10): linear fit = 1.11 x + 0.0 (4107 voxels, peak = 106), gca=106.1 gca peak = 0.13978 (88) mri peak = 0.09582 (106) Right_Thalamus_Proper (49): linear fit = 1.16 x + 0.0 (3744 voxels, overlap=0.121) Right_Thalamus_Proper (49): linear fit = 1.16 x + 0.0 (3744 voxels, peak = 103), gca=102.5 gca peak = 0.08514 (81) mri peak = 0.09146 (96) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1507 voxels, overlap=0.016) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1507 voxels, peak = 94), gca=93.6 gca peak = 0.09624 (82) mri peak = 0.08217 (97) Right_Putamen (51): linear fit = 1.16 x + 0.0 (1435 voxels, overlap=0.262) Right_Putamen (51): linear fit = 1.16 x + 0.0 (1435 voxels, peak = 96), gca=95.5 gca peak = 0.07543 (88) mri peak = 0.06056 (88) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10184 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10184 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.12961 (105) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (893 voxels, overlap=0.010) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (893 voxels, peak = 108), gca=107.8 gca peak = 0.17004 (92) mri peak = 0.11597 (108) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (956 voxels, overlap=0.008) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (956 voxels, peak = 104), gca=103.5 gca peak = 0.21361 (36) mri peak = 1.00000 (39) gca peak = 0.26069 (23) mri peak = 0.14634 (32) Fourth_Ventricle (15): linear fit = 1.28 x + 0.0 (328 voxels, overlap=0.404) Fourth_Ventricle (15): linear fit = 1.28 x + 0.0 (328 voxels, peak = 30), gca=29.6 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 1.27 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.38 x + 0.0 Left_Pallidum too bright - rescaling by 0.985 (from 1.125) to 106.4 (was 108.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12851 (37) mri peak = 0.12265 (34) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1064 voxels, overlap=0.831) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1064 voxels, peak = 36), gca=36.4 gca peak = 0.12219 (30) mri peak = 0.12931 (35) Right_Lateral_Ventricle (43): linear fit = 1.07 x + 0.0 (1239 voxels, overlap=0.720) Right_Lateral_Ventricle (43): linear fit = 1.07 x + 0.0 (1239 voxels, peak = 32), gca=32.0 gca peak = 0.22195 (106) mri peak = 0.16981 (106) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (370 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (370 voxels, peak = 106), gca=106.0 gca peak = 0.16121 (106) mri peak = 0.10104 (111) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (333 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (333 voxels, peak = 109), gca=108.6 gca peak = 0.22382 (82) mri peak = 0.10882 (83) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (766 voxels, overlap=0.874) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (766 voxels, peak = 82), gca=81.6 gca peak = 0.25361 (82) mri peak = 0.10357 (85) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (555 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (555 voxels, peak = 81), gca=80.8 gca peak = 0.08278 (109) mri peak = 0.16259 (110) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44723 voxels, overlap=0.599) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (44723 voxels, peak = 109), gca=109.0 gca peak = 0.08583 (111) mri peak = 0.10547 (112) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43401 voxels, overlap=0.689) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43401 voxels, peak = 111), gca=111.0 gca peak = 0.06365 (77) mri peak = 0.04658 (76) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (31800 voxels, overlap=0.871) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (31800 voxels, peak = 77), gca=77.0 gca peak = 0.07107 (77) mri peak = 0.05087 (77) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (27769 voxels, overlap=0.896) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (27769 voxels, peak = 78), gca=78.2 gca peak = 0.23545 (93) mri peak = 0.13566 (92) Right_Caudate (50): linear fit = 1.00 x + 0.0 (518 voxels, overlap=0.995) Right_Caudate (50): linear fit = 1.00 x + 0.0 (518 voxels, peak = 93), gca=93.0 gca peak = 0.14376 (89) mri peak = 0.14037 (91) Left_Caudate (11): linear fit = 1.00 x + 0.0 (925 voxels, overlap=0.785) Left_Caudate (11): linear fit = 1.00 x + 0.0 (925 voxels, peak = 89), gca=89.4 gca peak = 0.07957 (82) mri peak = 0.05820 (83) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (19242 voxels, overlap=0.944) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (19242 voxels, peak = 82), gca=81.6 gca peak = 0.09506 (79) mri peak = 0.05582 (79) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21941 voxels, overlap=0.969) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21941 voxels, peak = 79), gca=78.6 gca peak = 0.15191 (97) mri peak = 0.10631 (98) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4838 voxels, overlap=0.967) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4838 voxels, peak = 97), gca=97.5 gca peak = 0.16064 (92) mri peak = 0.11238 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5096 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5096 voxels, peak = 92), gca=91.5 gca peak = 0.30350 (83) mri peak = 0.13546 (85) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (285 voxels, overlap=1.011) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (285 voxels, peak = 84), gca=84.2 gca peak = 0.33776 (79) mri peak = 0.10776 (81) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (242 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (242 voxels, peak = 80), gca=80.2 gca peak = 0.09604 (104) mri peak = 0.10931 (107) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4107 voxels, overlap=0.860) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4107 voxels, peak = 104), gca=104.0 gca peak = 0.10240 (102) mri peak = 0.09582 (106) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3744 voxels, overlap=0.896) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3744 voxels, peak = 102), gca=102.0 gca peak = 0.08662 (95) mri peak = 0.09146 (96) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1507 voxels, overlap=0.773) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1507 voxels, peak = 96), gca=96.4 gca peak = 0.09926 (96) mri peak = 0.08217 (97) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1435 voxels, overlap=0.803) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1435 voxels, peak = 95), gca=94.6 gca peak = 0.07175 (88) mri peak = 0.06056 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10184 voxels, overlap=0.835) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10184 voxels, peak = 88), gca=87.6 gca peak = 0.11173 (103) mri peak = 0.12961 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (893 voxels, overlap=0.722) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (893 voxels, peak = 103), gca=103.0 gca peak = 0.14821 (104) mri peak = 0.11597 (108) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (956 voxels, overlap=0.752) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (956 voxels, peak = 102), gca=102.4 gca peak = 0.16821 (50) mri peak = 1.00000 (39) gca peak = 0.16053 (30) mri peak = 0.14634 (32) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (328 voxels, overlap=0.702) Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (328 voxels, peak = 29), gca=28.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21757 (46) gca peak Third_Ventricle = 0.16821 (50) gca peak CSF = 0.17842 (53) gca peak Left_Accumbens_area = 0.40676 (83) gca peak Left_undetermined = 0.95107 (42) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08662 (41) gca peak Right_Inf_Lat_Vent = 0.20689 (42) gca peak Right_Accumbens_area = 0.25801 (91) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.13262 (46) gca peak Fifth_Ventricle = 0.46296 (57) gca peak WM_hypointensities = 0.17821 (85) gca peak non_WM_hypointensities = 0.12111 (55) gca peak Optic_Chiasm = 0.34334 (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 Left_Pallidum too bright - rescaling by 0.982 (from 1.025) to 106.7 (was 108.6) Right_Pallidum too bright - rescaling by 1.007 (from 1.000) to 106.7 (was 106.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 33888 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 323 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 84534 changed. image ll: -2.236, PF=1.000 pass 2: 14457 changed. image ll: -2.232, PF=1.000 pass 3: 4753 changed. relabeling voxels using optimal scale estimates iter 1: nchanged = 10388 iter 2: nchanged = 2049 iter 3: nchanged = 670 iter 4: nchanged = 306 iter 5: nchanged = 157 iter 6: nchanged = 83 iter 7: nchanged = 42 writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 113 minutes and 21 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/cc_up.lta case018_tp2 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/case018_tp2/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/case018_tp2/mri/norm.mgz 62554 voxels in left wm, 27921 in right wm, xrange [124, 133] searching rotation angles z=[-6 8], y=[-6 8] searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 global minimum found at slice 126.4, rotations (1.20, 1.07) final transformation (x=126.4, yr=1.201, zr=1.072): 1.000 -0.019 0.021 0.927; 0.019 1.000 0.000 33.606; -0.021 -0.000 1.000 12.674; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 151 166 eigenvectors: 0.001 0.000 1.000; 0.094 -0.996 0.000; 0.996 0.094 -0.001; error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Sep 18 16:18:32 EDT 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Sep 18 16:18:32 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/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... 1643 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 23 (23) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 57 (57) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 9 seconds. #-------------------------------------------- #@# Mask BFS Thu Sep 18 16:22:45 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1577888 voxels in mask (pct= 9.40) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Sep 18 16:22:48 EDT 2014 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): 104.4 +- 5.4 [80.0 --> 125.0] GM (82.0) : 79.1 +- 11.9 [30.0 --> 96.0] setting bottom of white matter range to 91.0 setting top of gray matter range to 103.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8187 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4861 filled 2554 bright non-wm voxels segmented. 4378 diagonally connected voxels added... white matter segmentation took 2.1 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 0.79 minutes reading wm segmentation from wm.seg.mgz... 201 voxels added to wm to prevent paths from MTL structures to cortex 4326 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51128 voxels turned on, 41674 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 50 found - 50 modified | TOTAL: 50 pass 2 (xy+): 0 found - 50 modified | TOTAL: 50 pass 1 (xy-): 32 found - 32 modified | TOTAL: 82 pass 2 (xy-): 0 found - 32 modified | TOTAL: 82 pass 1 (yz+): 49 found - 49 modified | TOTAL: 131 pass 2 (yz+): 0 found - 49 modified | TOTAL: 131 pass 1 (yz-): 43 found - 43 modified | TOTAL: 174 pass 2 (yz-): 0 found - 43 modified | TOTAL: 174 pass 1 (xz+): 35 found - 35 modified | TOTAL: 209 pass 2 (xz+): 0 found - 35 modified | TOTAL: 209 pass 1 (xz-): 26 found - 26 modified | TOTAL: 235 pass 2 (xz-): 0 found - 26 modified | TOTAL: 235 Iteration Number : 1 pass 1 (+++): 26 found - 26 modified | TOTAL: 26 pass 2 (+++): 0 found - 26 modified | TOTAL: 26 pass 1 (+++): 34 found - 34 modified | TOTAL: 60 pass 2 (+++): 0 found - 34 modified | TOTAL: 60 pass 1 (+++): 45 found - 45 modified | TOTAL: 105 pass 2 (+++): 0 found - 45 modified | TOTAL: 105 pass 1 (+++): 30 found - 30 modified | TOTAL: 135 pass 2 (+++): 0 found - 30 modified | TOTAL: 135 Iteration Number : 1 pass 1 (++): 113 found - 113 modified | TOTAL: 113 pass 2 (++): 0 found - 113 modified | TOTAL: 113 pass 1 (+-): 150 found - 150 modified | TOTAL: 263 pass 2 (+-): 0 found - 150 modified | TOTAL: 263 pass 1 (--): 114 found - 114 modified | TOTAL: 377 pass 2 (--): 0 found - 114 modified | TOTAL: 377 pass 1 (-+): 123 found - 123 modified | TOTAL: 500 pass 2 (-+): 0 found - 123 modified | TOTAL: 500 Iteration Number : 2 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 10 found - 10 modified | TOTAL: 25 pass 2 (xy-): 0 found - 10 modified | TOTAL: 25 pass 1 (yz+): 14 found - 14 modified | TOTAL: 39 pass 2 (yz+): 0 found - 14 modified | TOTAL: 39 pass 1 (yz-): 2 found - 2 modified | TOTAL: 41 pass 2 (yz-): 0 found - 2 modified | TOTAL: 41 pass 1 (xz+): 12 found - 12 modified | TOTAL: 53 pass 2 (xz+): 0 found - 12 modified | TOTAL: 53 pass 1 (xz-): 8 found - 8 modified | TOTAL: 61 pass 2 (xz-): 0 found - 8 modified | TOTAL: 61 Iteration Number : 2 pass 1 (+++): 5 found - 5 modified | TOTAL: 5 pass 2 (+++): 0 found - 5 modified | TOTAL: 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 5 pass 1 (+++): 6 found - 6 modified | TOTAL: 11 pass 2 (+++): 0 found - 6 modified | TOTAL: 11 pass 1 (+++): 2 found - 2 modified | TOTAL: 13 pass 2 (+++): 0 found - 2 modified | TOTAL: 13 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 6 found - 6 modified | TOTAL: 9 pass 2 (+-): 0 found - 6 modified | TOTAL: 9 pass 1 (--): 2 found - 2 modified | TOTAL: 11 pass 2 (--): 0 found - 2 modified | TOTAL: 11 pass 1 (-+): 7 found - 7 modified | TOTAL: 18 pass 2 (-+): 0 found - 7 modified | TOTAL: 18 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 5 found - 5 modified | TOTAL: 6 pass 2 (xy-): 0 found - 5 modified | TOTAL: 6 pass 1 (yz+): 0 found - 0 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 3 found - 3 modified | TOTAL: 9 pass 2 (xz+): 0 found - 3 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 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 = 975 (out of 523837: 0.186127) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Sep 18 16:25:46 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/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 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.122 0.027 0.025 -21.856; -0.027 1.065 0.114 -4.937; -0.024 -0.126 0.991 6.131; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1007 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 122, 147), TAL = (2.0, 19.0, 6.0) talairach voxel to voxel transform 0.890 -0.025 -0.019 19.447; 0.020 0.926 -0.107 5.667; 0.024 0.117 0.995 -4.984; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 122, 147) --> (2.0, 19.0, 6.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, 19.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 19.00, 6.00) SRC: (109.71, 104.98, 158.17) search lh wm seed point around talairach space (-16.00, 19.00, 6.00), SRC: (141.75, 105.71, 159.05) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Sep 18 16:26:40 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 3 found - 3 modified | TOTAL: 10 pass 2 (xz-): 0 found - 3 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 255031: 0.005490) 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 40: 365 vertices, 425 faces slice 50: 4074 vertices, 4254 faces slice 60: 9810 vertices, 10034 faces slice 70: 17277 vertices, 17556 faces slice 80: 26380 vertices, 26736 faces slice 90: 35939 vertices, 36271 faces slice 100: 45874 vertices, 46239 faces slice 110: 57304 vertices, 57684 faces slice 120: 69045 vertices, 69457 faces slice 130: 79640 vertices, 79986 faces slice 140: 89492 vertices, 89865 faces slice 150: 98485 vertices, 98842 faces slice 160: 106767 vertices, 107101 faces slice 170: 113773 vertices, 114058 faces slice 180: 119594 vertices, 119879 faces slice 190: 124487 vertices, 124746 faces slice 200: 128192 vertices, 128379 faces slice 210: 129026 vertices, 129120 faces slice 220: 129026 vertices, 129120 faces slice 230: 129026 vertices, 129120 faces slice 240: 129026 vertices, 129120 faces slice 250: 129026 vertices, 129120 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... 129026 voxel in cpt #1: X=-94 [v=129026,e=387360,f=258240] located at (-24.049013, -11.313107, 28.121580) For the whole surface: X=-94 [v=129026,e=387360,f=258240] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Sep 18 16:26:52 EDT 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /usr/local/freesurfer/subjects/case018_tp2/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Sep 18 16:26:56 EDT 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /usr/local/freesurfer/subjects/case018_tp2/scripts avg radius = 46.4 mm, total surface area = 67971 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Sep 18 16:27:26 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/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 1.02 +- 0.60 (0.00-->7.82) (max @ vno 53663 --> 54783) face area 0.02 +- 0.03 (-0.22-->0.52) scaling brain by 0.306... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.551, avgs=0 005/300: dt: 0.9000, rms radial error=177.289, avgs=0 010/300: dt: 0.9000, rms radial error=176.729, avgs=0 015/300: dt: 0.9000, rms radial error=175.993, avgs=0 020/300: dt: 0.9000, rms radial error=175.156, avgs=0 025/300: dt: 0.9000, rms radial error=174.259, avgs=0 030/300: dt: 0.9000, rms radial error=173.329, avgs=0 035/300: dt: 0.9000, rms radial error=172.383, avgs=0 040/300: dt: 0.9000, rms radial error=171.429, avgs=0 045/300: dt: 0.9000, rms radial error=170.476, avgs=0 050/300: dt: 0.9000, rms radial error=169.524, avgs=0 055/300: dt: 0.9000, rms radial error=168.575, avgs=0 060/300: dt: 0.9000, rms radial error=167.630, avgs=0 065/300: dt: 0.9000, rms radial error=166.691, avgs=0 070/300: dt: 0.9000, rms radial error=165.758, avgs=0 075/300: dt: 0.9000, rms radial error=164.829, avgs=0 080/300: dt: 0.9000, rms radial error=163.906, avgs=0 085/300: dt: 0.9000, rms radial error=162.987, avgs=0 090/300: dt: 0.9000, rms radial error=162.074, avgs=0 095/300: dt: 0.9000, rms radial error=161.165, avgs=0 100/300: dt: 0.9000, rms radial error=160.260, avgs=0 105/300: dt: 0.9000, rms radial error=159.361, avgs=0 110/300: dt: 0.9000, rms radial error=158.467, avgs=0 115/300: dt: 0.9000, rms radial error=157.577, avgs=0 120/300: dt: 0.9000, rms radial error=156.693, avgs=0 125/300: dt: 0.9000, rms radial error=155.813, avgs=0 130/300: dt: 0.9000, rms radial error=154.937, avgs=0 135/300: dt: 0.9000, rms radial error=154.067, avgs=0 140/300: dt: 0.9000, rms radial error=153.201, avgs=0 145/300: dt: 0.9000, rms radial error=152.341, avgs=0 150/300: dt: 0.9000, rms radial error=151.484, avgs=0 155/300: dt: 0.9000, rms radial error=150.633, avgs=0 160/300: dt: 0.9000, rms radial error=149.786, avgs=0 165/300: dt: 0.9000, rms radial error=148.944, avgs=0 170/300: dt: 0.9000, rms radial error=148.107, avgs=0 175/300: dt: 0.9000, rms radial error=147.274, avgs=0 180/300: dt: 0.9000, rms radial error=146.445, avgs=0 185/300: dt: 0.9000, rms radial error=145.622, avgs=0 190/300: dt: 0.9000, rms radial error=144.802, avgs=0 195/300: dt: 0.9000, rms radial error=143.988, avgs=0 200/300: dt: 0.9000, rms radial error=143.177, avgs=0 205/300: dt: 0.9000, rms radial error=142.372, avgs=0 210/300: dt: 0.9000, rms radial error=141.570, avgs=0 215/300: dt: 0.9000, rms radial error=140.774, avgs=0 220/300: dt: 0.9000, rms radial error=139.981, avgs=0 225/300: dt: 0.9000, rms radial error=139.193, avgs=0 230/300: dt: 0.9000, rms radial error=138.410, avgs=0 235/300: dt: 0.9000, rms radial error=137.630, avgs=0 240/300: dt: 0.9000, rms radial error=136.856, avgs=0 245/300: dt: 0.9000, rms radial error=136.085, avgs=0 250/300: dt: 0.9000, rms radial error=135.319, avgs=0 255/300: dt: 0.9000, rms radial error=134.557, avgs=0 260/300: dt: 0.9000, rms radial error=133.799, avgs=0 265/300: dt: 0.9000, rms radial error=133.045, avgs=0 270/300: dt: 0.9000, rms radial error=132.296, avgs=0 275/300: dt: 0.9000, rms radial error=131.551, avgs=0 280/300: dt: 0.9000, rms radial error=130.810, avgs=0 285/300: dt: 0.9000, rms radial error=130.073, avgs=0 290/300: dt: 0.9000, rms radial error=129.340, avgs=0 295/300: dt: 0.9000, rms radial error=128.612, avgs=0 300/300: dt: 0.9000, rms radial error=127.887, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15183.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2570.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 278.79 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00717 epoch 4 (K=640.0), pass 1, starting sse = 19.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/13 = 0.00963 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Sep 18 16:31:04 EDT 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /usr/local/freesurfer/subjects/case018_tp2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 case018_tp2 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=-94 (nv=129026, nf=258240, ne=387360, g=48) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 6379 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 32 into 26 40 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7104 (-4.3552) -vertex loglikelihood: -5.5732 (-2.7866) -normal dot loglikelihood: -3.5484 (-3.5484) -quad curv loglikelihood: -6.5182 (-3.2591) Total Loglikelihood : -24.3501 CORRECTING DEFECT 0 (vertices=23, convex hull=61) After retessellation of defect 0, euler #=-36 (125215,374270,249019) : difference with theory (-37) = -1 CORRECTING DEFECT 1 (vertices=26, convex hull=62) After retessellation of defect 1, euler #=-35 (125228,374327,249064) : difference with theory (-36) = -1 CORRECTING DEFECT 2 (vertices=39, convex hull=58) After retessellation of defect 2, euler #=-34 (125241,374389,249114) : difference with theory (-35) = -1 CORRECTING DEFECT 3 (vertices=9, convex hull=22) After retessellation of defect 3, euler #=-33 (125243,374401,249125) : difference with theory (-34) = -1 CORRECTING DEFECT 4 (vertices=27, convex hull=83) After retessellation of defect 4, euler #=-32 (125259,374484,249193) : difference with theory (-33) = -1 CORRECTING DEFECT 5 (vertices=335, convex hull=220) After retessellation of defect 5, euler #=-31 (125275,374633,249327) : difference with theory (-32) = -1 CORRECTING DEFECT 6 (vertices=131, convex hull=128) After retessellation of defect 6, euler #=-30 (125325,374842,249487) : difference with theory (-31) = -1 CORRECTING DEFECT 7 (vertices=15, convex hull=14) After retessellation of defect 7, euler #=-29 (125325,374846,249492) : difference with theory (-30) = -1 CORRECTING DEFECT 8 (vertices=356, convex hull=137) After retessellation of defect 8, euler #=-28 (125396,375127,249703) : difference with theory (-29) = -1 CORRECTING DEFECT 9 (vertices=53, convex hull=85) After retessellation of defect 9, euler #=-27 (125424,375247,249796) : difference with theory (-28) = -1 CORRECTING DEFECT 10 (vertices=19, convex hull=47) After retessellation of defect 10, euler #=-26 (125437,375304,249841) : difference with theory (-27) = -1 CORRECTING DEFECT 11 (vertices=27, convex hull=49) After retessellation of defect 11, euler #=-25 (125455,375376,249896) : difference with theory (-26) = -1 CORRECTING DEFECT 12 (vertices=34, convex hull=55) After retessellation of defect 12, euler #=-24 (125473,375448,249951) : difference with theory (-25) = -1 CORRECTING DEFECT 13 (vertices=70, convex hull=99) After retessellation of defect 13, euler #=-23 (125510,375596,250063) : difference with theory (-24) = -1 CORRECTING DEFECT 14 (vertices=41, convex hull=88) After retessellation of defect 14, euler #=-22 (125533,375703,250148) : difference with theory (-23) = -1 CORRECTING DEFECT 15 (vertices=256, convex hull=60) After retessellation of defect 15, euler #=-21 (125549,375775,250205) : difference with theory (-22) = -1 CORRECTING DEFECT 16 (vertices=23, convex hull=43) After retessellation of defect 16, euler #=-20 (125558,375816,250238) : difference with theory (-21) = -1 CORRECTING DEFECT 17 (vertices=24, convex hull=56) After retessellation of defect 17, euler #=-19 (125571,375876,250286) : difference with theory (-20) = -1 CORRECTING DEFECT 18 (vertices=17, convex hull=27) After retessellation of defect 18, euler #=-18 (125577,375902,250307) : difference with theory (-19) = -1 CORRECTING DEFECT 19 (vertices=233, convex hull=145) After retessellation of defect 19, euler #=-17 (125587,375996,250392) : difference with theory (-18) = -1 CORRECTING DEFECT 20 (vertices=92, convex hull=73) After retessellation of defect 20, euler #=-16 (125597,376061,250448) : difference with theory (-17) = -1 CORRECTING DEFECT 21 (vertices=64, convex hull=28) After retessellation of defect 21, euler #=-15 (125605,376092,250472) : difference with theory (-16) = -1 CORRECTING DEFECT 22 (vertices=15, convex hull=24) Warning - incorrect dp selected!!!!(-83.589695 >= -83.589705 ) After retessellation of defect 22, euler #=-14 (125608,376108,250486) : difference with theory (-15) = -1 CORRECTING DEFECT 23 (vertices=900, convex hull=426) After retessellation of defect 23, euler #=-15 (125815,376967,251137) : difference with theory (-14) = 1 CORRECTING DEFECT 24 (vertices=6, convex hull=22) After retessellation of defect 24, euler #=-14 (125817,376981,251150) : difference with theory (-13) = 1 CORRECTING DEFECT 25 (vertices=30, convex hull=18) After retessellation of defect 25, euler #=-13 (125821,376996,251162) : difference with theory (-12) = 1 CORRECTING DEFECT 26 (vertices=164, convex hull=215) After retessellation of defect 26, euler #=-11 (125904,377350,251435) : difference with theory (-11) = 0 CORRECTING DEFECT 27 (vertices=35, convex hull=72) After retessellation of defect 27, euler #=-10 (125924,377440,251506) : difference with theory (-10) = 0 CORRECTING DEFECT 28 (vertices=28, convex hull=23) After retessellation of defect 28, euler #=-9 (125929,377461,251523) : difference with theory (-9) = 0 CORRECTING DEFECT 29 (vertices=102, convex hull=88) After retessellation of defect 29, euler #=-8 (125954,377571,251609) : difference with theory (-8) = 0 CORRECTING DEFECT 30 (vertices=127, convex hull=99) After retessellation of defect 30, euler #=-7 (125967,377654,251680) : difference with theory (-7) = 0 CORRECTING DEFECT 31 (vertices=127, convex hull=84) After retessellation of defect 31, euler #=-6 (125988,377752,251758) : difference with theory (-6) = 0 CORRECTING DEFECT 32 (vertices=109, convex hull=103) After retessellation of defect 32, euler #=-5 (126020,377896,251871) : difference with theory (-5) = 0 CORRECTING DEFECT 33 (vertices=16, convex hull=28) After retessellation of defect 33, euler #=-4 (126022,377912,251886) : difference with theory (-4) = 0 CORRECTING DEFECT 34 (vertices=45, convex hull=77) After retessellation of defect 34, euler #=-3 (126042,378002,251957) : difference with theory (-3) = 0 CORRECTING DEFECT 35 (vertices=119, convex hull=97) After retessellation of defect 35, euler #=-2 (126056,378088,252030) : difference with theory (-2) = 0 CORRECTING DEFECT 36 (vertices=22, convex hull=41) After retessellation of defect 36, euler #=-1 (126065,378127,252061) : difference with theory (-1) = 0 CORRECTING DEFECT 37 (vertices=16, convex hull=45) After retessellation of defect 37, euler #=0 (126073,378169,252096) : difference with theory (0) = 0 CORRECTING DEFECT 38 (vertices=29, convex hull=67) After retessellation of defect 38, euler #=1 (126089,378243,252155) : difference with theory (1) = 0 CORRECTING DEFECT 39 (vertices=19, convex hull=54) After retessellation of defect 39, euler #=2 (126095,378279,252186) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.06-->10.42) (max @ vno 115379 --> 119801) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.06-->10.42) (max @ vno 115379 --> 119801) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 163 mutations (32.5%), 339 crossovers (67.5%), 403 vertices were eliminated building final representation... 2931 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=126095, nf=252186, ne=378279, g=0) writing corrected surface to /usr/local/freesurfer/subjects/case018_tp2/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 34.8 minutes 0 defective edges removing intersecting faces 000: 402 intersecting 001: 7 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 126095 - 378279 + 252186 = 2 --> 0 holes F =2V-4: 252186 = 252190-4 (0) 2E=3F: 756558 = 756558 (0) total defect index = 0 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 58 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Sep 18 17:05:59 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs case018_tp2 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... 13243 bright wm thresholded. 3034 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/case018_tp2/surf/lh.orig... computing class statistics... border white: 252263 voxels (1.50%) border gray 277912 voxels (1.66%) WM (100.0): 101.0 +- 5.8 [70.0 --> 110.0] GM (92.0) : 90.1 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.9 (was 70) setting MAX_BORDER_WHITE to 112.8 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 62.8 (was 40) setting MAX_GRAY to 101.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.04-->5.12) (max @ vno 115379 --> 119801) face area 0.28 +- 0.13 (0.00-->3.34) mean absolute distance = 0.86 +- 1.01 3666 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=107, GM=83 mean inside = 100.9, mean outside = 88.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=89.9, 60 (60) missing vertices, mean dist 0.5 [0.8 (%26.2)->0.9 (%73.8))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.28 (0.09-->5.42) (max @ vno 47439 --> 47440) face area 0.28 +- 0.14 (0.00-->3.72) mean absolute distance = 0.44 +- 0.65 3711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3812450.8, rms=8.14 001: dt: 0.5000, sse=4342230.5, rms=6.040 (0.000%) 002: dt: 0.5000, sse=4405328.0, rms=4.611 (0.000%) 003: dt: 0.5000, sse=4516822.5, rms=3.626 (0.000%) 004: dt: 0.5000, sse=4573758.0, rms=2.992 (0.000%) 005: dt: 0.5000, sse=4620365.0, rms=2.602 (0.000%) 006: dt: 0.5000, sse=4639928.0, rms=2.369 (0.000%) 007: dt: 0.5000, sse=4659364.5, rms=2.234 (0.000%) 008: dt: 0.5000, sse=4672001.5, rms=2.148 (0.000%) 009: dt: 0.5000, sse=4679562.0, rms=2.095 (0.000%) rms = 2.05, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=4701904.5, rms=2.054 (0.000%) 011: dt: 0.2500, sse=3293625.0, rms=1.667 (0.000%) 012: dt: 0.2500, sse=3180004.0, rms=1.617 (0.000%) rms = 1.60, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3133707.5, rms=1.602 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3103250.8, rms=1.589 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.4, 55 (6) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.3 (%28.1))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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 (0.08-->5.84) (max @ vno 47439 --> 47440) face area 0.35 +- 0.17 (0.00-->5.09) mean absolute distance = 0.32 +- 0.41 4427 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3477471.8, rms=3.78 015: dt: 0.5000, sse=3664751.2, rms=2.382 (0.000%) 016: dt: 0.5000, sse=3955330.8, rms=1.874 (0.000%) 017: dt: 0.5000, sse=4000320.0, rms=1.677 (0.000%) rms = 1.64, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=4308198.0, rms=1.639 (0.000%) 019: dt: 0.2500, sse=3479885.2, rms=1.345 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3370892.0, rms=1.307 (0.000%) rms = 1.30, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3336657.0, rms=1.300 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=94.7, 62 (4) missing vertices, mean dist -0.2 [0.4 (%75.3)->0.2 (%24.7))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, 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 0.88 +- 0.25 (0.04-->6.07) (max @ vno 47439 --> 47440) face area 0.33 +- 0.17 (0.00-->5.12) mean absolute distance = 0.23 +- 0.32 3084 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3487296.8, rms=3.05 022: dt: 0.5000, sse=3668285.0, rms=1.725 (0.000%) 023: dt: 0.5000, sse=3894555.0, rms=1.504 (0.000%) rms = 1.45, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=3953673.0, rms=1.454 (0.000%) 025: dt: 0.2500, sse=3568826.8, rms=1.204 (0.000%) rms = 1.19, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3453941.8, rms=1.188 (0.000%) rms = 1.19, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3425951.2, rms=1.185 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=95.4, 72 (3) missing vertices, mean dist -0.1 [0.2 (%58.7)->0.2 (%41.3))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3431246.0, rms=1.46 028: dt: 0.5000, sse=4213838.0, rms=1.032 (0.000%) rms = 1.28, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3928198.5, rms=0.958 (0.000%) rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3901971.8, rms=0.953 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 9 non-cortical segments detected only using segment with 1960 vertices erasing segment 1 (vno[0] = 53116) erasing segment 2 (vno[0] = 72200) erasing segment 3 (vno[0] = 75278) erasing segment 4 (vno[0] = 89544) erasing segment 5 (vno[0] = 92944) erasing segment 6 (vno[0] = 94402) erasing segment 7 (vno[0] = 98539) erasing segment 8 (vno[0] = 125627) writing cortex label to /usr/local/freesurfer/subjects/case018_tp2/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/lh.area vertex spacing 0.88 +- 0.26 (0.06-->6.13) (max @ vno 47439 --> 47440) face area 0.33 +- 0.17 (0.00-->5.06) refinement took 4.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu Sep 18 17:10:42 EDT 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /usr/local/freesurfer/subjects/case018_tp2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Sep 18 17:10:46 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.7 mm, total surface area = 75928 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.016 (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 172 vertices thresholded to be in k1 ~ [-0.22 0.45], k2 ~ [-0.11 0.06] total integrated curvature = 0.549*4pi (6.898) --> 0 handles ICI = 1.5, FI = 9.8, variation=165.901 93 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.14 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Thu Sep 18 17:12:28 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm case018_tp2 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 [ case018_tp2/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 [ 246 ] Gb_filter = 0 WARN: S lookup min: -0.514868 WARN: S explicit min: 0.000000 vertex = 414 #-------------------------------------------- #@# Sphere lh Thu Sep 18 17:12:32 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/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 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=ubunt, 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 %20.31 pass 1: epoch 2 of 3 starting distance error %20.26 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 0.50 hours #-------------------------------------------- #@# Surf Reg lh Thu Sep 18 17:42:45 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=ubunt, 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=ubunt, 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 = 0.561 curvature mean = 0.027, std = 0.934 curvature mean = 0.023, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 317876.4, tmin=0.7570 d=32.00 min @ (0.00, 8.00, -8.00) sse = 227881.3, tmin=1.5194 d=16.00 min @ (0.00, 0.00, 4.00) sse = 224969.4, tmin=2.2926 d=8.00 min @ (2.00, 0.00, -2.00) sse = 220091.8, tmin=3.0896 d=4.00 min @ (-1.00, 1.00, 1.00) sse = 218722.3, tmin=3.8787 d=2.00 min @ (0.50, -0.50, -0.50) sse = 218091.5, tmin=4.7051 d=1.00 min @ (0.00, 0.25, 0.25) sse = 218042.9, tmin=5.5481 d=0.50 min @ (-0.12, -0.12, -0.12) sse = 218014.2, tmin=6.3707 tol=1.0e+00, sigma=0.5, host=ubunt, 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 6.37 min curvature mean = -0.004, std = 0.952 curvature mean = 0.010, std = 0.937 curvature mean = -0.005, std = 0.965 curvature mean = 0.004, std = 0.972 curvature mean = -0.007, std = 0.967 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.028, std = 0.292 curvature mean = 0.003, std = 0.067 curvature mean = 0.062, std = 0.353 curvature mean = 0.003, std = 0.079 curvature mean = 0.027, std = 0.543 curvature mean = 0.003, std = 0.086 curvature mean = 0.014, std = 0.676 curvature mean = 0.003, std = 0.088 curvature mean = 0.005, std = 0.775 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Sep 18 18:02:42 EDT 2014 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 Thu Sep 18 18:02:44 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Sep 18 18:02:45 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1134 labels changed using aseg relabeling using gibbs priors... 000: 2993 changed, 126095 examined... 001: 704 changed, 12678 examined... 002: 181 changed, 3836 examined... 003: 71 changed, 1067 examined... 004: 31 changed, 395 examined... 005: 24 changed, 185 examined... 006: 15 changed, 125 examined... 007: 9 changed, 75 examined... 008: 4 changed, 50 examined... 009: 3 changed, 26 examined... 010: 4 changed, 18 examined... 011: 1 changed, 17 examined... 012: 3 changed, 9 examined... 013: 0 changed, 13 examined... 277 labels changed using aseg 000: 117 total segments, 68 labels (222 vertices) changed 001: 47 total segments, 3 labels (8 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 959 vertices marked for relabeling... 959 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 55 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Sep 18 18:03:41 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs case018_tp2 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... 13243 bright wm thresholded. 3034 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/case018_tp2/surf/lh.orig... computing class statistics... border white: 252263 voxels (1.50%) border gray 277912 voxels (1.66%) WM (100.0): 101.0 +- 5.8 [70.0 --> 110.0] GM (92.0) : 90.1 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.9 (was 70) setting MAX_BORDER_WHITE to 112.8 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 62.8 (was 40) setting MAX_GRAY to 101.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.7 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=83 mean inside = 100.9, mean outside = 88.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.04-->5.12) (max @ vno 115379 --> 119801) face area 0.28 +- 0.13 (0.00-->3.34) mean absolute distance = 0.86 +- 1.02 3756 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 552 points - only 0.00% unknown mean border=89.9, 60 (60) missing vertices, mean dist 0.5 [0.8 (%26.3)->0.9 (%73.7))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.09-->5.42) (max @ vno 47439 --> 47440) face area 0.28 +- 0.14 (0.00-->3.72) mean absolute distance = 0.44 +- 0.65 3754 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3820520.8, rms=8.13 001: dt: 0.5000, sse=4358648.5, rms=6.031 (0.000%) 002: dt: 0.5000, sse=4419841.5, rms=4.604 (0.000%) 003: dt: 0.5000, sse=4532069.5, rms=3.622 (0.000%) 004: dt: 0.5000, sse=4589242.5, rms=2.989 (0.000%) 005: dt: 0.5000, sse=4636915.5, rms=2.601 (0.000%) 006: dt: 0.5000, sse=4656515.5, rms=2.369 (0.000%) 007: dt: 0.5000, sse=4676889.5, rms=2.234 (0.000%) 008: dt: 0.5000, sse=4689922.5, rms=2.148 (0.000%) 009: dt: 0.5000, sse=4697427.0, rms=2.094 (0.000%) rms = 2.05, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=4719225.5, rms=2.053 (0.000%) 011: dt: 0.2500, sse=3308591.8, rms=1.667 (0.000%) 012: dt: 0.2500, sse=3194661.2, rms=1.617 (0.000%) rms = 1.60, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3148274.5, rms=1.603 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3117386.5, rms=1.589 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 5 with 342 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown deleting segment 9 with 72 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=92.4, 55 (6) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.3 (%28.1))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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 (0.08-->5.84) (max @ vno 47439 --> 47440) face area 0.35 +- 0.17 (0.00-->5.09) mean absolute distance = 0.32 +- 0.41 4465 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3493015.5, rms=3.78 015: dt: 0.5000, sse=3681761.2, rms=2.379 (0.000%) 016: dt: 0.5000, sse=3975671.0, rms=1.872 (0.000%) 017: dt: 0.5000, sse=4016710.5, rms=1.676 (0.000%) rms = 1.64, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=4327429.0, rms=1.638 (0.000%) 019: dt: 0.2500, sse=3495615.8, rms=1.345 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3386565.0, rms=1.308 (0.000%) rms = 1.30, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3352573.0, rms=1.301 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 365 points - only 0.00% unknown deleting segment 2 with 87 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown mean border=94.7, 62 (4) missing vertices, mean dist -0.2 [0.4 (%75.2)->0.2 (%24.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->6.07) (max @ vno 47439 --> 47440) face area 0.34 +- 0.17 (0.00-->5.12) mean absolute distance = 0.23 +- 0.32 3134 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3504982.8, rms=3.05 022: dt: 0.5000, sse=3685093.8, rms=1.723 (0.000%) 023: dt: 0.5000, sse=3915110.0, rms=1.503 (0.000%) rms = 1.45, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=3971744.0, rms=1.454 (0.000%) 025: dt: 0.2500, sse=3586173.0, rms=1.205 (0.000%) rms = 1.19, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3470610.8, rms=1.189 (0.000%) rms = 1.19, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3442950.2, rms=1.186 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 364 points - only 0.00% unknown deleting segment 2 with 89 points - only 0.00% unknown deleting segment 3 with 18 points - only 0.00% unknown mean border=95.4, 74 (3) missing vertices, mean dist -0.1 [0.2 (%58.7)->0.2 (%41.3))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, 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=3448313.2, rms=1.46 028: dt: 0.5000, sse=4235429.5, rms=1.032 (0.000%) rms = 1.28, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3948328.5, rms=0.958 (0.000%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3922033.8, rms=0.953 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=73.7, 59 (59) missing vertices, mean dist 1.9 [0.3 (%0.0)->2.5 (%100.0))] %22 local maxima, %51 large gradients and %23 min vals, 1452 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, 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=14422774.0, rms=22.43 001: dt: 0.5000, sse=11742768.0, rms=19.783 (0.000%) 002: dt: 0.5000, sse=9660253.0, rms=17.484 (0.000%) 003: dt: 0.5000, sse=8111384.5, rms=15.534 (0.000%) 004: dt: 0.5000, sse=7053261.5, rms=13.885 (0.000%) 005: dt: 0.5000, sse=6356875.5, rms=12.489 (0.000%) 006: dt: 0.5000, sse=5909209.0, rms=11.259 (0.000%) 007: dt: 0.5000, sse=5604596.0, rms=10.107 (0.000%) 008: dt: 0.5000, sse=5378086.0, rms=9.032 (0.000%) 009: dt: 0.5000, sse=5246731.0, rms=8.069 (0.000%) 010: dt: 0.5000, sse=5166848.5, rms=7.201 (0.000%) 011: dt: 0.5000, sse=5134458.0, rms=6.376 (0.000%) 012: dt: 0.5000, sse=5106417.5, rms=5.593 (0.000%) 013: dt: 0.5000, sse=5095988.5, rms=4.884 (0.000%) 014: dt: 0.5000, sse=5147661.0, rms=4.346 (0.000%) 015: dt: 0.5000, sse=5195804.5, rms=3.963 (0.000%) 016: dt: 0.5000, sse=5257806.0, rms=3.753 (0.000%) 017: dt: 0.5000, sse=5314225.0, rms=3.600 (0.000%) 018: dt: 0.5000, sse=5323549.5, rms=3.535 (0.000%) 019: dt: 0.5000, sse=5379114.5, rms=3.471 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=5394706.0, rms=3.456 (0.000%) 021: dt: 0.2500, sse=3715280.0, rms=2.723 (0.000%) 022: dt: 0.2500, sse=3552293.2, rms=2.552 (0.000%) rms = 2.54, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3458451.5, rms=2.536 (0.000%) 024: dt: 0.1250, sse=3326078.8, rms=2.406 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3308540.2, rms=2.391 (0.000%) positioning took 2.1 minutes mean border=71.5, 701 (14) missing vertices, mean dist 0.2 [0.2 (%43.0)->0.5 (%57.0))] %48 local maxima, %30 large gradients and %17 min vals, 498 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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=3820985.5, rms=4.25 026: dt: 0.5000, sse=4023866.5, rms=3.520 (0.000%) 027: dt: 0.5000, sse=4997875.5, rms=3.463 (0.000%) rms = 3.51, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4190232.8, rms=2.819 (0.000%) 029: dt: 0.2500, sse=3884109.0, rms=2.556 (0.000%) rms = 2.51, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3859741.2, rms=2.512 (0.000%) 031: dt: 0.1250, sse=3711586.2, rms=2.351 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3689616.5, rms=2.322 (0.000%) positioning took 0.7 minutes mean border=69.9, 1017 (13) missing vertices, mean dist 0.1 [0.2 (%35.6)->0.3 (%64.4))] %66 local maxima, %12 large gradients and %17 min vals, 591 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, 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=3819297.5, rms=3.17 rms = 3.25, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3677522.5, rms=2.699 (0.000%) 034: dt: 0.2500, sse=3682007.2, rms=2.403 (0.000%) 035: dt: 0.2500, sse=3799885.8, rms=2.334 (0.000%) rms = 2.33, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=3851236.2, rms=2.327 (0.000%) 037: dt: 0.1250, sse=3753029.5, rms=2.207 (0.000%) rms = 2.18, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3759748.2, rms=2.184 (0.000%) positioning took 0.6 minutes mean border=69.2, 1979 (12) missing vertices, mean dist 0.0 [0.2 (%45.0)->0.3 (%55.0))] %67 local maxima, %10 large gradients and %16 min vals, 480 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3775986.2, rms=2.35 rms = 2.71, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3717702.0, rms=2.181 (0.000%) 040: dt: 0.2500, sse=3847303.8, rms=2.117 (0.000%) rms = 2.11, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=3903093.2, rms=2.109 (0.000%) 042: dt: 0.1250, sse=3841101.0, rms=2.032 (0.000%) rms = 2.01, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=3848967.8, rms=2.014 (0.000%) positioning took 0.5 minutes writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.07-->7.08) (max @ vno 110454 --> 109840) face area 0.40 +- 0.31 (0.00-->6.81) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 126095 vertices processed 25000 of 126095 vertices processed 50000 of 126095 vertices processed 75000 of 126095 vertices processed 100000 of 126095 vertices processed 125000 of 126095 vertices processed 0 of 126095 vertices processed 25000 of 126095 vertices processed 50000 of 126095 vertices processed 75000 of 126095 vertices processed 100000 of 126095 vertices processed 125000 of 126095 vertices processed thickness calculation complete, 506:1011 truncations. 28594 vertices at 0 distance 84344 vertices at 1 distance 76096 vertices at 2 distance 34731 vertices at 3 distance 11674 vertices at 4 distance 3405 vertices at 5 distance 1062 vertices at 6 distance 414 vertices at 7 distance 163 vertices at 8 distance 75 vertices at 9 distance 47 vertices at 10 distance 34 vertices at 11 distance 27 vertices at 12 distance 20 vertices at 13 distance 17 vertices at 14 distance 15 vertices at 15 distance 7 vertices at 16 distance 5 vertices at 17 distance 5 vertices at 18 distance 4 vertices at 19 distance 5 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/lh.thickness positioning took 9.6 minutes #-------------------------------------------- #@# Surf Volume lh Thu Sep 18 18:13:15 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/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 ] #-------------------------------------------- #@# Tessellate rh Thu Sep 18 18:13:15 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 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+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 258897: 0.001545) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 348 vertices, 395 faces slice 50: 3700 vertices, 3866 faces slice 60: 10161 vertices, 10441 faces slice 70: 18759 vertices, 19075 faces slice 80: 28315 vertices, 28688 faces slice 90: 38154 vertices, 38445 faces slice 100: 48279 vertices, 48628 faces slice 110: 60090 vertices, 60525 faces slice 120: 71332 vertices, 71745 faces slice 130: 81973 vertices, 82355 faces slice 140: 92226 vertices, 92623 faces slice 150: 101406 vertices, 101760 faces slice 160: 108903 vertices, 109187 faces slice 170: 115732 vertices, 115997 faces slice 180: 121454 vertices, 121709 faces slice 190: 126558 vertices, 126795 faces slice 200: 130288 vertices, 130456 faces slice 210: 131284 vertices, 131356 faces slice 220: 131284 vertices, 131356 faces slice 230: 131284 vertices, 131356 faces slice 240: 131284 vertices, 131356 faces slice 250: 131284 vertices, 131356 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 131284 voxel in cpt #1: X=-72 [v=131284,e=394068,f=262712] located at (27.507298, -12.196162, 26.925056) For the whole surface: X=-72 [v=131284,e=394068,f=262712] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Sep 18 18:13:27 EDT 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /usr/local/freesurfer/subjects/case018_tp2/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Sep 18 18:13:31 EDT 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /usr/local/freesurfer/subjects/case018_tp2/scripts avg radius = 46.8 mm, total surface area = 69038 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.040 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.030 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Sep 18 18:14:02 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.59 (0.00-->7.48) (max @ vno 49066 --> 49067) face area 0.02 +- 0.03 (-0.22-->0.69) scaling brain by 0.304... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.456, avgs=0 005/300: dt: 0.9000, rms radial error=177.194, avgs=0 010/300: dt: 0.9000, rms radial error=176.633, avgs=0 015/300: dt: 0.9000, rms radial error=175.895, avgs=0 020/300: dt: 0.9000, rms radial error=175.055, avgs=0 025/300: dt: 0.9000, rms radial error=174.157, avgs=0 030/300: dt: 0.9000, rms radial error=173.226, avgs=0 035/300: dt: 0.9000, rms radial error=172.279, avgs=0 040/300: dt: 0.9000, rms radial error=171.326, avgs=0 045/300: dt: 0.9000, rms radial error=170.371, avgs=0 050/300: dt: 0.9000, rms radial error=169.420, avgs=0 055/300: dt: 0.9000, rms radial error=168.472, avgs=0 060/300: dt: 0.9000, rms radial error=167.529, avgs=0 065/300: dt: 0.9000, rms radial error=166.590, avgs=0 070/300: dt: 0.9000, rms radial error=165.660, avgs=0 075/300: dt: 0.9000, rms radial error=164.733, avgs=0 080/300: dt: 0.9000, rms radial error=163.812, avgs=0 085/300: dt: 0.9000, rms radial error=162.895, avgs=0 090/300: dt: 0.9000, rms radial error=161.983, avgs=0 095/300: dt: 0.9000, rms radial error=161.075, avgs=0 100/300: dt: 0.9000, rms radial error=160.174, avgs=0 105/300: dt: 0.9000, rms radial error=159.277, avgs=0 110/300: dt: 0.9000, rms radial error=158.385, avgs=0 115/300: dt: 0.9000, rms radial error=157.498, avgs=0 120/300: dt: 0.9000, rms radial error=156.616, avgs=0 125/300: dt: 0.9000, rms radial error=155.738, avgs=0 130/300: dt: 0.9000, rms radial error=154.866, avgs=0 135/300: dt: 0.9000, rms radial error=153.997, avgs=0 140/300: dt: 0.9000, rms radial error=153.134, avgs=0 145/300: dt: 0.9000, rms radial error=152.274, avgs=0 150/300: dt: 0.9000, rms radial error=151.421, avgs=0 155/300: dt: 0.9000, rms radial error=150.571, avgs=0 160/300: dt: 0.9000, rms radial error=149.726, avgs=0 165/300: dt: 0.9000, rms radial error=148.885, avgs=0 170/300: dt: 0.9000, rms radial error=148.048, avgs=0 175/300: dt: 0.9000, rms radial error=147.217, avgs=0 180/300: dt: 0.9000, rms radial error=146.390, avgs=0 185/300: dt: 0.9000, rms radial error=145.567, avgs=0 190/300: dt: 0.9000, rms radial error=144.750, avgs=0 195/300: dt: 0.9000, rms radial error=143.936, avgs=0 200/300: dt: 0.9000, rms radial error=143.127, avgs=0 205/300: dt: 0.9000, rms radial error=142.320, avgs=0 210/300: dt: 0.9000, rms radial error=141.521, avgs=0 215/300: dt: 0.9000, rms radial error=140.726, avgs=0 220/300: dt: 0.9000, rms radial error=139.934, avgs=0 225/300: dt: 0.9000, rms radial error=139.147, avgs=0 230/300: dt: 0.9000, rms radial error=138.364, avgs=0 235/300: dt: 0.9000, rms radial error=137.586, avgs=0 240/300: dt: 0.9000, rms radial error=136.812, avgs=0 245/300: dt: 0.9000, rms radial error=136.043, avgs=0 250/300: dt: 0.9000, rms radial error=135.277, avgs=0 255/300: dt: 0.9000, rms radial error=134.515, avgs=0 260/300: dt: 0.9000, rms radial error=133.758, avgs=0 265/300: dt: 0.9000, rms radial error=133.005, avgs=0 270/300: dt: 0.9000, rms radial error=132.256, avgs=0 275/300: dt: 0.9000, rms radial error=131.511, avgs=0 280/300: dt: 0.9000, rms radial error=130.770, avgs=0 285/300: dt: 0.9000, rms radial error=130.034, avgs=0 290/300: dt: 0.9000, rms radial error=129.302, avgs=0 295/300: dt: 0.9000, rms radial error=128.574, avgs=0 300/300: dt: 0.9000, rms radial error=127.850, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15475.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2622.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 285.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/13 = 0.00868 epoch 4 (K=640.0), pass 1, starting sse = 17.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00720 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Sep 18 18:17:51 EDT 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /usr/local/freesurfer/subjects/case018_tp2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 case018_tp2 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-72 (nv=131284, nf=262712, ne=394068, g=37) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 4860 ambiguous faces found in tessellation segmenting defects... 42 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 24 41 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7232 (-4.3616) -vertex loglikelihood: -5.5802 (-2.7901) -normal dot loglikelihood: -3.6006 (-3.6006) -quad curv loglikelihood: -6.1517 (-3.0759) Total Loglikelihood : -24.0558 CORRECTING DEFECT 0 (vertices=23, convex hull=56) After retessellation of defect 0, euler #=-39 (128309,383701,255353) : difference with theory (-38) = 1 CORRECTING DEFECT 1 (vertices=18, convex hull=27) After retessellation of defect 1, euler #=-38 (128310,383713,255365) : difference with theory (-37) = 1 CORRECTING DEFECT 2 (vertices=43, convex hull=78) After retessellation of defect 2, euler #=-37 (128340,383834,255457) : difference with theory (-36) = 1 CORRECTING DEFECT 3 (vertices=24, convex hull=55) After retessellation of defect 3, euler #=-36 (128352,383890,255502) : difference with theory (-35) = 1 CORRECTING DEFECT 4 (vertices=31, convex hull=80) After retessellation of defect 4, euler #=-35 (128362,383954,255557) : difference with theory (-34) = 1 CORRECTING DEFECT 5 (vertices=36, convex hull=49) After retessellation of defect 5, euler #=-34 (128375,384013,255604) : difference with theory (-33) = 1 CORRECTING DEFECT 6 (vertices=29, convex hull=61) After retessellation of defect 6, euler #=-33 (128384,384062,255645) : difference with theory (-32) = 1 CORRECTING DEFECT 7 (vertices=30, convex hull=68) After retessellation of defect 7, euler #=-32 (128404,384150,255714) : difference with theory (-31) = 1 CORRECTING DEFECT 8 (vertices=23, convex hull=53) After retessellation of defect 8, euler #=-31 (128413,384201,255757) : difference with theory (-30) = 1 CORRECTING DEFECT 9 (vertices=35, convex hull=76) After retessellation of defect 9, euler #=-30 (128422,384260,255808) : difference with theory (-29) = 1 CORRECTING DEFECT 10 (vertices=76, convex hull=118) After retessellation of defect 10, euler #=-29 (128458,384421,255934) : difference with theory (-28) = 1 CORRECTING DEFECT 11 (vertices=27, convex hull=41) After retessellation of defect 11, euler #=-28 (128468,384465,255969) : difference with theory (-27) = 1 CORRECTING DEFECT 12 (vertices=27, convex hull=30) After retessellation of defect 12, euler #=-27 (128470,384481,255984) : difference with theory (-26) = 1 CORRECTING DEFECT 13 (vertices=24, convex hull=53) After retessellation of defect 13, euler #=-26 (128482,384537,256029) : difference with theory (-25) = 1 CORRECTING DEFECT 14 (vertices=36, convex hull=59) After retessellation of defect 14, euler #=-25 (128501,384618,256092) : difference with theory (-24) = 1 CORRECTING DEFECT 15 (vertices=51, convex hull=100) After retessellation of defect 15, euler #=-24 (128517,384709,256168) : difference with theory (-23) = 1 CORRECTING DEFECT 16 (vertices=23, convex hull=72) After retessellation of defect 16, euler #=-23 (128528,384767,256216) : difference with theory (-22) = 1 CORRECTING DEFECT 17 (vertices=208, convex hull=56) After retessellation of defect 17, euler #=-22 (128571,384920,256327) : difference with theory (-21) = 1 CORRECTING DEFECT 18 (vertices=9, convex hull=14) After retessellation of defect 18, euler #=-21 (128573,384930,256336) : difference with theory (-20) = 1 CORRECTING DEFECT 19 (vertices=9, convex hull=22) After retessellation of defect 19, euler #=-20 (128574,384943,256349) : difference with theory (-19) = 1 CORRECTING DEFECT 20 (vertices=25, convex hull=19) After retessellation of defect 20, euler #=-19 (128578,384959,256362) : difference with theory (-18) = 1 CORRECTING DEFECT 21 (vertices=198, convex hull=169) After retessellation of defect 21, euler #=-18 (128589,385071,256464) : difference with theory (-17) = 1 CORRECTING DEFECT 22 (vertices=49, convex hull=43) After retessellation of defect 22, euler #=-17 (128598,385116,256501) : difference with theory (-16) = 1 CORRECTING DEFECT 23 (vertices=10, convex hull=30) After retessellation of defect 23, euler #=-16 (128602,385135,256517) : difference with theory (-15) = 1 CORRECTING DEFECT 24 (vertices=126, convex hull=55) After retessellation of defect 24, euler #=-14 (128615,385199,256570) : difference with theory (-14) = 0 CORRECTING DEFECT 25 (vertices=76, convex hull=25) Warning - incorrect dp selected!!!!(-72.404868 >= -72.404875 ) After retessellation of defect 25, euler #=-13 (128617,385213,256583) : difference with theory (-13) = 0 CORRECTING DEFECT 26 (vertices=91, convex hull=68) After retessellation of defect 26, euler #=-12 (128628,385277,256637) : difference with theory (-12) = 0 CORRECTING DEFECT 27 (vertices=512, convex hull=208) After retessellation of defect 27, euler #=-11 (128785,385846,257050) : difference with theory (-11) = 0 CORRECTING DEFECT 28 (vertices=17, convex hull=53) After retessellation of defect 28, euler #=-10 (128794,385897,257093) : difference with theory (-10) = 0 CORRECTING DEFECT 29 (vertices=67, convex hull=28) After retessellation of defect 29, euler #=-9 (128800,385924,257115) : difference with theory (-9) = 0 CORRECTING DEFECT 30 (vertices=27, convex hull=42) After retessellation of defect 30, euler #=-8 (128804,385952,257140) : difference with theory (-8) = 0 CORRECTING DEFECT 31 (vertices=75, convex hull=103) After retessellation of defect 31, euler #=-7 (128813,386023,257203) : difference with theory (-7) = 0 CORRECTING DEFECT 32 (vertices=84, convex hull=138) After retessellation of defect 32, euler #=-6 (128856,386218,257356) : difference with theory (-6) = 0 CORRECTING DEFECT 33 (vertices=350, convex hull=182) After retessellation of defect 33, euler #=-5 (128921,386503,257577) : difference with theory (-5) = 0 CORRECTING DEFECT 34 (vertices=157, convex hull=242) After retessellation of defect 34, euler #=-4 (129038,386962,257920) : difference with theory (-4) = 0 CORRECTING DEFECT 35 (vertices=25, convex hull=66) After retessellation of defect 35, euler #=-3 (129049,387019,257967) : difference with theory (-3) = 0 CORRECTING DEFECT 36 (vertices=20, convex hull=55) After retessellation of defect 36, euler #=-2 (129060,387071,258009) : difference with theory (-2) = 0 CORRECTING DEFECT 37 (vertices=171, convex hull=63) After retessellation of defect 37, euler #=-1 (129082,387162,258079) : difference with theory (-1) = 0 CORRECTING DEFECT 38 (vertices=35, convex hull=52) After retessellation of defect 38, euler #=0 (129096,387226,258130) : difference with theory (0) = 0 CORRECTING DEFECT 39 (vertices=44, convex hull=75) After retessellation of defect 39, euler #=1 (129105,387283,258179) : difference with theory (1) = 0 CORRECTING DEFECT 40 (vertices=43, convex hull=63) After retessellation of defect 40, euler #=2 (129121,387357,258238) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.06-->10.97) (max @ vno 108841 --> 130709) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.06-->10.97) (max @ vno 108841 --> 130709) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 136 mutations (32.8%), 279 crossovers (67.2%), 181 vertices were eliminated building final representation... 2163 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=129121, nf=258238, ne=387357, g=0) writing corrected surface to /usr/local/freesurfer/subjects/case018_tp2/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.0 minutes 0 defective edges removing intersecting faces 000: 214 intersecting 001: 3 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 129121 - 387357 + 258238 = 2 --> 0 holes F =2V-4: 258238 = 258242-4 (0) 2E=3F: 774714 = 774714 (0) total defect index = 0 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 44 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Sep 18 18:43:57 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs case018_tp2 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... 12947 bright wm thresholded. 3033 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/case018_tp2/surf/rh.orig... computing class statistics... border white: 252263 voxels (1.50%) border gray 277912 voxels (1.66%) WM (100.0): 101.0 +- 5.9 [70.0 --> 110.0] GM (92.0) : 90.2 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 75.1 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 65.2 (was 40) setting MAX_GRAY to 101.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 80.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 55.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->7.17) (max @ vno 108841 --> 128906) face area 0.28 +- 0.12 (0.00-->2.23) mean absolute distance = 0.84 +- 1.01 3460 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=107, GM=85 mean inside = 100.9, mean outside = 88.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=91.2, 115 (115) missing vertices, mean dist 0.4 [0.8 (%28.4)->0.9 (%71.6))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.08-->6.19) (max @ vno 108841 --> 128906) face area 0.28 +- 0.14 (0.00-->1.85) mean absolute distance = 0.44 +- 0.66 3581 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3663010.0, rms=7.50 001: dt: 0.5000, sse=4255564.5, rms=5.476 (0.000%) 002: dt: 0.5000, sse=4374624.0, rms=4.125 (0.000%) 003: dt: 0.5000, sse=4461578.5, rms=3.211 (0.000%) 004: dt: 0.5000, sse=4526138.0, rms=2.625 (0.000%) 005: dt: 0.5000, sse=4557000.0, rms=2.288 (0.000%) 006: dt: 0.5000, sse=4570127.5, rms=2.103 (0.000%) 007: dt: 0.5000, sse=4580020.0, rms=2.004 (0.000%) 008: dt: 0.5000, sse=4585963.0, rms=1.944 (0.000%) rms = 1.91, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=4592432.5, rms=1.913 (0.000%) 010: dt: 0.2500, sse=3320273.2, rms=1.558 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3207411.5, rms=1.518 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3163188.5, rms=1.507 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=93.4, 97 (69) missing vertices, mean dist -0.3 [0.5 (%70.6)->0.3 (%29.4))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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 +- 0.25 (0.07-->5.87) (max @ vno 108841 --> 128906) face area 0.34 +- 0.16 (0.00-->2.35) mean absolute distance = 0.33 +- 0.42 3845 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3504940.2, rms=3.46 013: dt: 0.5000, sse=3712542.2, rms=2.203 (0.000%) 014: dt: 0.5000, sse=3960120.8, rms=1.772 (0.000%) 015: dt: 0.5000, sse=4012296.0, rms=1.616 (0.000%) rms = 1.58, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4262044.5, rms=1.580 (0.000%) 017: dt: 0.2500, sse=3525667.5, rms=1.330 (0.000%) rms = 1.30, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3422536.5, rms=1.300 (0.000%) rms = 1.29, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3388709.2, rms=1.291 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=95.6, 112 (64) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.2 (%25.3))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, 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 0.88 +- 0.25 (0.07-->5.67) (max @ vno 108841 --> 128906) face area 0.33 +- 0.16 (0.00-->2.29) mean absolute distance = 0.23 +- 0.32 3380 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3525628.0, rms=2.89 020: dt: 0.5000, sse=3745297.0, rms=1.607 (0.000%) 021: dt: 0.5000, sse=3962856.0, rms=1.414 (0.000%) rms = 1.40, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=3982090.0, rms=1.395 (0.000%) 023: dt: 0.2500, sse=3617888.8, rms=1.187 (0.000%) rms = 1.18, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3521667.8, rms=1.177 (0.000%) rms = 1.18, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3493489.0, rms=1.176 (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 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=96.2, 128 (64) missing vertices, mean dist -0.1 [0.2 (%58.6)->0.2 (%41.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3498687.5, rms=1.44 026: dt: 0.5000, sse=4287637.5, rms=0.994 (0.000%) rms = 1.24, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4011203.8, rms=0.941 (0.000%) rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.94, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3984928.5, rms=0.939 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2087 vertices erasing segment 1 (vno[0] = 53306) erasing segment 2 (vno[0] = 54523) erasing segment 3 (vno[0] = 86973) erasing segment 4 (vno[0] = 87030) erasing segment 5 (vno[0] = 90022) erasing segment 6 (vno[0] = 90031) erasing segment 7 (vno[0] = 91822) erasing segment 8 (vno[0] = 93889) erasing segment 9 (vno[0] = 95765) erasing segment 10 (vno[0] = 96573) erasing segment 11 (vno[0] = 98994) erasing segment 12 (vno[0] = 101542) erasing segment 13 (vno[0] = 128406) writing cortex label to /usr/local/freesurfer/subjects/case018_tp2/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/rh.area vertex spacing 0.88 +- 0.25 (0.07-->5.56) (max @ vno 108841 --> 128906) face area 0.32 +- 0.16 (0.00-->2.19) refinement took 4.8 minutes #-------------------------------------------- #@# Smooth2 rh Thu Sep 18 18:48:42 EDT 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /usr/local/freesurfer/subjects/case018_tp2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Sep 18 18:48:46 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.8 mm, total surface area = 76651 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 147 vertices thresholded to be in k1 ~ [-0.39 0.41], k2 ~ [-0.13 0.13] total integrated curvature = 0.508*4pi (6.385) --> 0 handles ICI = 1.4, FI = 8.4, variation=144.488 116 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 129 vertices thresholded to be in [-0.18 0.20] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Thu Sep 18 18:50:31 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm case018_tp2 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ case018_tp2/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 261 ] Gb_filter = 0 WARN: S lookup min: -0.146430 WARN: S explicit min: 0.000000 vertex = 344 #-------------------------------------------- #@# Sphere rh Thu Sep 18 18:50:35 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 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 0.287... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=ubunt, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %42.78 pass 1: epoch 2 of 3 starting distance error %20.53 unfolding complete - removing small folds... starting distance error %20.40 removing remaining folds... final distance error %20.42 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.35 hours #-------------------------------------------- #@# Surf Reg rh Thu Sep 18 19:11:49 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=ubunt, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=ubunt, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 0.575 curvature mean = 0.023, std = 0.936 curvature mean = 0.022, std = 0.856 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 405551.4, tmin=0.7740 d=32.00 min @ (-8.00, 0.00, 8.00) sse = 333816.3, tmin=1.5503 d=16.00 min @ (0.00, -4.00, 0.00) sse = 325903.4, tmin=2.3332 d=8.00 min @ (0.00, 0.00, 2.00) sse = 323329.8, tmin=3.1227 d=2.00 min @ (-0.50, 0.50, 0.50) sse = 323040.2, tmin=4.7040 d=1.00 min @ (0.00, -0.25, -0.25) sse = 322980.8, tmin=5.5022 d=0.50 min @ (0.00, 0.00, -0.12) sse = 322975.9, tmin=6.3236 tol=1.0e+00, sigma=0.5, host=ubunt, 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 6.32 min curvature mean = 0.010, std = 0.957 curvature mean = 0.011, std = 0.939 curvature mean = 0.010, std = 0.970 curvature mean = 0.005, std = 0.973 curvature mean = 0.007, std = 0.971 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.026, std = 0.279 curvature mean = 0.006, std = 0.070 curvature mean = 0.063, std = 0.371 curvature mean = 0.005, std = 0.083 curvature mean = 0.025, std = 0.563 curvature mean = 0.005, std = 0.089 curvature mean = 0.013, std = 0.701 curvature mean = 0.005, std = 0.092 curvature mean = 0.005, std = 0.806 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Sep 18 19:33:02 EDT 2014 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Sep 18 19:33:04 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Sep 18 19:33:05 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1152 labels changed using aseg relabeling using gibbs priors... 000: 2758 changed, 129121 examined... 001: 644 changed, 11917 examined... 002: 161 changed, 3541 examined... 003: 52 changed, 980 examined... 004: 26 changed, 313 examined... 005: 5 changed, 150 examined... 006: 0 changed, 37 examined... 190 labels changed using aseg 000: 89 total segments, 47 labels (326 vertices) changed 001: 44 total segments, 2 labels (2 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 72 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1235 vertices marked for relabeling... 1235 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 57 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Sep 18 19:34:03 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs case018_tp2 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... 12947 bright wm thresholded. 3033 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/case018_tp2/surf/rh.orig... computing class statistics... border white: 252263 voxels (1.50%) border gray 277912 voxels (1.66%) WM (100.0): 101.0 +- 5.9 [70.0 --> 110.0] GM (92.0) : 90.2 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 75.1 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 65.2 (was 40) setting MAX_GRAY to 101.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 80.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 55.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=85 mean inside = 100.9, mean outside = 88.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->7.17) (max @ vno 108841 --> 128906) face area 0.28 +- 0.12 (0.00-->2.23) mean absolute distance = 0.84 +- 1.02 3537 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 237 points - only 0.00% unknown deleting segment 5 with 40 points - only 0.00% unknown mean border=91.2, 115 (115) missing vertices, mean dist 0.4 [0.8 (%28.5)->0.9 (%71.5))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.08-->6.19) (max @ vno 108841 --> 128906) face area 0.28 +- 0.14 (0.00-->1.84) mean absolute distance = 0.44 +- 0.67 3645 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3670478.5, rms=7.50 001: dt: 0.5000, sse=4269858.0, rms=5.482 (0.000%) 002: dt: 0.5000, sse=4385776.0, rms=4.133 (0.000%) 003: dt: 0.5000, sse=4473561.0, rms=3.220 (0.000%) 004: dt: 0.5000, sse=4537650.0, rms=2.634 (0.000%) 005: dt: 0.5000, sse=4567610.0, rms=2.297 (0.000%) 006: dt: 0.5000, sse=4582244.5, rms=2.111 (0.000%) 007: dt: 0.5000, sse=4592129.5, rms=2.011 (0.000%) 008: dt: 0.5000, sse=4599126.0, rms=1.951 (0.000%) rms = 1.92, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=4606443.5, rms=1.920 (0.000%) 010: dt: 0.2500, sse=3332643.5, rms=1.567 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3220438.5, rms=1.527 (0.000%) rms = 1.52, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3175889.8, rms=1.517 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 50.00% unknown deleting segment 6 with 159 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 34 points - only 20.59% unknown deleting segment 12 with 45 points - only 0.00% unknown mean border=93.4, 98 (69) missing vertices, mean dist -0.3 [0.5 (%70.6)->0.3 (%29.4))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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 +- 0.25 (0.07-->5.87) (max @ vno 108841 --> 128906) face area 0.34 +- 0.16 (0.00-->2.35) mean absolute distance = 0.33 +- 0.42 3916 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3521341.5, rms=3.46 013: dt: 0.5000, sse=3734478.2, rms=2.208 (0.000%) 014: dt: 0.5000, sse=3982655.8, rms=1.779 (0.000%) 015: dt: 0.5000, sse=4032144.0, rms=1.624 (0.000%) rms = 1.59, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4283632.0, rms=1.587 (0.000%) 017: dt: 0.2500, sse=3543246.2, rms=1.338 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3440893.0, rms=1.308 (0.000%) rms = 1.30, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3406218.8, rms=1.300 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 198 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 34 points - only 20.59% unknown deleting segment 7 with 43 points - only 0.00% unknown mean border=95.6, 111 (64) missing vertices, mean dist -0.2 [0.4 (%74.7)->0.2 (%25.3))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, 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 0.88 +- 0.25 (0.07-->5.67) (max @ vno 108841 --> 128906) face area 0.33 +- 0.16 (0.00-->2.29) mean absolute distance = 0.24 +- 0.33 3454 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3543193.2, rms=2.89 020: dt: 0.5000, sse=3763338.2, rms=1.612 (0.000%) 021: dt: 0.5000, sse=3981047.2, rms=1.420 (0.000%) rms = 1.40, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=4000243.8, rms=1.400 (0.000%) 023: dt: 0.2500, sse=3633986.2, rms=1.193 (0.000%) rms = 1.18, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3537268.8, rms=1.184 (0.000%) rms = 1.18, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3508762.5, rms=1.182 (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 deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 219 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 34 points - only 20.59% unknown deleting segment 9 with 43 points - only 0.00% unknown mean border=96.2, 128 (64) missing vertices, mean dist -0.1 [0.2 (%58.6)->0.2 (%41.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, 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=3514057.0, rms=1.44 026: dt: 0.5000, sse=4310298.0, rms=0.999 (0.000%) rms = 1.24, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4031856.8, rms=0.946 (0.000%) rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.94, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4004895.5, rms=0.944 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=75.7, 87 (87) missing vertices, mean dist 1.9 [0.3 (%0.0)->2.4 (%100.0))] %24 local maxima, %50 large gradients and %21 min vals, 1628 gradients ignored tol=1.0e-04, sigma=2.0, host=ubunt, 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=13481103.0, rms=21.26 001: dt: 0.5000, sse=11036369.0, rms=18.783 (0.000%) 002: dt: 0.5000, sse=9132161.0, rms=16.640 (0.000%) 003: dt: 0.5000, sse=7743717.5, rms=14.833 (0.000%) 004: dt: 0.5000, sse=6809902.5, rms=13.292 (0.000%) 005: dt: 0.5000, sse=6224645.5, rms=11.991 (0.000%) 006: dt: 0.5000, sse=5876770.0, rms=10.883 (0.000%) 007: dt: 0.5000, sse=5664608.0, rms=9.874 (0.000%) 008: dt: 0.5000, sse=5460861.5, rms=8.907 (0.000%) 009: dt: 0.5000, sse=5381634.5, rms=7.974 (0.000%) 010: dt: 0.5000, sse=5220344.0, rms=7.039 (0.000%) 011: dt: 0.5000, sse=5174807.5, rms=6.170 (0.000%) 012: dt: 0.5000, sse=5111648.0, rms=5.379 (0.000%) 013: dt: 0.5000, sse=5154403.5, rms=4.728 (0.000%) 014: dt: 0.5000, sse=5188517.5, rms=4.214 (0.000%) 015: dt: 0.5000, sse=5269990.0, rms=3.902 (0.000%) 016: dt: 0.5000, sse=5328963.5, rms=3.686 (0.000%) 017: dt: 0.5000, sse=5367184.5, rms=3.572 (0.000%) 018: dt: 0.5000, sse=5410886.5, rms=3.491 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5441357.5, rms=3.461 (0.000%) 020: dt: 0.2500, sse=3756012.5, rms=2.748 (0.000%) 021: dt: 0.2500, sse=3604733.8, rms=2.577 (0.000%) rms = 2.56, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3524856.2, rms=2.559 (0.000%) 023: dt: 0.1250, sse=3376220.0, rms=2.414 (0.000%) rms = 2.40, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3358142.5, rms=2.396 (0.000%) positioning took 2.1 minutes mean border=73.3, 768 (10) missing vertices, mean dist 0.2 [0.2 (%39.6)->0.5 (%60.4))] %51 local maxima, %28 large gradients and %16 min vals, 476 gradients ignored tol=1.0e-04, sigma=1.0, host=ubunt, 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=3935154.2, rms=4.49 025: dt: 0.5000, sse=4080842.2, rms=3.639 (0.000%) 026: dt: 0.5000, sse=5056683.5, rms=3.507 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4236839.0, rms=2.847 (0.000%) 028: dt: 0.2500, sse=3926175.5, rms=2.597 (0.000%) rms = 2.55, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3897888.5, rms=2.552 (0.000%) 030: dt: 0.1250, sse=3747930.8, rms=2.366 (0.000%) rms = 2.34, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3729201.5, rms=2.335 (0.000%) positioning took 0.7 minutes mean border=71.6, 999 (10) missing vertices, mean dist 0.1 [0.2 (%33.4)->0.3 (%66.6))] %66 local maxima, %12 large gradients and %16 min vals, 517 gradients ignored tol=1.0e-04, sigma=0.5, host=ubunt, 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=3872686.0, rms=3.25 rms = 3.29, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3726646.2, rms=2.746 (0.000%) 033: dt: 0.2500, sse=3709037.2, rms=2.408 (0.000%) 034: dt: 0.2500, sse=3821969.0, rms=2.334 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... rms = 2.29, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3787032.8, rms=2.288 (0.000%) positioning took 0.5 minutes mean border=70.8, 1898 (10) missing vertices, mean dist 0.1 [0.2 (%42.4)->0.3 (%57.6))] %68 local maxima, %10 large gradients and %16 min vals, 427 gradients ignored tol=1.0e-04, sigma=0.2, host=ubunt, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3808603.5, rms=2.49 rms = 3.02, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3728865.0, rms=2.258 (0.000%) 037: dt: 0.2500, sse=3855836.5, rms=2.176 (0.000%) rms = 2.19, time step reduction 2 of 3 to 0.125... rms = 2.15, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3830600.2, rms=2.146 (0.000%) positioning took 0.4 minutes writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/rh.area.pial vertex spacing 1.00 +- 0.43 (0.02-->7.01) (max @ vno 89051 --> 88011) face area 0.40 +- 0.30 (0.00-->6.10) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 129121 vertices processed 25000 of 129121 vertices processed 50000 of 129121 vertices processed 75000 of 129121 vertices processed 100000 of 129121 vertices processed 125000 of 129121 vertices processed 0 of 129121 vertices processed 25000 of 129121 vertices processed 50000 of 129121 vertices processed 75000 of 129121 vertices processed 100000 of 129121 vertices processed 125000 of 129121 vertices processed thickness calculation complete, 375:951 truncations. 32745 vertices at 0 distance 90044 vertices at 1 distance 77689 vertices at 2 distance 32371 vertices at 3 distance 9973 vertices at 4 distance 2576 vertices at 5 distance 780 vertices at 6 distance 280 vertices at 7 distance 128 vertices at 8 distance 69 vertices at 9 distance 26 vertices at 10 distance 21 vertices at 11 distance 10 vertices at 12 distance 16 vertices at 13 distance 14 vertices at 14 distance 7 vertices at 15 distance 7 vertices at 16 distance 8 vertices at 17 distance 5 vertices at 18 distance 4 vertices at 19 distance 7 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/case018_tp2/surf/rh.thickness positioning took 9.2 minutes #-------------------------------------------- #@# Surf Volume rh Thu Sep 18 19:43:12 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Thu Sep 18 19:43:13 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab case018_tp2 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1610 1122 2852 2.552 0.472 0.126 0.037 15 2.5 bankssts 1001 634 2032 3.103 0.601 0.145 0.072 16 1.9 caudalanteriorcingulate 3004 1955 6224 2.758 0.620 0.134 0.048 37 5.8 caudalmiddlefrontal 2389 1527 2967 1.786 0.381 0.158 0.060 39 6.1 cuneus 505 349 1655 3.311 0.879 0.173 0.078 9 1.7 entorhinal 4542 3066 9936 2.730 0.637 0.150 0.068 76 12.2 fusiform 6008 4015 11684 2.535 0.513 0.136 0.071 95 11.0 inferiorparietal 4488 3029 10252 2.787 0.654 0.158 0.093 160 19.1 inferiortemporal 1367 859 2299 2.424 0.640 0.149 0.058 23 3.2 isthmuscingulate 7599 4592 11610 2.183 0.569 0.138 0.063 137 15.8 lateraloccipital 3251 2202 7178 2.913 0.771 0.167 0.096 86 10.5 lateralorbitofrontal 4683 2991 6364 1.982 0.647 0.158 0.075 118 15.4 lingual 2326 1625 4682 2.521 0.704 0.178 0.108 80 10.5 medialorbitofrontal 3993 2751 10891 3.122 0.653 0.146 0.048 76 7.9 middletemporal 1026 670 2328 3.009 0.856 0.134 0.049 12 2.1 parahippocampal 1983 1251 3148 2.368 0.577 0.138 0.086 37 6.7 paracentral 1671 1131 3547 2.785 0.535 0.124 0.042 20 2.8 parsopercularis 934 627 2587 3.155 0.587 0.172 0.077 21 2.8 parsorbitalis 1558 1050 3067 2.567 0.580 0.124 0.038 18 2.3 parstriangularis 2202 1380 2218 1.756 0.508 0.148 0.070 32 6.3 pericalcarine 5506 3442 7451 1.918 0.617 0.137 0.068 146 12.9 postcentral 1718 1171 3422 2.719 0.479 0.168 0.060 37 4.3 posteriorcingulate 7471 4510 12945 2.601 0.493 0.122 0.097 206 24.3 precentral 4644 3084 8327 2.505 0.538 0.145 0.056 78 10.4 precuneus 1337 869 3003 3.146 0.571 0.168 0.078 36 4.2 rostralanteriorcingulate 8827 5948 17752 2.503 0.642 0.151 0.060 180 20.2 rostralmiddlefrontal 9134 6000 19885 2.842 0.636 0.147 0.069 211 24.3 superiorfrontal 7490 4849 12325 2.238 0.500 0.127 0.043 89 12.6 superiorparietal 4792 3207 11286 2.926 0.679 0.126 0.040 53 7.8 superiortemporal 6507 4318 13093 2.634 0.613 0.147 0.135 200 14.6 supramarginal 357 237 1014 2.883 0.670 0.244 0.157 18 2.3 frontalpole 696 506 2849 3.712 0.753 0.205 0.124 21 3.9 temporalpole 639 408 1158 2.581 0.402 0.153 0.065 12 1.7 transversetemporal 2723 1803 5837 3.160 0.885 0.132 0.182 156 6.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Sep 18 19:43:37 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 132 labels changed using aseg relabeling using gibbs priors... 000: 8627 changed, 126095 examined... 001: 2024 changed, 33154 examined... 002: 628 changed, 10499 examined... 003: 293 changed, 3610 examined... 004: 126 changed, 1602 examined... 005: 60 changed, 687 examined... 006: 24 changed, 313 examined... 007: 10 changed, 133 examined... 008: 1 changed, 58 examined... 009: 1 changed, 7 examined... 010: 1 changed, 9 examined... 011: 0 changed, 7 examined... 49 labels changed using aseg 000: 289 total segments, 207 labels (2471 vertices) changed 001: 103 total segments, 22 labels (123 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 432 vertices marked for relabeling... 432 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 2 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Sep 18 19:44:39 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab case018_tp2 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1149 797 2471 2.405 0.806 0.177 0.091 37 3.7 G_and_S_frontomargin 1755 1144 3521 2.458 0.681 0.146 0.047 29 3.3 G_and_S_occipital_inf 1664 972 2489 2.160 0.508 0.152 0.119 44 8.1 G_and_S_paracentral 1418 956 3207 2.671 0.538 0.156 0.056 26 3.3 G_and_S_subcentral 828 572 2096 2.630 0.642 0.212 0.114 39 3.4 G_and_S_transv_frontopol 2285 1520 4495 2.925 0.678 0.147 0.060 44 5.7 G_and_S_cingul-Ant 1502 979 3009 2.911 0.539 0.131 0.043 18 2.5 G_and_S_cingul-Mid-Ant 1271 876 2451 2.632 0.422 0.139 0.045 18 2.4 G_and_S_cingul-Mid-Post 496 329 1087 2.825 0.607 0.182 0.088 13 1.7 G_cingul-Post-dorsal 294 178 588 2.524 0.612 0.157 0.063 6 0.7 G_cingul-Post-ventral 2231 1377 2897 1.795 0.485 0.165 0.072 42 6.8 G_cuneus 1069 716 2921 3.052 0.458 0.143 0.059 19 2.3 G_front_inf-Opercular 278 172 791 3.219 0.495 0.155 0.082 5 0.8 G_front_inf-Orbital 765 512 1907 2.787 0.538 0.139 0.052 13 1.5 G_front_inf-Triangul 4469 2946 10648 2.811 0.629 0.157 0.064 98 11.3 G_front_middle 5849 3779 14602 3.020 0.594 0.160 0.082 174 18.9 G_front_sup 332 246 898 3.483 0.853 0.144 0.093 7 0.8 G_Ins_lg_and_S_cent_ins 674 405 1895 3.594 0.814 0.152 0.082 15 2.1 G_insular_short 1953 1279 4569 2.631 0.540 0.152 0.129 45 4.1 G_occipital_middle 1369 886 2304 2.063 0.647 0.138 0.042 18 2.4 G_occipital_sup 1790 1201 4626 2.954 0.610 0.166 0.084 39 5.7 G_oc-temp_lat-fusifor 3200 1994 4620 1.982 0.677 0.173 0.092 104 12.9 G_oc-temp_med-Lingual 1302 886 4016 3.396 0.836 0.173 0.075 23 4.4 G_oc-temp_med-Parahip 2292 1570 6471 3.123 0.763 0.181 0.091 68 8.1 G_orbital 2652 1747 5928 2.684 0.605 0.155 0.058 54 6.1 G_pariet_inf-Angular 3306 2210 7992 2.868 0.587 0.154 0.217 135 8.1 G_pariet_inf-Supramar 2716 1782 5223 2.371 0.483 0.145 0.056 47 5.9 G_parietal_sup 2047 1164 2674 1.862 0.493 0.143 0.070 40 6.4 G_postcentral 2791 1544 5964 2.878 0.469 0.136 0.138 121 14.1 G_precentral 1935 1279 4674 2.777 0.451 0.170 0.075 53 5.5 G_precuneus 945 650 2432 2.791 0.593 0.214 0.154 48 5.2 G_rectus 341 228 544 2.486 1.003 0.185 0.191 18 3.4 G_subcallosal 455 292 964 2.638 0.379 0.151 0.066 10 1.2 G_temp_sup-G_T_transv 1835 1212 6133 3.398 0.652 0.157 0.062 34 4.3 G_temp_sup-Lateral 682 482 1850 3.406 0.768 0.117 0.045 5 1.3 G_temp_sup-Plan_polar 1012 672 2022 2.589 0.484 0.125 0.049 33 2.2 G_temp_sup-Plan_tempo 2529 1736 7149 2.914 0.727 0.184 0.126 140 15.2 G_temporal_inf 2313 1609 7707 3.292 0.634 0.162 0.056 60 5.4 G_temporal_middle 320 213 564 2.735 0.493 0.129 0.031 3 0.4 Lat_Fis-ant-Horizont 172 117 220 2.073 0.270 0.110 0.021 1 0.2 Lat_Fis-ant-Vertical 1040 680 1355 2.450 0.443 0.139 0.049 10 2.2 Lat_Fis-post 2721 1409 3227 2.018 0.497 0.143 0.104 74 7.8 Pole_occipital 1555 1079 5101 3.353 0.783 0.193 0.115 42 7.6 Pole_temporal 2677 1742 2938 1.890 0.598 0.140 0.054 34 6.5 S_calcarine 2994 1891 3229 1.993 0.616 0.114 0.084 63 6.0 S_central 980 673 1391 2.149 0.435 0.121 0.039 9 1.6 S_cingul-Marginalis 492 307 915 3.172 0.645 0.163 0.110 11 2.3 S_circular_insula_ant 1175 783 1959 2.852 0.732 0.095 0.023 6 1.2 S_circular_insula_inf 1442 967 2098 2.575 0.506 0.099 0.027 7 1.6 S_circular_insula_sup 1005 659 1545 2.524 0.434 0.105 0.035 6 1.4 S_collat_transv_ant 407 264 583 2.413 0.509 0.136 0.047 4 0.7 S_collat_transv_post 1942 1299 3293 2.443 0.492 0.117 0.034 22 2.7 S_front_inf 1885 1294 2759 2.181 0.411 0.131 0.041 20 3.0 S_front_middle 2600 1728 4696 2.546 0.579 0.134 0.049 32 4.8 S_front_sup 622 416 797 2.258 0.267 0.099 0.021 3 0.6 S_interm_prim-Jensen 3183 2039 4503 2.160 0.488 0.123 0.039 35 4.9 S_intrapariet_and_P_trans 1275 839 1578 1.990 0.364 0.116 0.030 9 1.6 S_oc_middle_and_Lunatus 1023 685 1348 2.133 0.349 0.113 0.028 7 1.2 S_oc_sup_and_transversal 524 356 696 2.229 0.321 0.106 0.023 3 0.6 S_occipital_ant 841 575 1306 2.513 0.355 0.127 0.044 8 1.6 S_oc-temp_lat 1961 1334 2859 2.244 0.506 0.121 0.035 16 2.8 S_oc-temp_med_and_Lingual 516 365 747 2.188 0.416 0.117 0.026 3 0.6 S_orbital_lateral 529 397 890 2.306 0.773 0.203 0.683 135 1.3 S_orbital_med-olfact 1144 777 2094 2.686 0.634 0.138 0.089 15 2.4 S_orbital-H_Shaped 2233 1462 3040 2.206 0.529 0.123 0.043 20 3.6 S_parieto_occipital 982 579 1149 2.500 0.732 0.160 0.077 20 2.2 S_pericallosal 2816 1824 3664 2.087 0.475 0.122 0.067 91 4.3 S_postcentral 1421 952 2060 2.415 0.457 0.099 0.023 7 1.5 S_precentral-inf-part 1432 926 2125 2.487 0.450 0.122 0.051 13 3.1 S_precentral-sup-part 835 576 1442 2.557 0.688 0.159 0.055 16 2.0 S_suborbital 911 600 1456 2.562 0.472 0.143 0.050 12 1.9 S_subparietal 1455 980 2293 2.641 0.422 0.133 0.050 16 2.8 S_temporal_inf 4742 3267 7677 2.514 0.448 0.111 0.028 34 5.6 S_temporal_sup 335 226 438 2.348 0.395 0.144 0.045 4 0.7 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Sep 18 19:45:05 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1257 labels changed using aseg relabeling using gibbs priors... 000: 2597 changed, 126095 examined... 001: 609 changed, 10970 examined... 002: 162 changed, 3374 examined... 003: 55 changed, 962 examined... 004: 23 changed, 328 examined... 005: 8 changed, 130 examined... 006: 6 changed, 54 examined... 007: 5 changed, 27 examined... 008: 5 changed, 22 examined... 009: 4 changed, 20 examined... 010: 1 changed, 23 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 1 changed, 6 examined... 014: 2 changed, 9 examined... 015: 2 changed, 13 examined... 016: 0 changed, 13 examined... 164 labels changed using aseg 000: 71 total segments, 38 labels (166 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 391 vertices marked for relabeling... 391 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 54 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Sep 18 19:45:59 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab case018_tp2 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1673 1079 3370 3.065 0.589 0.138 0.058 23 3.0 caudalanteriorcingulate 3098 2014 6401 2.747 0.622 0.133 0.048 39 5.9 caudalmiddlefrontal 3351 2132 4443 1.887 0.464 0.147 0.054 48 7.6 cuneus 464 322 1534 3.324 0.862 0.172 0.079 8 1.5 entorhinal 4218 2851 9138 2.724 0.617 0.145 0.059 63 10.2 fusiform 5958 3943 11529 2.536 0.521 0.138 0.072 97 11.2 inferiorparietal 4745 3192 11114 2.785 0.668 0.162 0.099 172 21.3 inferiortemporal 1364 857 2305 2.438 0.647 0.150 0.059 23 3.2 isthmuscingulate 7605 4592 11511 2.167 0.575 0.138 0.063 138 15.7 lateraloccipital 3441 2382 8063 2.906 0.818 0.178 0.195 216 11.2 lateralorbitofrontal 4641 2961 6295 1.978 0.640 0.158 0.075 117 15.2 lingual 2094 1447 4212 2.510 0.716 0.185 0.117 78 10.5 medialorbitofrontal 5171 3580 12941 3.007 0.663 0.141 0.047 88 10.2 middletemporal 1072 704 2407 3.006 0.874 0.133 0.048 12 2.2 parahippocampal 2195 1394 3617 2.415 0.589 0.136 0.081 38 7.0 paracentral 1577 1050 3277 2.783 0.537 0.123 0.043 19 2.7 parsopercularis 982 649 2346 2.907 0.586 0.152 0.061 16 2.3 parsorbitalis 1891 1272 3575 2.500 0.593 0.125 0.035 22 2.7 parstriangularis 2216 1394 2245 1.754 0.508 0.149 0.071 32 6.4 pericalcarine 6175 3877 8415 1.961 0.615 0.138 0.067 155 14.3 postcentral 1781 1215 3486 2.712 0.483 0.166 0.060 37 4.4 posteriorcingulate 7294 4392 12621 2.605 0.497 0.122 0.098 204 24.1 precentral 4330 2895 8074 2.546 0.526 0.147 0.057 76 9.8 precuneus 1641 1085 3598 3.089 0.595 0.165 0.074 41 5.0 rostralanteriorcingulate 6170 4148 12752 2.604 0.628 0.151 0.060 122 14.5 rostralmiddlefrontal 10880 7169 23371 2.729 0.673 0.153 0.072 269 29.8 superiorfrontal 5968 3876 9848 2.250 0.477 0.124 0.041 70 9.8 superiorparietal 6829 4649 16752 2.957 0.727 0.135 0.048 89 13.4 superiortemporal 6228 4129 12347 2.619 0.607 0.147 0.140 195 14.2 supramarginal 583 371 1060 2.558 0.378 0.156 0.067 11 1.6 transversetemporal 2346 1556 5220 3.178 0.873 0.123 0.060 33 5.3 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Sep 18 19:46:23 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts pctsurfcon --s case018_tp2 --lh-only Log file is /usr/local/freesurfer/subjects/case018_tp2/scripts/pctsurfcon.log Thu Sep 18 19:46:23 EDT 2014 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/case018_tp2/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.wm.mgh --regheader case018_tp2 --cortex srcvol = /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/case018_tp2/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/case018_tp2/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 = 100496 Masking with /usr/local/freesurfer/subjects/case018_tp2/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.wm.mgh Dim: 126095 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.gm.mgh --projfrac 0.3 --regheader case018_tp2 --cortex srcvol = /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/case018_tp2/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/case018_tp2/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 113975 Masking with /usr/local/freesurfer/subjects/case018_tp2/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.gm.mgh Dim: 126095 1 1 mri_concat /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.wm.mgh /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23381/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/case018_tp2/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/case018_tp2/surf/lh.w-g.pct.mgh --annot case018_tp2 lh aparc --sum /usr/local/freesurfer/subjects/case018_tp2/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --in /usr/local/freesurfer/subjects/case018_tp2/surf/lh.w-g.pct.mgh --annot case018_tp2 lh aparc --sum /usr/local/freesurfer/subjects/case018_tp2/stats/lh.w-g.pct.stats --snr sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /usr/local/freesurfer/subjects/case018_tp2/surf/lh.w-g.pct.mgh Vertex Area is 0.656093 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 8114 5555.167 1 1001 bankssts 1610 1121.662 2 1002 caudalanteriorcingulate 1001 633.706 3 1003 caudalmiddlefrontal 3004 1955.473 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2389 1526.884 6 1006 entorhinal 505 348.560 7 1007 fusiform 4542 3065.808 8 1008 inferiorparietal 6008 4014.830 9 1009 inferiortemporal 4488 3028.500 10 1010 isthmuscingulate 1367 859.298 11 1011 lateraloccipital 7599 4591.529 12 1012 lateralorbitofrontal 3251 2201.946 13 1013 lingual 4683 2990.707 14 1014 medialorbitofrontal 2326 1624.587 15 1015 middletemporal 3993 2750.995 16 1016 parahippocampal 1026 670.271 17 1017 paracentral 1983 1251.362 18 1018 parsopercularis 1671 1130.545 19 1019 parsorbitalis 934 626.949 20 1020 parstriangularis 1558 1049.990 21 1021 pericalcarine 2202 1379.704 22 1022 postcentral 5506 3442.439 23 1023 posteriorcingulate 1718 1171.391 24 1024 precentral 7471 4509.831 25 1025 precuneus 4644 3083.720 26 1026 rostralanteriorcingulate 1337 868.896 27 1027 rostralmiddlefrontal 8827 5947.566 28 1028 superiorfrontal 9134 6000.449 29 1029 superiorparietal 7490 4848.759 30 1030 superiortemporal 4792 3206.599 31 1031 supramarginal 6507 4317.992 32 1032 frontalpole 357 237.404 33 1033 temporalpole 696 506.000 34 1034 transversetemporal 639 407.701 35 1035 insula 2723 1802.718 Reporting on 35 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Sep 18 19:46:35 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab case018_tp2 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1274 874 2078 2.445 0.377 0.116 0.029 10 1.6 bankssts 1187 756 2268 2.789 0.730 0.150 0.053 22 2.6 caudalanteriorcingulate 2671 1768 4915 2.563 0.508 0.130 0.039 31 4.5 caudalmiddlefrontal 2524 1507 2948 1.762 0.428 0.154 0.065 41 6.7 cuneus 690 444 2114 3.215 0.878 0.165 0.078 13 2.4 entorhinal 5040 3331 10425 2.657 0.655 0.160 0.070 103 14.8 fusiform 8483 5504 15897 2.535 0.601 0.135 0.049 130 16.3 inferiorparietal 5174 3407 11635 2.803 0.742 0.157 0.082 153 16.9 inferiortemporal 1185 714 1947 2.483 0.686 0.161 0.082 26 3.6 isthmuscingulate 6884 4134 10503 2.293 0.604 0.148 0.064 125 18.4 lateraloccipital 3003 2001 7004 2.972 0.789 0.169 0.088 94 10.4 lateralorbitofrontal 4704 2899 6047 1.907 0.567 0.155 0.080 93 16.4 lingual 2290 1637 4682 2.542 0.742 0.168 0.070 61 7.0 medialorbitofrontal 4544 3052 10637 2.852 0.718 0.133 0.052 66 9.8 middletemporal 1069 682 2002 2.568 0.730 0.125 0.054 13 2.2 parahippocampal 2422 1456 3689 2.377 0.476 0.137 0.095 154 10.4 paracentral 1758 1171 3461 2.661 0.481 0.125 0.047 22 3.0 parsopercularis 1079 728 2700 2.865 0.752 0.148 0.051 19 2.3 parsorbitalis 1498 1053 3476 2.683 0.712 0.128 0.036 16 2.3 parstriangularis 2643 1628 2603 1.692 0.480 0.157 0.129 67 13.9 pericalcarine 5489 3411 7922 2.018 0.603 0.133 0.053 82 11.7 postcentral 1577 1059 2800 2.461 0.544 0.158 0.054 29 3.5 posteriorcingulate 7104 4200 12382 2.648 0.583 0.120 0.054 89 16.2 precentral 4800 3163 8354 2.427 0.512 0.145 0.055 74 11.0 precuneus 797 533 1689 2.769 0.847 0.137 0.051 14 1.7 rostralanteriorcingulate 9842 6626 20061 2.500 0.601 0.156 0.066 223 24.6 rostralmiddlefrontal 9513 6284 20166 2.692 0.649 0.143 0.066 174 23.6 superiorfrontal 7362 4785 11677 2.149 0.525 0.134 0.050 97 14.9 superiorparietal 4357 2797 9396 2.739 0.649 0.119 0.050 82 8.4 superiortemporal 5223 3481 10331 2.580 0.593 0.139 0.046 73 10.1 supramarginal 383 272 1098 2.732 0.669 0.214 0.077 15 1.1 frontalpole 717 476 2399 3.527 0.937 0.211 0.171 35 5.4 temporalpole 485 287 836 2.695 0.505 0.121 0.041 4 0.8 transversetemporal 3169 2066 6206 2.939 0.886 0.140 0.085 70 10.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Sep 18 19:47:01 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 46 labels changed using aseg relabeling using gibbs priors... 000: 9338 changed, 129121 examined... 001: 2181 changed, 35573 examined... 002: 720 changed, 11345 examined... 003: 292 changed, 3964 examined... 004: 155 changed, 1718 examined... 005: 67 changed, 853 examined... 006: 30 changed, 392 examined... 007: 25 changed, 176 examined... 008: 7 changed, 120 examined... 009: 5 changed, 36 examined... 010: 5 changed, 28 examined... 011: 2 changed, 29 examined... 012: 2 changed, 8 examined... 013: 1 changed, 9 examined... 014: 1 changed, 7 examined... 015: 2 changed, 6 examined... 016: 2 changed, 13 examined... 017: 0 changed, 9 examined... 33 labels changed using aseg 000: 268 total segments, 187 labels (2105 vertices) changed 001: 95 total segments, 15 labels (31 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 823 vertices marked for relabeling... 823 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 4 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Sep 18 19:48:05 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab case018_tp2 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1177 815 2519 2.396 0.663 0.188 0.120 43 4.5 G_and_S_frontomargin 1690 1090 2936 2.484 0.599 0.146 0.062 25 4.1 G_and_S_occipital_inf 1535 849 2176 2.166 0.474 0.139 0.067 31 4.2 G_and_S_paracentral 1221 800 2445 2.622 0.536 0.147 0.058 18 2.9 G_and_S_subcentral 1248 847 2625 2.435 0.586 0.167 0.065 35 2.9 G_and_S_transv_frontopol 2797 1879 5341 2.638 0.699 0.144 0.064 51 7.2 G_and_S_cingul-Ant 1485 988 2809 2.658 0.562 0.132 0.044 20 2.9 G_and_S_cingul-Mid-Ant 1408 954 2548 2.533 0.461 0.141 0.046 17 2.7 G_and_S_cingul-Mid-Post 361 235 847 2.823 0.489 0.190 0.080 10 1.1 G_cingul-Post-dorsal 288 185 666 2.750 0.644 0.194 0.137 10 1.3 G_cingul-Post-ventral 2455 1457 2820 1.712 0.427 0.162 0.134 51 12.3 G_cuneus 1155 730 2968 2.997 0.515 0.136 0.050 19 2.2 G_front_inf-Opercular 227 157 681 2.939 0.552 0.144 0.039 4 0.4 G_front_inf-Orbital 620 436 2114 3.251 0.565 0.162 0.072 13 1.4 G_front_inf-Triangul 3975 2649 10109 2.820 0.517 0.167 0.070 97 10.9 G_front_middle 5893 3760 14642 2.908 0.639 0.157 0.099 257 22.4 G_front_sup 343 218 699 3.132 0.743 0.121 0.104 4 1.1 G_Ins_lg_and_S_cent_ins 613 358 1724 3.444 0.749 0.165 0.107 22 2.5 G_insular_short 2276 1399 4926 2.656 0.550 0.149 0.058 45 5.6 G_occipital_middle 1554 955 2443 2.087 0.499 0.135 0.057 23 3.0 G_occipital_sup 2431 1538 5473 2.818 0.586 0.173 0.078 59 8.0 G_oc-temp_lat-fusifor 2662 1616 3720 1.891 0.605 0.162 0.094 64 11.0 G_oc-temp_med-Lingual 1743 1122 4384 3.007 0.840 0.176 0.112 50 8.0 G_oc-temp_med-Parahip 2488 1695 7296 3.178 0.770 0.184 0.100 104 10.5 G_orbital 3465 2172 8760 2.991 0.587 0.160 0.071 85 9.3 G_pariet_inf-Angular 2605 1727 5710 2.729 0.511 0.147 0.062 78 5.7 G_pariet_inf-Supramar 2099 1324 4161 2.451 0.565 0.147 0.057 35 5.4 G_parietal_sup 2129 1213 3192 2.065 0.498 0.141 0.069 44 5.7 G_postcentral 2873 1507 5883 2.943 0.456 0.118 0.062 44 7.5 G_precentral 2076 1350 4598 2.617 0.539 0.174 0.079 50 6.8 G_precuneus 373 322 945 2.330 0.611 0.284 0.118 26 1.9 G_rectus 304 205 445 2.022 1.037 0.084 0.030 2 0.3 G_subcallosal 333 212 677 2.769 0.483 0.129 0.042 3 0.6 G_temp_sup-G_T_transv 1410 869 3909 3.002 0.610 0.142 0.068 25 4.0 G_temp_sup-Lateral 763 509 1950 3.357 0.797 0.089 0.026 3 0.9 G_temp_sup-Plan_polar 601 403 1158 2.590 0.487 0.109 0.032 4 0.8 G_temp_sup-Plan_tempo 2895 1899 7585 2.931 0.798 0.184 0.112 131 13.3 G_temporal_inf 2356 1590 7118 3.242 0.665 0.163 0.072 53 7.3 G_temporal_middle 329 230 531 2.308 0.547 0.103 0.020 2 0.3 Lat_Fis-ant-Horizont 97 72 167 2.571 0.517 0.130 0.036 1 0.1 Lat_Fis-ant-Vertical 1521 1003 2139 2.466 0.578 0.119 0.035 12 2.3 Lat_Fis-post 3895 2184 4533 1.947 0.592 0.158 0.078 100 13.7 Pole_occipital 1945 1265 6105 3.272 0.804 0.193 0.128 70 10.4 Pole_temporal 2663 1723 2980 1.890 0.582 0.146 0.062 40 7.0 S_calcarine 2845 1835 3244 2.000 0.634 0.119 0.048 28 6.1 S_central 1227 835 1754 2.213 0.401 0.111 0.032 8 1.7 S_cingul-Marginalis 509 318 835 2.764 0.653 0.125 0.057 6 1.3 S_circular_insula_ant 958 611 1551 2.926 0.815 0.090 0.033 6 1.2 S_circular_insula_inf 1059 717 1572 2.553 0.381 0.110 0.030 6 1.3 S_circular_insula_sup 963 656 1655 2.492 0.581 0.119 0.040 8 1.7 S_collat_transv_ant 480 295 642 2.271 0.335 0.154 0.060 6 1.2 S_collat_transv_post 1875 1287 2797 2.342 0.491 0.131 0.040 19 3.1 S_front_inf 2914 1932 4470 2.275 0.489 0.123 0.034 32 4.2 S_front_middle 2698 1845 4881 2.458 0.539 0.138 0.046 34 5.4 S_front_sup 213 143 305 2.078 0.279 0.110 0.032 2 0.3 S_interm_prim-Jensen 3237 2181 4158 1.974 0.415 0.125 0.040 32 5.2 S_intrapariet_and_P_trans 415 285 609 2.398 0.372 0.137 0.040 4 0.7 S_oc_middle_and_Lunatus 1760 1143 2176 2.039 0.367 0.112 0.031 13 2.2 S_oc_sup_and_transversal 572 366 985 2.535 0.392 0.139 0.049 7 1.1 S_occipital_ant 1135 736 1566 2.333 0.505 0.130 0.048 13 1.9 S_oc-temp_lat 1818 1250 2538 2.157 0.431 0.123 0.038 15 2.9 S_oc-temp_med_and_Lingual 420 283 540 2.181 0.332 0.128 0.038 4 0.6 S_orbital_lateral 637 455 1042 2.054 0.792 0.133 0.061 14 1.2 S_orbital_med-olfact 1237 822 2234 2.702 0.737 0.140 0.050 17 2.5 S_orbital-H_Shaped 1939 1256 2494 2.223 0.424 0.124 0.039 16 3.3 S_parieto_occipital 1500 897 1574 2.230 0.725 0.150 0.056 27 3.3 S_pericallosal 2303 1548 3230 2.032 0.489 0.127 0.038 23 3.8 S_postcentral 1655 1127 2585 2.393 0.424 0.115 0.034 14 2.5 S_precentral-inf-part 916 613 1332 2.319 0.457 0.114 0.038 7 1.3 S_precentral-sup-part 333 226 675 2.909 0.410 0.158 0.045 6 0.6 S_suborbital 946 628 1527 2.294 0.583 0.147 0.049 13 2.0 S_subparietal 1666 1131 2513 2.376 0.448 0.106 0.030 11 2.2 S_temporal_inf 6113 4093 9056 2.334 0.411 0.109 0.028 43 7.5 S_temporal_sup 220 163 352 2.284 0.352 0.142 0.049 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Sep 18 19:48:31 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 case018_tp2 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1147 labels changed using aseg relabeling using gibbs priors... 000: 2597 changed, 129121 examined... 001: 628 changed, 11132 examined... 002: 168 changed, 3440 examined... 003: 65 changed, 978 examined... 004: 32 changed, 379 examined... 005: 9 changed, 191 examined... 006: 10 changed, 49 examined... 007: 10 changed, 62 examined... 008: 4 changed, 45 examined... 009: 4 changed, 26 examined... 010: 1 changed, 18 examined... 011: 2 changed, 7 examined... 012: 5 changed, 14 examined... 013: 4 changed, 20 examined... 014: 2 changed, 21 examined... 015: 1 changed, 12 examined... 016: 0 changed, 7 examined... 216 labels changed using aseg 000: 53 total segments, 20 labels (178 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 611 vertices marked for relabeling... 611 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 55 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Sep 18 19:49:26 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab case018_tp2 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /usr/local/freesurfer/subjects/case018_tp2/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1323 842 2512 2.767 0.721 0.151 0.057 26 3.1 caudalanteriorcingulate 2773 1827 4999 2.544 0.507 0.130 0.042 33 4.8 caudalmiddlefrontal 3026 1830 3623 1.807 0.426 0.150 0.061 47 7.6 cuneus 695 453 2116 3.228 0.917 0.166 0.079 14 2.4 entorhinal 4374 2897 9070 2.670 0.658 0.157 0.066 81 12.1 fusiform 8059 5216 15035 2.534 0.604 0.138 0.051 127 16.0 inferiorparietal 5849 3842 13096 2.785 0.731 0.159 0.084 175 20.0 inferiortemporal 1160 698 1917 2.487 0.683 0.161 0.083 25 3.5 isthmuscingulate 7058 4248 10670 2.280 0.605 0.147 0.063 126 18.5 lateraloccipital 3811 2570 8752 2.820 0.838 0.174 0.099 124 13.4 lateralorbitofrontal 4722 2913 6091 1.909 0.564 0.155 0.080 93 16.5 lingual 1699 1257 3560 2.521 0.820 0.178 0.071 54 5.3 medialorbitofrontal 5588 3746 12516 2.801 0.681 0.130 0.048 76 11.3 middletemporal 1054 670 1974 2.558 0.722 0.124 0.053 13 2.2 parahippocampal 2508 1497 3878 2.392 0.493 0.136 0.094 155 10.6 paracentral 1715 1145 3373 2.671 0.477 0.125 0.041 21 2.9 parsopercularis 1032 696 2398 2.669 0.717 0.136 0.039 13 1.8 parsorbitalis 1676 1172 3784 2.693 0.684 0.138 0.049 22 3.0 parstriangularis 2639 1624 2610 1.700 0.489 0.157 0.131 67 14.1 pericalcarine 5859 3666 8522 2.026 0.600 0.133 0.052 86 12.4 postcentral 1743 1160 3096 2.477 0.543 0.156 0.053 31 3.8 posteriorcingulate 6880 4076 12113 2.651 0.586 0.120 0.054 87 15.9 precentral 4929 3261 8633 2.414 0.537 0.148 0.058 79 12.1 precuneus 872 583 1885 2.835 0.772 0.139 0.054 15 2.0 rostralanteriorcingulate 6186 4163 13078 2.606 0.619 0.154 0.060 126 15.1 rostralmiddlefrontal 13236 8780 27361 2.601 0.653 0.146 0.065 263 32.2 superiorfrontal 6271 4080 10173 2.170 0.531 0.132 0.048 82 12.1 superiorparietal 6189 4008 13580 2.789 0.726 0.135 0.071 145 18.1 superiortemporal 4995 3335 9806 2.582 0.586 0.137 0.045 67 9.4 supramarginal 449 267 786 2.715 0.496 0.124 0.042 4 0.8 transversetemporal 2570 1667 5342 3.077 0.787 0.124 0.066 40 6.4 insula #----------------------------------------- #@# WM/GM Contrast rh Thu Sep 18 19:49:50 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/scripts pctsurfcon --s case018_tp2 --rh-only Log file is /usr/local/freesurfer/subjects/case018_tp2/scripts/pctsurfcon.log Thu Sep 18 19:49:50 EDT 2014 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/case018_tp2/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.wm.mgh --regheader case018_tp2 --cortex srcvol = /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/case018_tp2/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 102623 Masking with /usr/local/freesurfer/subjects/case018_tp2/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.wm.mgh Dim: 129121 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.gm.mgh --projfrac 0.3 --regheader case018_tp2 --cortex srcvol = /usr/local/freesurfer/subjects/case018_tp2/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/case018_tp2/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/case018_tp2/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/case018_tp2/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 116615 Masking with /usr/local/freesurfer/subjects/case018_tp2/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.gm.mgh Dim: 129121 1 1 mri_concat /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.wm.mgh /usr/local/freesurfer/subjects/case018_tp2/surf/tmp.pctsurfcon.23547/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/case018_tp2/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /usr/local/freesurfer/subjects/case018_tp2/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/case018_tp2/surf/rh.w-g.pct.mgh --annot case018_tp2 rh aparc --sum /usr/local/freesurfer/subjects/case018_tp2/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --in /usr/local/freesurfer/subjects/case018_tp2/surf/rh.w-g.pct.mgh --annot case018_tp2 rh aparc --sum /usr/local/freesurfer/subjects/case018_tp2/stats/rh.w-g.pct.stats --snr sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /usr/local/freesurfer/subjects/case018_tp2/surf/rh.w-g.pct.mgh Vertex Area is 0.646236 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 8181 5255.596 1 2001 bankssts 1274 874.208 2 2002 caudalanteriorcingulate 1187 756.331 3 2003 caudalmiddlefrontal 2671 1768.100 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2524 1507.076 6 2006 entorhinal 690 444.119 7 2007 fusiform 5040 3331.276 8 2008 inferiorparietal 8483 5504.389 9 2009 inferiortemporal 5174 3406.562 10 2010 isthmuscingulate 1185 714.102 11 2011 lateraloccipital 6884 4133.590 12 2012 lateralorbitofrontal 3003 2000.600 13 2013 lingual 4704 2899.381 14 2014 medialorbitofrontal 2290 1637.380 15 2015 middletemporal 4544 3051.842 16 2016 parahippocampal 1069 681.519 17 2017 paracentral 2422 1455.519 18 2018 parsopercularis 1758 1171.059 19 2019 parsorbitalis 1079 727.971 20 2020 parstriangularis 1498 1053.413 21 2021 pericalcarine 2643 1628.308 22 2022 postcentral 5489 3410.614 23 2023 posteriorcingulate 1577 1059.130 24 2024 precentral 7104 4199.880 25 2025 precuneus 4800 3163.035 26 2026 rostralanteriorcingulate 797 533.118 27 2027 rostralmiddlefrontal 9842 6626.501 28 2028 superiorfrontal 9513 6284.267 29 2029 superiorparietal 7362 4785.414 30 2030 superiortemporal 4357 2797.449 31 2031 supramarginal 5223 3481.024 32 2032 frontalpole 383 272.427 33 2033 temporalpole 717 475.878 34 2034 transversetemporal 485 287.127 35 2035 insula 3169 2065.511 Reporting on 35 segmentations mri_segstats done Cleaning up #-------------------------------------------- #@# Cortical ribbon mask Thu Sep 18 19:50:02 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon case018_tp2 SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 34 writing volume /usr/local/freesurfer/subjects/case018_tp2/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Sep 18 20:03:14 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject case018_tp2 $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject case018_tp2 sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 atlas_icv (eTIV) = 1517003 mm^3 (det: 1.284181 ) Computing euler number orig.nofix lheno = -94, rheno = -72 orig.nofix lhholes = 48, rhholes = 37 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 226635.378 226652.000 diff= -16.6 pctdiff=-0.007 rhCtxGM: 225475.491 225472.000 diff= 3.5 pctdiff= 0.002 lhCtxWM: 221431.625 221445.500 diff= -13.9 pctdiff=-0.006 rhCtxWM: 221252.166 221653.500 diff= -401.3 pctdiff=-0.181 SubCortGMVol 57277.000 SupraTentVol 969496.660 (968798.000) diff=698.660 pctdiff=0.072 SupraTentVolNotVent 953222.660 (952524.000) diff=698.660 pctdiff=0.073 BrainSegVol 1103897.000 (1100516.000) diff=3381.000 pctdiff=0.306 BrainSegVolNotVent 1082523.000 (1081833.660) diff=689.340 pctdiff=0.064 BrainSegVolNotVent 1082523.000 CerebellumVol 129738.000 VentChorVol 16274.000 3rd4th5thCSF 5100.000 CSFVol 1745.000, OptChiasmVol 235.000 MaskVol 1599767.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 5810 5810.380 4 5 Left-Inf-Lat-Vent 266 265.722 5 7 Left-Cerebellum-White-Matter 13150 13150.320 6 8 Left-Cerebellum-Cortex 49066 49066.152 7 10 Left-Thalamus-Proper 7897 7896.711 8 11 Left-Caudate 4280 4279.624 9 12 Left-Putamen 5463 5463.219 10 13 Left-Pallidum 1584 1583.794 11 14 3rd-Ventricle 1050 1050.415 12 15 4th-Ventricle 2472 2471.688 13 16 Brain-Stem 19438 19438.357 14 17 Left-Hippocampus 3894 3894.174 15 18 Left-Amygdala 1541 1540.725 16 24 CSF 1678 1678.198 17 26 Left-Accumbens-area 510 509.636 18 28 Left-VentralDC 3525 3524.991 19 30 Left-vessel 19 18.614 20 31 Left-choroid-plexus 1385 1385.164 23 43 Right-Lateral-Ventricle 7684 7683.817 24 44 Right-Inf-Lat-Vent 246 246.451 25 46 Right-Cerebellum-White-Matter 15192 15191.952 26 47 Right-Cerebellum-Cortex 53048 53048.395 27 49 Right-Thalamus-Proper 6983 6982.895 28 50 Right-Caudate 3904 3904.193 29 51 Right-Putamen 4587 4586.802 30 52 Right-Pallidum 1723 1723.486 31 53 Right-Hippocampus 4001 4000.740 32 54 Right-Amygdala 1562 1562.182 33 58 Right-Accumbens-area 617 616.881 34 60 Right-VentralDC 3686 3686.483 35 62 Right-vessel 29 28.810 36 63 Right-choroid-plexus 1328 1328.460 37 72 5th-Ventricle 22 22.117 38 77 WM-hypointensities 1026 1026.009 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 21 20.685 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 234 234.206 45 251 CC_Posterior 998 997.882 46 252 CC_Mid_Posterior 405 405.080 47 253 CC_Central 464 464.087 48 254 CC_Mid_Anterior 490 490.452 49 255 CC_Anterior 997 996.919 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Thu Sep 18 20:06:55 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2 mri_aparc2aseg --s case018_tp2 --volmask SUBJECTS_DIR /usr/local/freesurfer/subjects subject case018_tp2 outvol /usr/local/freesurfer/subjects/case018_tp2/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/case018_tp2/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 450179 Used brute-force search on 0 voxels Writing output aseg to /usr/local/freesurfer/subjects/case018_tp2/mri/aparc+aseg.mgz /usr/local/freesurfer/subjects/case018_tp2 mri_aparc2aseg --s case018_tp2 --volmask --a2009s SUBJECTS_DIR /usr/local/freesurfer/subjects subject case018_tp2 outvol /usr/local/freesurfer/subjects/case018_tp2/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/case018_tp2/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 450179 Used brute-force search on 0 voxels Writing output aseg to /usr/local/freesurfer/subjects/case018_tp2/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Sep 18 20:11:18 EDT 2014 /usr/local/freesurfer/subjects/case018_tp2 mri_aparc2aseg --s case018_tp2 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /usr/local/freesurfer/subjects subject case018_tp2 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /usr/local/freesurfer/subjects/case018_tp2/mri/aparc+aseg.mgz Reading lh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/case018_tp2/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/case018_tp2/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/case018_tp2/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/case018_tp2/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8114 vertices from left hemi Ripped 8181 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/case018_tp2/mri/aseg.mgz Loading Ctx Seg File /usr/local/freesurfer/subjects/case018_tp2/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 891681 Used brute-force search on 259 voxels Fixing Parahip LH WM Found 15 clusters 0 k 1.000000 1 k 1457.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 3.000000 7 k 2.000000 8 k 1.000000 9 k 2.000000 10 k 51.000000 11 k 1.000000 12 k 1.000000 13 k 1.000000 14 k 1.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1663.000000 1 k 1.000000 2 k 2.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 42.000000 7 k 1.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /usr/local/freesurfer/subjects/case018_tp2 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject case018_tp2 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject case018_tp2 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname ubuntu machine x86_64 user mahmoud UseRobust 0 atlas_icv (eTIV) = 1517003 mm^3 (det: 1.284181 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 226635.378 226652.000 diff= -16.6 pctdiff=-0.007 rhCtxGM: 225475.491 225472.000 diff= 3.5 pctdiff= 0.002 lhCtxWM: 221431.625 221445.500 diff= -13.9 pctdiff=-0.006 rhCtxWM: 221252.166 221653.500 diff= -401.3 pctdiff=-0.181 SubCortGMVol 57277.000 SupraTentVol 969496.660 (968798.000) diff=698.660 pctdiff=0.072 SupraTentVolNotVent 953222.660 (952524.000) diff=698.660 pctdiff=0.073 BrainSegVol 1103897.000 (1100516.000) diff=3381.000 pctdiff=0.306 BrainSegVolNotVent 1082523.000 (1081833.660) diff=689.340 pctdiff=0.064 BrainSegVolNotVent 1082523.000 CerebellumVol 129738.000 VentChorVol 16274.000 3rd4th5thCSF 5100.000 CSFVol 1745.000, OptChiasmVol 235.000 MaskVol 1599767.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 3499 3499.090 2 3002 wm-lh-caudalanteriorcingulate 3087 3087.428 3 3003 wm-lh-caudalmiddlefrontal 5549 5549.435 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2778 2777.884 6 3006 wm-lh-entorhinal 683 682.636 7 3007 wm-lh-fusiform 7204 7203.704 8 3008 wm-lh-inferiorparietal 8684 8683.582 9 3009 wm-lh-inferiortemporal 5447 5446.789 10 3010 wm-lh-isthmuscingulate 3205 3204.569 11 3011 wm-lh-lateraloccipital 9636 9636.354 12 3012 wm-lh-lateralorbitofrontal 6296 6296.249 13 3013 wm-lh-lingual 5685 5684.612 14 3014 wm-lh-medialorbitofrontal 3176 3175.867 15 3015 wm-lh-middletemporal 4951 4951.039 16 3016 wm-lh-parahippocampal 1571 1571.044 17 3017 wm-lh-paracentral 3570 3569.580 18 3018 wm-lh-parsopercularis 2665 2664.821 19 3019 wm-lh-parsorbitalis 996 995.957 20 3020 wm-lh-parstriangularis 2397 2397.393 21 3021 wm-lh-pericalcarine 3583 3582.928 22 3022 wm-lh-postcentral 6138 6137.604 23 3023 wm-lh-posteriorcingulate 4405 4405.156 24 3024 wm-lh-precentral 12160 12160.498 25 3025 wm-lh-precuneus 8580 8580.197 26 3026 wm-lh-rostralanteriorcingulate 2642 2642.396 27 3027 wm-lh-rostralmiddlefrontal 14586 14585.542 28 3028 wm-lh-superiorfrontal 15033 15032.953 29 3029 wm-lh-superiorparietal 11904 11904.457 30 3030 wm-lh-superiortemporal 6686 6686.487 31 3031 wm-lh-supramarginal 9528 9528.309 32 3032 wm-lh-frontalpole 268 268.218 33 3033 wm-lh-temporalpole 754 754.493 34 3034 wm-lh-transversetemporal 768 768.017 35 3035 wm-lh-insula 7193 7193.250 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 3001 3000.981 120 4002 wm-rh-caudalanteriorcingulate 3203 3203.359 121 4003 wm-rh-caudalmiddlefrontal 5521 5521.045 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2634 2633.892 124 4006 wm-rh-entorhinal 950 950.024 125 4007 wm-rh-fusiform 6936 6936.078 126 4008 wm-rh-inferiorparietal 12680 12680.454 127 4009 wm-rh-inferiortemporal 5921 5920.716 128 4010 wm-rh-isthmuscingulate 2919 2918.839 129 4011 wm-rh-lateraloccipital 8489 8489.499 130 4012 wm-rh-lateralorbitofrontal 5705 5705.474 131 4013 wm-rh-lingual 5477 5476.661 132 4014 wm-rh-medialorbitofrontal 3135 3134.786 133 4015 wm-rh-middletemporal 6093 6092.567 134 4016 wm-rh-parahippocampal 1738 1737.641 135 4017 wm-rh-paracentral 4766 4766.265 136 4018 wm-rh-parsopercularis 3020 3020.017 137 4019 wm-rh-parsorbitalis 1101 1100.905 138 4020 wm-rh-parstriangularis 2600 2599.558 139 4021 wm-rh-pericalcarine 3720 3720.001 140 4022 wm-rh-postcentral 6536 6536.125 141 4023 wm-rh-posteriorcingulate 4211 4211.358 142 4024 wm-rh-precentral 11792 11792.188 143 4025 wm-rh-precuneus 8275 8274.547 144 4026 wm-rh-rostralanteriorcingulate 2196 2196.046 145 4027 wm-rh-rostralmiddlefrontal 15278 15278.484 146 4028 wm-rh-superiorfrontal 15871 15870.527 147 4029 wm-rh-superiorparietal 10478 10478.235 148 4030 wm-rh-superiortemporal 4924 4923.795 149 4031 wm-rh-supramarginal 8157 8156.858 150 4032 wm-rh-frontalpole 277 276.994 151 4033 wm-rh-temporalpole 684 684.370 152 4034 wm-rh-transversetemporal 531 531.177 153 4035 wm-rh-insula 8089 8088.661 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 37740 37740.188 237 5002 Right-UnsegmentedWhiteMatter 36393 36392.715 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /usr/local/freesurfer/subjects/case018_tp2/label #-------------------------------------------- #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /usr/local/freesurfer/subjects; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case018_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting