Fri Nov 6 09:39:16 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02 /usr/local/freesurfer/stable5_3_0/bin/recon-all -i /cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE/926000-000004-000001.dcm -subject PBR_CON_010_02 -all subjid PBR_CON_010_02 setenv SUBJECTS_DIR /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux pyrrha 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 515818 total used free shared buffers cached Mem: 132080476 43122028 88958448 19776 146660 41036228 -/+ buffers/cache: 1939140 130141336 Swap: 131073860 0 131073860 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:16-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 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: 2015/11/06-14:39:17-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 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: 2015/11/06-14:39:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:19-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:19-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:19-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:20-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:20-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:20-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:21-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:21-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 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: 2015/11/06-14:39:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 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: 2015/11/06-14:39:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/06-14:39:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: zurcher Machine: pyrrha Platform: Linux PlatformVersion: 2.6.32-573.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02 mri_convert /autofs/cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE/926000-000004-000001.dcm /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig/001.mgz mri_convert /autofs/cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE/926000-000004-000001.dcm /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE/926000-000004-000001.dcm... Getting Series No INFO: Found 212 files in /autofs/cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE INFO: Scanning for Series Number 4 Scanning Directory INFO: found 208 files in series INFO: loading series header info. RunNo = 3 INFO: sorting. INFO: (280 280 208), 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 /autofs/cluster/hookerlab/Users/Nicole/Autism/PET/PBR_CON_010_02/MR/MPRAGE/926000-000004-000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName PBR_CON_010_02 Date and time StudyDate 20140807 StudyTime 151513.125000 SeriesTime 152531.926000 AcqTime 151852.925000 Acquisition parameters PulseSeq tfl3d4_ns Protocol MEMPRAGE_4e_1mm_iso_LFOV PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.63 InversionTime 1200 RepetitionTime 2530 PhEncFOV 280 ReadoutFOV 280 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 280 NImageCols 280 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 114.1478 159.0503 130.1881 VolRes 1.0000 1.0000 1.0000 VolDim 280 280 208 Vc -0.0000 -1.0000 0.0000 Vr -0.0541 -0.0000 -0.9985 Vs -0.9985 -0.0000 0.0541 VolCenter 2.7289 19.0503 -3.9828 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2530.00, TE=1.63, TI=1200.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0.0540789, -0, -0.998537) k_ras = (-0.998537, -0, 0.0540788) writing to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Nov 6 09:40:45 EST 2015 Found 1 runs /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig/001.mgz /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/rawavg.mgz /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02 mri_convert /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/rawavg.mgz /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig.mgz --conform mri_convert /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/rawavg.mgz /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/rawavg.mgz... TR=2530.00, TE=1.63, TI=1200.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0.0540789, -0, -0.998537) k_ras = (-0.998537, -0, 0.0540788) Original Data has (1, 1, 1) mm size and (280, 280, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/talairach.xfm /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig.mgz /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 6 09:41:01 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 6 09:43:15 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5265, pval=0.2115 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable5_3_0/bin/extract_talairach_avi_QA.awk /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/talairach_avi.log TalAviQA: 0.97809 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 6 09:43:16 EST 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri /usr/local/freesurfer/stable5_3_0/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 pyrrha 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 6 09:43:16 EST 2015 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.16288 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16288/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16288/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=2530.00, TE=1.63, TI=1200.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (7.82311e-08, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.16288/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 6 09:43:19 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.16288/nu0.mnc ./tmp.mri_nu_correct.mni.16288/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16288/0/ [zurcher@pyrrha:/autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/] [2015-11-06 09:43:19] running: /usr/local/freesurfer/stable5_3_0/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.16288/0/ ./tmp.mri_nu_correct.mni.16288/nu0.mnc ./tmp.mri_nu_correct.mni.16288/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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[zurcher@pyrrha:/autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/] [2015-11-06 09:44:04] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16288/nu0.mnc ./tmp.mri_nu_correct.mni.16288/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Nov 6 09:44:09 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.16288/nu1.mnc ./tmp.mri_nu_correct.mni.16288/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.16288/1/ [zurcher@pyrrha:/autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/] [2015-11-06 09:44:09] running: /usr/local/freesurfer/stable5_3_0/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.16288/1/ ./tmp.mri_nu_correct.mni.16288/nu1.mnc ./tmp.mri_nu_correct.mni.16288/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.000977619 [zurcher@pyrrha:/autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/] [2015-11-06 09:44:59] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16288/nu1.mnc ./tmp.mri_nu_correct.mni.16288/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.16288/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16288/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.16288/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16288/ones.mgz sysname Linux hostname pyrrha machine x86_64 user zurcher input ./tmp.mri_nu_correct.mni.16288/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.16288/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.16288/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16288/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16288/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16288/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16288/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16288/input.mean.dat sysname Linux hostname pyrrha machine x86_64 user zurcher UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16288/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.16288/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16288/ones.mgz --i ./tmp.mri_nu_correct.mni.16288/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16288/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16288/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16288/ones.mgz --i ./tmp.mri_nu_correct.mni.16288/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16288/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16288/output.mean.dat sysname Linux hostname pyrrha machine x86_64 user zurcher UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16288/ones.mgz Loading ./tmp.mri_nu_correct.mni.16288/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.16288/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.16288/nu2.mnc ./tmp.mri_nu_correct.mni.16288/nu2.mnc mul .86919042352017697220 Saving result to './tmp.mri_nu_correct.mni.16288/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.16288/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.16288/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.16288/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (7.82311e-08, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (24, 144) to ( 3, 110) Fri Nov 6 09:45:45 EST 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Nov 6 09:45:46 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.007 0.030 -0.056 1.099; 0.008 0.881 0.406 -5.793; 0.030 -0.385 1.020 10.320; 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 = 18 Starting OpenSpline(): npoints = 18 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 72 (72), valley at 59 (59) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 74 (74), valley at 59 (59) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 11 seconds. #-------------------------------------------- #@# Skull Stripping Fri Nov 6 09:47:59 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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=31.9 skull bounding box = (51, 46, 0) --> (216, 255, 224) using (106, 116, 112) as brain centroid... mean wm in atlas = 126, using box (86,90,84) --> (126, 141,139) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 initial log_p = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.342466 @ (-9.091, -27.273, 9.091) max log p = -4.288688 @ (4.545, 13.636, -4.545) max log p = -4.288116 @ (-2.273, -2.273, 2.273) max log p = -4.261283 @ (1.136, 3.409, 1.136) max log p = -4.250820 @ (-0.568, -0.568, -0.568) max log p = -4.250820 @ (0.000, 0.000, 0.000) Found translation: (-6.3, -13.1, 7.4): log p = -4.251 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.3 (thresh=-4.2) 1.000 0.000 0.000 -6.250; 0.000 0.987 0.390 -49.819; 0.000 -0.402 0.919 69.281; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.000 0.000 0.000 -6.250; 0.000 1.062 0.419 -62.638; 0.000 -0.402 0.919 69.281; 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.979 -0.068 -0.027 8.295; 0.064 1.039 0.410 -65.269; 0.000 -0.402 0.919 71.156; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.979 -0.068 -0.027 8.295; 0.064 1.039 0.410 -65.269; 0.000 -0.402 0.919 71.156; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.978 -0.060 -0.024 6.478; 0.056 1.041 0.402 -64.737; 0.000 -0.394 0.925 69.948; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.978 -0.060 -0.024 6.478; 0.056 1.041 0.402 -64.737; 0.000 -0.394 0.925 69.948; 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 0.97848 -0.05969 -0.02356 6.47828; 0.05618 1.04131 0.40170 -64.73661; 0.00033 -0.39422 0.92547 69.94838; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.97848 -0.05969 -0.02356 6.47828; 0.05618 1.04131 0.40170 -64.73661; 0.00033 -0.39422 0.92547 69.94838; 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: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.978 -0.060 -0.024 6.478; 0.056 1.041 0.402 -64.737; 0.000 -0.394 0.925 69.948; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.6) transform before final EM align: 0.978 -0.060 -0.024 6.478; 0.056 1.041 0.402 -64.737; 0.000 -0.394 0.925 69.948; 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 0.97848 -0.05969 -0.02356 6.47828; 0.05618 1.04131 0.40170 -64.73661; 0.00033 -0.39422 0.92547 69.94838; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.97848 -0.05969 -0.02356 6.47828; 0.05618 1.04131 0.40170 -64.73661; 0.00033 -0.39422 0.92547 69.94838; 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: 010: -log(p) = 4.4 tol 0.000000 final transform: 0.978 -0.060 -0.024 6.478; 0.056 1.041 0.402 -64.737; 0.000 -0.394 0.925 69.948; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 23 minutes and 2 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/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=134 y=121 z=99 r=90 first estimation of the main basin volume: 3148820 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=152, y=120, z=56, Imax=255 CSF=15, 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=22760796495 voxels, voxel volume =1.000 = 22760796495 mmm3 = 22760796.160 cm3 done. PostAnalyze...Basin Prior 87 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=131,y=131, z=92, r=10260 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44724 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=39 , nb = -1028618836 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1051782991 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1098332561 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1070531086 OTHER CSF_MIN=2, CSF_intensity=20, CSF_MAX=38 , nb = 1083024218 Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 8, 53, 72 after analyzing : 4, 38, 53, 46 RIGHT_CER before analyzing : 39, 72, 83, 94 after analyzing : 39, 79, 83, 82 LEFT_CER before analyzing : 5, 10, 53, 76 after analyzing : 5, 38, 53, 47 RIGHT_BRAIN before analyzing : 4, 8, 52, 72 after analyzing : 4, 37, 52, 45 LEFT_BRAIN before analyzing : 4, 8, 53, 71 after analyzing : 4, 38, 53, 46 OTHER before analyzing : 38, 4, 0, 2 after analyzing : 4, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 73.444, std = 7.228 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.57, sigma = 5.93 after rotation: sse = 3.57, sigma = 5.93 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.13, its var is 6.61 before Erosion-Dilatation 2.18% of inacurate vertices after Erosion-Dilatation 1.50% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1903362 voxels, voxel volume = 1.000 mm3 = 1903362 mmm3 = 1903.362 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Nov 6 10:11:24 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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=21.0 skull bounding box = (62, 67, 17) --> (201, 210, 183) using (108, 115, 100) as brain centroid... mean wm in atlas = 107, using box (91,97,80) --> (125, 132,120) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.967489 @ (-9.091, -9.091, 9.091) max log p = -3.853374 @ (4.545, -4.545, -4.545) max log p = -3.832726 @ (-2.273, -2.273, 2.273) max log p = -3.813982 @ (-1.136, 3.409, -1.136) max log p = -3.777381 @ (0.568, -1.705, 1.705) max log p = -3.777381 @ (0.000, 0.000, 0.000) Found translation: (-7.4, -14.2, 7.4): log p = -3.777 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.8 (thresh=-3.8) 1.000 0.000 0.000 -7.386; 0.000 1.111 0.298 -58.101; 0.000 -0.239 0.893 49.676; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.000 0.000 0.000 -7.386; 0.000 1.028 0.275 -44.829; 0.000 -0.257 0.960 45.503; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.000 0.000 0.000 -7.386; 0.000 1.028 0.275 -44.829; 0.000 -0.257 0.960 45.503; 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 0.981 -0.034 -0.011 0.651; 0.033 1.065 0.357 -58.477; 0.000 -0.324 0.940 60.087; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.981 -0.034 -0.011 0.651; 0.033 1.065 0.357 -58.477; 0.000 -0.324 0.940 60.087; 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=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 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 0.98174 -0.02832 -0.02666 2.19797; 0.03322 1.06159 0.35533 -58.79045; 0.01603 -0.32414 0.93902 58.08398; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.98174 -0.02832 -0.02666 2.19797; 0.03322 1.06159 0.35533 -58.79045; 0.01603 -0.32414 0.93902 58.08398; 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: 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.4) transform before final EM align: 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 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 0.98174 -0.02832 -0.02666 2.19797; 0.03322 1.06159 0.35533 -58.79045; 0.01603 -0.32414 0.93902 58.08398; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.98174 -0.02832 -0.02666 2.19797; 0.03322 1.06159 0.35533 -58.79045; 0.01603 -0.32414 0.93902 58.08398; 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: 011: -log(p) = 3.8 tol 0.000000 final transform: 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 0 seconds. #-------------------------------------- #@# CA Normalize Fri Nov 6 10:32:25 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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=21.0 skull bounding box = (62, 67, 17) --> (201, 210, 183) using (108, 115, 100) as brain centroid... mean wm in atlas = 107, using box (91,97,80) --> (125, 132,120) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 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 (129, 72, 19) --> (200, 182, 181) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 236.0 0 of 294 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 72, 19) --> (134, 175, 183) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 236.0 0 of 339 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 155, 50) --> (184, 195, 102) Left_Cerebellum_White_Matter: limiting intensities to 107.0 --> 236.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 155, 48) --> (133, 195, 105) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 236.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 142, 83) --> (150, 205, 113) Brain_Stem: limiting intensities to 88.0 --> 236.0 0 of 12 (0.0%) samples deleted using 662 total control points for intensity normalization... bias field = 0.992 +- 0.061 0 of 662 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 72, 19) --> (200, 182, 181) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 203.0 0 of 347 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 72, 19) --> (134, 175, 183) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 203.0 1 of 401 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 155, 50) --> (184, 195, 102) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 203.0 6 of 55 (10.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 155, 48) --> (133, 195, 105) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 203.0 0 of 63 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 142, 83) --> (150, 205, 113) Brain_Stem: limiting intensities to 87.0 --> 203.0 25 of 80 (31.2%) samples deleted using 946 total control points for intensity normalization... bias field = 1.002 +- 0.053 0 of 914 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 72, 19) --> (200, 182, 181) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 187.0 0 of 456 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 72, 19) --> (134, 175, 183) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 187.0 1 of 433 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 155, 50) --> (184, 195, 102) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 187.0 0 of 84 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 155, 48) --> (133, 195, 105) Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 187.0 0 of 65 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 142, 83) --> (150, 205, 113) Brain_Stem: limiting intensities to 70.0 --> 187.0 0 of 194 (0.0%) samples deleted using 1232 total control points for intensity normalization... bias field = 1.011 +- 0.041 1 of 1231 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 36 seconds. #-------------------------------------- #@# CA Reg Fri Nov 6 10:34:02 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.09 (predicted orig area = 7.3) 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=0.794, neg=0, invalid=96777 0001: dt=129.472000, rms=0.749 (5.729%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.727 (2.839%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.710 (2.329%), neg=0, invalid=96777 0004: dt=73.984000, rms=0.708 (0.343%), neg=0, invalid=96777 0005: dt=1183.744000, rms=0.687 (2.936%), neg=0, invalid=96777 0006: dt=73.984000, rms=0.686 (0.196%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.684 (0.270%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.682 (0.340%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.680 (0.266%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.679 (0.170%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.678 (0.132%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.677 (0.149%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.676 (0.153%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.675 (0.175%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.673 (0.237%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.671 (0.338%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.668 (0.338%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.667 (0.273%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.665 (0.203%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.664 (0.148%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.664 (0.112%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.663 (0.113%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.662 (0.076%), neg=0, invalid=96777 0024: dt=517.888000, rms=0.661 (0.133%), neg=0, invalid=96777 0025: dt=221.952000, rms=0.661 (0.029%), neg=0, invalid=96777 0026: dt=221.952000, rms=0.661 (0.005%), neg=0, invalid=96777 0027: dt=221.952000, rms=0.661 (0.092%), neg=0, invalid=96777 0028: dt=221.952000, rms=0.660 (0.071%), neg=0, invalid=96777 0029: dt=221.952000, rms=0.660 (0.054%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.660, neg=0, invalid=96777 0030: dt=369.920000, rms=0.657 (0.456%), neg=0, invalid=96777 0031: dt=55.488000, rms=0.656 (0.053%), neg=0, invalid=96777 0032: dt=55.488000, rms=0.656 (0.011%), neg=0, invalid=96777 0033: dt=55.488000, rms=0.656 (0.011%), neg=0, invalid=96777 0034: dt=55.488000, rms=0.656 (0.017%), neg=0, invalid=96777 0035: dt=55.488000, rms=0.656 (0.053%), neg=0, invalid=96777 0036: dt=55.488000, rms=0.655 (0.092%), neg=0, invalid=96777 0037: dt=55.488000, rms=0.655 (0.094%), neg=0, invalid=96777 0038: dt=55.488000, rms=0.654 (0.077%), neg=0, invalid=96777 0039: dt=0.000000, rms=0.654 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.659, neg=0, invalid=96777 0040: dt=82.944000, rms=0.655 (0.585%), neg=0, invalid=96777 0041: dt=145.152000, rms=0.646 (1.357%), neg=0, invalid=96777 0042: dt=36.288000, rms=0.643 (0.545%), neg=0, invalid=96777 0043: dt=36.288000, rms=0.641 (0.217%), neg=0, invalid=96777 0044: dt=36.288000, rms=0.639 (0.376%), neg=0, invalid=96777 0045: dt=36.288000, rms=0.636 (0.510%), neg=0, invalid=96777 0046: dt=36.288000, rms=0.632 (0.594%), neg=0, invalid=96777 0047: dt=36.288000, rms=0.628 (0.655%), neg=0, invalid=96777 0048: dt=36.288000, rms=0.623 (0.757%), neg=0, invalid=96777 0049: dt=36.288000, rms=0.619 (0.655%), neg=0, invalid=96777 0050: dt=36.288000, rms=0.616 (0.530%), neg=0, invalid=96777 0051: dt=36.288000, rms=0.613 (0.433%), neg=0, invalid=96777 0052: dt=36.288000, rms=0.610 (0.410%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.608 (0.443%), neg=0, invalid=96777 0054: dt=36.288000, rms=0.605 (0.379%), neg=0, invalid=96777 0055: dt=36.288000, rms=0.604 (0.320%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.602 (0.264%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.600 (0.253%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.599 (0.201%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.598 (0.146%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.598 (0.122%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.597 (0.127%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.596 (0.178%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.595 (0.154%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.594 (0.123%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.593 (0.133%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.592 (0.172%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.591 (0.141%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.591 (0.071%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.591 (0.039%), neg=0, invalid=96777 0070: dt=103.680000, rms=0.590 (0.113%), neg=0, invalid=96777 0071: dt=5.184000, rms=0.590 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=96777 0072: dt=36.288000, rms=0.589 (0.121%), neg=0, invalid=96777 0073: dt=82.944000, rms=0.588 (0.275%), neg=0, invalid=96777 0074: dt=9.072000, rms=0.588 (0.023%), neg=0, invalid=96777 0075: dt=9.072000, rms=0.588 (0.016%), neg=0, invalid=96777 0076: dt=9.072000, rms=0.588 (0.005%), neg=0, invalid=96777 0077: dt=9.072000, rms=0.588 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0078: dt=3.600000, rms=0.615 (0.050%), neg=0, invalid=96777 0079: dt=2.400000, rms=0.615 (0.011%), neg=0, invalid=96777 0080: dt=2.400000, rms=0.615 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0081: dt=2.400000, rms=0.615 (0.010%), neg=0, invalid=96777 0082: dt=0.700000, rms=0.615 (0.000%), neg=0, invalid=96777 0083: dt=0.700000, 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=0.687, neg=0, invalid=96777 0084: dt=5.336761, rms=0.666 (3.097%), neg=0, invalid=96777 0085: dt=3.617647, rms=0.664 (0.238%), neg=0, invalid=96777 0086: dt=3.617647, rms=0.664 (-0.052%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=96777 0087: dt=0.000000, rms=0.664 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0088: dt=0.972906, rms=0.723 (0.415%), neg=0, invalid=96777 0089: dt=2.241379, rms=0.717 (0.784%), neg=0, invalid=96777 0090: dt=0.533333, rms=0.716 (0.069%), neg=0, invalid=96777 0091: dt=0.533333, rms=0.716 (0.070%), neg=0, invalid=96777 0092: dt=0.533333, rms=0.715 (0.095%), neg=0, invalid=96777 0093: dt=0.533333, rms=0.715 (0.072%), neg=0, invalid=96777 0094: dt=0.533333, rms=0.715 (0.000%), neg=0, invalid=96777 0095: dt=1.536000, rms=0.715 (0.029%), neg=0, invalid=96777 0096: dt=0.448000, rms=0.715 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.715, neg=0, invalid=96777 0097: dt=1.280000, rms=0.714 (0.106%), neg=0, invalid=96777 0098: dt=0.000000, rms=0.714 (0.000%), neg=0, invalid=96777 0099: dt=0.100000, rms=0.714 (-0.002%), 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=0.681, neg=0, invalid=96777 0100: dt=0.448000, rms=0.665 (2.383%), neg=0, invalid=96777 0101: dt=0.000000, rms=0.665 (0.005%), neg=0, invalid=96777 0102: dt=0.050000, rms=0.665 (-0.361%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=96777 0103: dt=0.000000, rms=0.665 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11429 (22) Left_Lateral_Ventricle (4): linear fit = 0.83 x + 0.0 (1683 voxels, overlap=0.434) Left_Lateral_Ventricle (4): linear fit = 0.83 x + 0.0 (1683 voxels, peak = 20), gca=20.0 gca peak = 0.14022 (22) mri peak = 0.10315 (20) Right_Lateral_Ventricle (43): linear fit = 0.85 x + 0.0 (800 voxels, overlap=0.587) Right_Lateral_Ventricle (43): linear fit = 0.85 x + 0.0 (800 voxels, peak = 19), gca=18.6 gca peak = 0.24234 (100) mri peak = 0.06641 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (529 voxels, overlap=0.767) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (529 voxels, peak = 100), gca=100.5 gca peak = 0.19192 (97) mri peak = 0.06452 (105) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (432 voxels, overlap=0.865) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (432 voxels, peak = 105), gca=105.2 gca peak = 0.24007 (63) mri peak = 0.05300 (69) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (788 voxels, overlap=0.713) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (788 voxels, peak = 68), gca=68.4 gca peak = 0.29892 (64) mri peak = 0.08651 (78) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (783 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (783 voxels, peak = 76), gca=76.5 gca peak = 0.12541 (104) mri peak = 0.07558 (109) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (89085 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (89085 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.08541 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (91416 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (91416 voxels, peak = 110), gca=109.7 gca peak = 0.11691 (63) mri peak = 0.05156 (72) Left_Cerebral_Cortex (3): linear fit = 1.11 x + 0.0 (29077 voxels, overlap=0.621) Left_Cerebral_Cortex (3): linear fit = 1.11 x + 0.0 (29077 voxels, peak = 70), gca=69.6 gca peak = 0.13270 (63) mri peak = 0.04761 (72) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (31538 voxels, overlap=0.361) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (31538 voxels, peak = 72), gca=71.5 gca peak = 0.15182 (70) mri peak = 0.08923 (88) Right_Caudate (50): linear fit = 1.18 x + 0.0 (400 voxels, overlap=0.043) Right_Caudate (50): linear fit = 1.18 x + 0.0 (400 voxels, peak = 83), gca=82.9 gca peak = 0.14251 (76) mri peak = 0.13793 (93) Left_Caudate (11): linear fit = 1.18 x + 0.0 (734 voxels, overlap=0.014) Left_Caudate (11): linear fit = 1.18 x + 0.0 (734 voxels, peak = 90), gca=90.1 gca peak = 0.12116 (60) mri peak = 0.03470 (68) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (20345 voxels, overlap=0.380) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (20345 voxels, peak = 71), gca=71.1 gca peak = 0.12723 (61) mri peak = 0.03690 (72) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (23602 voxels, overlap=0.395) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (23602 voxels, peak = 76), gca=75.9 gca peak = 0.22684 (88) mri peak = 0.07945 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9968 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9968 voxels, peak = 93), gca=92.8 gca peak = 0.21067 (87) mri peak = 0.09398 (84) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (9841 voxels, overlap=0.975) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (9841 voxels, peak = 86), gca=85.7 gca peak = 0.25455 (62) mri peak = 0.11009 (81) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (368 voxels, overlap=0.059) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (368 voxels, peak = 82), gca=81.5 gca peak = 0.39668 (62) mri peak = 0.09678 (70) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (368 voxels, overlap=0.400) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (368 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.05718 (101) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6211 voxels, overlap=0.340) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6211 voxels, peak = 105), gca=104.6 gca peak = 0.12071 (89) mri peak = 0.07259 (93) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4426 voxels, overlap=0.782) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (4426 voxels, peak = 92), gca=92.1 gca peak = 0.13716 (82) mri peak = 0.05815 (98) Left_Putamen (12): linear fit = 1.20 x + 0.0 (2640 voxels, overlap=0.019) Left_Putamen (12): linear fit = 1.20 x + 0.0 (2640 voxels, peak = 98), gca=98.0 gca peak = 0.15214 (84) mri peak = 0.06988 (93) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2847 voxels, overlap=0.555) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2847 voxels, peak = 92), gca=92.0 gca peak = 0.08983 (85) mri peak = 0.07290 (88) Brain_Stem (16): linear fit = 1.03 x + 0.0 (14043 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.03 x + 0.0 (14043 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.06913 (91) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (992 voxels, overlap=0.796) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (992 voxels, peak = 91), gca=90.6 gca peak = 0.12914 (94) mri peak = 0.07889 (101) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1097 voxels, overlap=0.677) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1097 voxels, peak = 100), gca=100.1 gca peak = 0.21100 (36) mri peak = 1.00000 (41) Third_Ventricle (14): linear fit = 1.11 x + 0.0 (142 voxels, overlap=2.064) Third_Ventricle (14): linear fit = 1.11 x + 0.0 (142 voxels, peak = 40), gca=39.8 gca peak = 0.13542 (27) mri peak = 0.11834 (18) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (422 voxels, overlap=0.130) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (422 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Fourth_Ventricle = 0.13542 (27) 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 1.16 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.93 x + 0.0 Left_Putamen too bright - rescaling by 1.003 (from 1.195) to 98.3 (was 98.0) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.675, neg=0, invalid=96777 0104: dt=129.472000, rms=0.660 (2.186%), neg=0, invalid=96777 0105: dt=295.936000, rms=0.653 (1.051%), neg=0, invalid=96777 0106: dt=129.472000, rms=0.650 (0.587%), neg=0, invalid=96777 0107: dt=73.984000, rms=0.649 (0.162%), neg=0, invalid=96777 0108: dt=517.888000, rms=0.643 (0.853%), neg=0, invalid=96777 0109: dt=55.488000, rms=0.642 (0.095%), neg=0, invalid=96777 0110: dt=517.888000, rms=0.641 (0.249%), neg=0, invalid=96777 0111: dt=110.976000, rms=0.639 (0.322%), neg=0, invalid=96777 0112: dt=92.480000, rms=0.638 (0.052%), neg=0, invalid=96777 0113: dt=517.888000, rms=0.636 (0.351%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.636 (0.066%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.636 (0.024%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.635 (0.017%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.635 (0.016%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.635 (0.027%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.635 (0.054%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.634 (0.082%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.634 (0.093%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.633 (0.089%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.633 (0.093%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.632 (0.095%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.631 (0.094%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.631 (0.095%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.630 (0.092%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.630 (0.095%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.629 (0.097%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.628 (0.097%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.628 (0.092%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.627 (0.090%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.627 (0.083%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.626 (0.078%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.626 (0.071%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.625 (0.071%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.625 (0.069%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.624 (0.067%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.624 (0.064%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.624 (0.063%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.623 (0.065%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.623 (0.062%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.622 (0.061%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.622 (0.057%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.622 (0.057%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.621 (0.054%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.621 (0.052%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.621 (0.046%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.621 (0.047%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.620 (0.043%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.620 (0.044%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.620 (0.050%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.619 (0.047%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.619 (0.050%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.619 (0.045%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.619 (0.047%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.618 (0.047%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.618 (0.045%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.618 (0.044%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.617 (0.044%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.617 (0.044%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.617 (0.042%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.617 (0.040%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.616 (0.036%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.616 (0.036%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.616 (0.031%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.616 (0.030%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.616 (0.031%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.615 (0.032%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.615 (0.033%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.615 (0.037%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.615 (0.035%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.615 (0.038%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.614 (0.038%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.614 (0.036%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.614 (0.034%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.614 (0.033%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.613 (0.033%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.613 (0.034%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.613 (0.033%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.613 (0.035%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.613 (0.032%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.612 (0.031%), neg=0, invalid=96777 0184: dt=32.368000, rms=0.612 (0.030%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.612 (0.027%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.612 (0.025%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.612 (0.024%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.612 (0.024%), neg=0, invalid=96777 0189: dt=517.888000, rms=0.612 (0.020%), neg=0, invalid=96777 0190: dt=517.888000, rms=0.612 (-0.541%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.612, neg=0, invalid=96777 0191: dt=129.472000, rms=0.610 (0.193%), neg=0, invalid=96777 0192: dt=129.472000, rms=0.610 (0.106%), neg=0, invalid=96777 0193: dt=129.472000, rms=0.609 (0.077%), neg=0, invalid=96777 0194: dt=110.976000, rms=0.609 (0.035%), neg=0, invalid=96777 0195: dt=110.976000, rms=0.609 (0.046%), neg=0, invalid=96777 0196: dt=110.976000, rms=0.608 (0.051%), neg=0, invalid=96777 0197: dt=110.976000, rms=0.608 (0.064%), neg=0, invalid=96777 0198: dt=110.976000, rms=0.608 (0.062%), neg=0, invalid=96777 0199: dt=110.976000, rms=0.607 (0.073%), neg=0, invalid=96777 0200: dt=110.976000, rms=0.607 (0.069%), neg=0, invalid=96777 0201: dt=110.976000, rms=0.607 (0.049%), neg=0, invalid=96777 0202: dt=110.976000, rms=0.606 (0.052%), neg=0, invalid=96777 0203: dt=110.976000, rms=0.606 (0.047%), neg=0, invalid=96777 0204: dt=110.976000, rms=0.606 (0.051%), neg=0, invalid=96777 0205: dt=110.976000, rms=0.605 (0.049%), neg=0, invalid=96777 0206: dt=110.976000, rms=0.605 (0.050%), neg=0, invalid=96777 0207: dt=110.976000, rms=0.605 (0.053%), neg=0, invalid=96777 0208: dt=110.976000, rms=0.604 (0.056%), neg=0, invalid=96777 0209: dt=110.976000, rms=0.604 (0.066%), neg=0, invalid=96777 0210: dt=110.976000, rms=0.604 (0.056%), neg=0, invalid=96777 0211: dt=110.976000, rms=0.603 (0.041%), neg=0, invalid=96777 0212: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=96777 0213: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=96777 0214: dt=110.976000, rms=0.603 (0.043%), neg=0, invalid=96777 0215: dt=110.976000, rms=0.602 (0.044%), neg=0, invalid=96777 0216: dt=110.976000, rms=0.602 (0.044%), neg=0, invalid=96777 0217: dt=110.976000, rms=0.602 (0.038%), neg=0, invalid=96777 0218: dt=110.976000, rms=0.602 (0.035%), neg=0, invalid=96777 0219: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=96777 0220: dt=110.976000, rms=0.601 (0.037%), neg=0, invalid=96777 0221: dt=110.976000, rms=0.601 (0.033%), neg=0, invalid=96777 0222: dt=110.976000, rms=0.601 (0.040%), neg=0, invalid=96777 0223: dt=110.976000, rms=0.601 (0.038%), neg=0, invalid=96777 0224: dt=110.976000, rms=0.600 (0.043%), neg=0, invalid=96777 0225: dt=110.976000, rms=0.600 (0.028%), neg=0, invalid=96777 0226: dt=110.976000, rms=0.600 (0.030%), neg=0, invalid=96777 0227: dt=110.976000, rms=0.600 (0.037%), neg=0, invalid=96777 0228: dt=110.976000, rms=0.600 (0.033%), neg=0, invalid=96777 0229: dt=110.976000, rms=0.599 (0.038%), neg=0, invalid=96777 0230: dt=110.976000, rms=0.599 (0.039%), neg=0, invalid=96777 0231: dt=110.976000, rms=0.599 (0.042%), neg=0, invalid=96777 0232: dt=110.976000, rms=0.599 (0.023%), neg=0, invalid=96777 0233: dt=110.976000, rms=0.599 (0.017%), neg=0, invalid=96777 0234: dt=369.920000, rms=0.599 (0.020%), neg=0, invalid=96777 0235: dt=32.368000, rms=0.598 (0.004%), neg=0, invalid=96777 0236: dt=32.368000, rms=0.598 (0.002%), neg=0, invalid=96777 0237: dt=32.368000, rms=0.598 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0238: dt=103.680000, rms=0.597 (0.398%), neg=0, invalid=96777 0239: dt=82.944000, rms=0.594 (0.587%), neg=0, invalid=96777 0240: dt=31.104000, rms=0.592 (0.307%), neg=0, invalid=96777 0241: dt=145.152000, rms=0.589 (0.529%), neg=0, invalid=96777 0242: dt=25.920000, rms=0.587 (0.404%), neg=0, invalid=96777 0243: dt=414.720000, rms=0.581 (1.033%), neg=0, invalid=96777 0244: dt=25.920000, rms=0.577 (0.693%), neg=0, invalid=96777 0245: dt=36.288000, rms=0.576 (0.152%), neg=0, invalid=96777 0246: dt=145.152000, rms=0.574 (0.234%), neg=0, invalid=96777 0247: dt=25.920000, rms=0.573 (0.177%), neg=0, invalid=96777 0248: dt=124.416000, rms=0.572 (0.248%), neg=0, invalid=96777 0249: dt=20.736000, rms=0.571 (0.118%), neg=0, invalid=96777 0250: dt=497.664000, rms=0.568 (0.577%), neg=0, invalid=96777 0251: dt=25.920000, rms=0.565 (0.456%), neg=0, invalid=96777 0252: dt=124.416000, rms=0.564 (0.223%), neg=0, invalid=96777 0253: dt=20.736000, rms=0.564 (0.054%), neg=0, invalid=96777 0254: dt=248.832000, rms=0.562 (0.241%), neg=0, invalid=96777 0255: dt=31.104000, rms=0.562 (0.110%), neg=0, invalid=96777 0256: dt=124.416000, rms=0.561 (0.204%), neg=0, invalid=96777 0257: dt=15.552000, rms=0.560 (0.049%), neg=0, invalid=96777 0258: dt=15.552000, rms=0.560 (0.027%), neg=0, invalid=96777 0259: dt=15.552000, rms=0.560 (0.026%), neg=0, invalid=96777 0260: dt=15.552000, rms=0.560 (0.038%), neg=0, invalid=96777 0261: dt=15.552000, rms=0.560 (0.059%), neg=0, invalid=96777 0262: dt=15.552000, rms=0.559 (0.075%), neg=0, invalid=96777 0263: dt=15.552000, rms=0.559 (0.095%), neg=0, invalid=96777 0264: dt=15.552000, rms=0.558 (0.096%), neg=0, invalid=96777 0265: dt=15.552000, rms=0.557 (0.099%), neg=0, invalid=96777 0266: dt=15.552000, rms=0.557 (0.106%), neg=0, invalid=96777 0267: dt=15.552000, rms=0.556 (0.113%), neg=0, invalid=96777 0268: dt=15.552000, rms=0.556 (0.118%), neg=0, invalid=96777 0269: dt=15.552000, rms=0.555 (0.117%), neg=0, invalid=96777 0270: dt=15.552000, rms=0.554 (0.109%), neg=0, invalid=96777 0271: dt=15.552000, rms=0.554 (0.107%), neg=0, invalid=96777 0272: dt=15.552000, rms=0.553 (0.104%), neg=0, invalid=96777 0273: dt=15.552000, rms=0.553 (0.107%), neg=0, invalid=96777 0274: dt=15.552000, rms=0.552 (0.116%), neg=0, invalid=96777 0275: dt=15.552000, rms=0.551 (0.120%), neg=0, invalid=96777 0276: dt=15.552000, rms=0.551 (0.119%), neg=0, invalid=96777 0277: dt=15.552000, rms=0.550 (0.114%), neg=0, invalid=96777 0278: dt=15.552000, rms=0.549 (0.105%), neg=0, invalid=96777 0279: dt=15.552000, rms=0.549 (0.096%), neg=0, invalid=96777 0280: dt=15.552000, rms=0.548 (0.093%), neg=0, invalid=96777 0281: dt=15.552000, rms=0.548 (0.092%), neg=0, invalid=96777 0282: dt=15.552000, rms=0.547 (0.093%), neg=0, invalid=96777 0283: dt=15.552000, rms=0.547 (0.090%), neg=0, invalid=96777 0284: dt=15.552000, rms=0.546 (0.083%), neg=0, invalid=96777 0285: dt=15.552000, rms=0.546 (0.073%), neg=0, invalid=96777 0286: dt=15.552000, rms=0.546 (0.074%), neg=0, invalid=96777 0287: dt=15.552000, rms=0.545 (0.075%), neg=0, invalid=96777 0288: dt=15.552000, rms=0.545 (0.080%), neg=0, invalid=96777 0289: dt=15.552000, rms=0.544 (0.082%), neg=0, invalid=96777 0290: dt=15.552000, rms=0.544 (0.076%), neg=0, invalid=96777 0291: dt=15.552000, rms=0.544 (0.072%), neg=0, invalid=96777 0292: dt=15.552000, rms=0.543 (0.069%), neg=0, invalid=96777 0293: dt=15.552000, rms=0.543 (0.064%), neg=0, invalid=96777 0294: dt=15.552000, rms=0.542 (0.060%), neg=0, invalid=96777 0295: dt=15.552000, rms=0.542 (0.067%), neg=0, invalid=96777 0296: dt=15.552000, rms=0.542 (0.065%), neg=0, invalid=96777 0297: dt=15.552000, rms=0.541 (0.061%), neg=0, invalid=96777 0298: dt=15.552000, rms=0.541 (0.060%), neg=0, invalid=96777 0299: dt=15.552000, rms=0.541 (0.056%), neg=0, invalid=96777 0300: dt=15.552000, rms=0.541 (0.054%), neg=0, invalid=96777 0301: dt=15.552000, rms=0.540 (0.056%), neg=0, invalid=96777 0302: dt=15.552000, rms=0.540 (0.055%), neg=0, invalid=96777 0303: dt=15.552000, rms=0.540 (0.053%), neg=0, invalid=96777 0304: dt=15.552000, rms=0.539 (0.048%), neg=0, invalid=96777 0305: dt=15.552000, rms=0.539 (0.051%), neg=0, invalid=96777 0306: dt=15.552000, rms=0.539 (0.046%), neg=0, invalid=96777 0307: dt=15.552000, rms=0.539 (0.043%), neg=0, invalid=96777 0308: dt=15.552000, rms=0.538 (0.038%), neg=0, invalid=96777 0309: dt=15.552000, rms=0.538 (0.040%), neg=0, invalid=96777 0310: dt=15.552000, rms=0.538 (0.044%), neg=0, invalid=96777 0311: dt=15.552000, rms=0.538 (0.048%), neg=0, invalid=96777 0312: dt=15.552000, rms=0.537 (0.042%), neg=0, invalid=96777 0313: dt=15.552000, rms=0.537 (0.040%), neg=0, invalid=96777 0314: dt=15.552000, rms=0.537 (0.040%), neg=0, invalid=96777 0315: dt=15.552000, rms=0.537 (0.039%), neg=0, invalid=96777 0316: dt=15.552000, rms=0.537 (0.038%), neg=0, invalid=96777 0317: dt=15.552000, rms=0.536 (0.037%), neg=0, invalid=96777 0318: dt=15.552000, rms=0.536 (0.041%), neg=0, invalid=96777 0319: dt=15.552000, rms=0.536 (0.034%), neg=0, invalid=96777 0320: dt=15.552000, rms=0.536 (0.034%), neg=0, invalid=96777 0321: dt=15.552000, rms=0.536 (0.034%), neg=0, invalid=96777 0322: dt=15.552000, rms=0.536 (0.030%), neg=0, invalid=96777 0323: dt=15.552000, rms=0.535 (0.027%), neg=0, invalid=96777 0324: dt=15.552000, rms=0.535 (0.033%), neg=0, invalid=96777 0325: dt=15.552000, rms=0.535 (0.032%), neg=0, invalid=96777 0326: dt=15.552000, rms=0.535 (0.033%), neg=0, invalid=96777 0327: dt=15.552000, rms=0.535 (0.031%), neg=0, invalid=96777 0328: dt=15.552000, rms=0.535 (0.030%), neg=0, invalid=96777 0329: dt=15.552000, rms=0.534 (0.028%), neg=0, invalid=96777 0330: dt=15.552000, rms=0.534 (0.026%), neg=0, invalid=96777 0331: dt=15.552000, rms=0.534 (0.031%), neg=0, invalid=96777 0332: dt=15.552000, rms=0.534 (0.023%), neg=0, invalid=96777 0333: dt=15.552000, rms=0.534 (0.026%), neg=0, invalid=96777 0334: dt=15.552000, rms=0.534 (0.028%), neg=0, invalid=96777 0335: dt=15.552000, rms=0.533 (0.032%), neg=0, invalid=96777 0336: dt=15.552000, rms=0.533 (0.028%), neg=0, invalid=96777 0337: dt=15.552000, rms=0.533 (0.029%), neg=0, invalid=96777 0338: dt=15.552000, rms=0.533 (0.024%), neg=0, invalid=96777 0339: dt=15.552000, rms=0.533 (0.022%), neg=0, invalid=96777 0340: dt=36.288000, rms=0.533 (0.007%), neg=0, invalid=96777 0341: dt=36.288000, rms=0.533 (0.006%), neg=0, invalid=96777 0342: dt=36.288000, rms=0.533 (0.009%), neg=0, invalid=96777 0343: dt=36.288000, rms=0.533 (0.014%), neg=0, invalid=96777 0344: dt=36.288000, rms=0.533 (0.015%), neg=0, invalid=96777 0345: dt=36.288000, rms=0.533 (0.021%), neg=0, invalid=96777 0346: dt=36.288000, rms=0.532 (0.027%), neg=0, invalid=96777 0347: dt=36.288000, rms=0.532 (0.029%), neg=0, invalid=96777 0348: dt=36.288000, rms=0.532 (0.028%), neg=0, invalid=96777 0349: dt=36.288000, rms=0.532 (0.039%), neg=0, invalid=96777 0350: dt=36.288000, rms=0.532 (0.044%), neg=0, invalid=96777 0351: dt=36.288000, rms=0.531 (0.028%), neg=0, invalid=96777 0352: dt=36.288000, rms=0.531 (0.024%), neg=0, invalid=96777 0353: dt=36.288000, rms=0.531 (0.039%), neg=0, invalid=96777 0354: dt=36.288000, rms=0.531 (0.039%), neg=0, invalid=96777 0355: dt=36.288000, rms=0.531 (0.039%), neg=0, invalid=96777 0356: dt=36.288000, rms=0.531 (0.031%), neg=0, invalid=96777 0357: dt=36.288000, rms=0.530 (0.049%), neg=0, invalid=96777 0358: dt=36.288000, rms=0.530 (0.040%), neg=0, invalid=96777 0359: dt=36.288000, rms=0.530 (0.031%), neg=0, invalid=96777 0360: dt=36.288000, rms=0.530 (0.035%), neg=0, invalid=96777 0361: dt=36.288000, rms=0.530 (0.030%), neg=0, invalid=96777 0362: dt=36.288000, rms=0.529 (0.048%), neg=0, invalid=96777 0363: dt=36.288000, rms=0.529 (0.044%), neg=0, invalid=96777 0364: dt=36.288000, rms=0.529 (0.040%), neg=0, invalid=96777 0365: dt=36.288000, rms=0.529 (0.035%), neg=0, invalid=96777 0366: dt=36.288000, rms=0.529 (0.032%), neg=0, invalid=96777 0367: dt=36.288000, rms=0.528 (0.025%), neg=0, invalid=96777 0368: dt=36.288000, rms=0.528 (0.042%), neg=0, invalid=96777 0369: dt=36.288000, rms=0.528 (0.054%), neg=0, invalid=96777 0370: dt=36.288000, rms=0.528 (0.043%), neg=0, invalid=96777 0371: dt=36.288000, rms=0.527 (0.035%), neg=0, invalid=96777 0372: dt=36.288000, rms=0.527 (0.020%), neg=0, invalid=96777 0373: dt=36.288000, rms=0.527 (0.030%), neg=0, invalid=96777 0374: dt=36.288000, rms=0.527 (0.037%), neg=0, invalid=96777 0375: dt=36.288000, rms=0.527 (0.039%), neg=0, invalid=96777 0376: dt=36.288000, rms=0.527 (0.025%), neg=0, invalid=96777 0377: dt=36.288000, rms=0.527 (0.018%), neg=0, invalid=96777 0378: dt=36.288000, rms=0.526 (0.046%), neg=0, invalid=96777 0379: dt=36.288000, rms=0.526 (0.037%), neg=0, invalid=96777 0380: dt=36.288000, rms=0.526 (0.020%), neg=0, invalid=96777 0381: dt=36.288000, rms=0.526 (0.022%), neg=0, invalid=96777 0382: dt=36.288000, rms=0.526 (0.029%), neg=0, invalid=96777 0383: dt=36.288000, rms=0.526 (0.044%), neg=0, invalid=96777 0384: dt=36.288000, rms=0.525 (0.034%), neg=0, invalid=96777 0385: dt=36.288000, rms=0.525 (0.016%), neg=0, invalid=96777 0386: dt=36.288000, rms=0.525 (0.013%), neg=0, invalid=96777 0387: dt=124.416000, rms=0.525 (0.051%), neg=0, invalid=96777 0388: dt=0.000000, rms=0.525 (-0.003%), neg=0, invalid=96777 0389: dt=0.450000, rms=0.525 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=96777 0390: dt=36.288000, rms=0.524 (0.117%), neg=0, invalid=96777 0391: dt=82.944000, rms=0.523 (0.250%), neg=0, invalid=96777 0392: dt=9.072000, rms=0.523 (0.035%), neg=0, invalid=96777 0393: dt=9.072000, rms=0.523 (0.021%), neg=0, invalid=96777 0394: dt=9.072000, rms=0.523 (-0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=96777 0395: dt=25.600000, rms=0.534 (0.251%), neg=0, invalid=96777 0396: dt=19.200000, rms=0.532 (0.381%), neg=0, invalid=96777 0397: dt=4.954839, rms=0.531 (0.111%), neg=0, invalid=96777 0398: dt=32.000000, rms=0.529 (0.284%), neg=0, invalid=96777 0399: dt=11.250000, rms=0.528 (0.323%), neg=0, invalid=96777 0400: dt=6.400000, rms=0.527 (0.073%), neg=0, invalid=96777 0401: dt=153.600000, rms=0.520 (1.306%), neg=0, invalid=96777 0402: dt=10.016260, rms=0.519 (0.236%), neg=0, invalid=96777 0403: dt=11.200000, rms=0.518 (0.188%), neg=0, invalid=96777 0404: dt=11.200000, rms=0.518 (0.138%), neg=0, invalid=96777 0405: dt=44.800000, rms=0.516 (0.319%), neg=0, invalid=96777 0406: dt=2.400000, rms=0.516 (0.039%), neg=0, invalid=96777 0407: dt=2.400000, rms=0.515 (0.044%), neg=0, invalid=96777 0408: dt=2.400000, rms=0.515 (0.050%), neg=0, invalid=96777 0409: dt=2.400000, rms=0.515 (0.045%), neg=0, invalid=96777 0410: dt=2.400000, rms=0.515 (0.048%), neg=0, invalid=96777 0411: dt=2.400000, rms=0.514 (0.071%), neg=0, invalid=96777 0412: dt=2.400000, rms=0.514 (0.089%), neg=0, invalid=96777 0413: dt=2.400000, rms=0.513 (0.100%), neg=0, invalid=96777 0414: dt=2.400000, rms=0.513 (0.091%), neg=0, invalid=96777 0415: dt=2.400000, rms=0.512 (0.089%), neg=0, invalid=96777 0416: dt=2.400000, rms=0.512 (0.088%), neg=0, invalid=96777 0417: dt=2.400000, rms=0.512 (0.091%), neg=0, invalid=96777 0418: dt=2.400000, rms=0.511 (0.088%), neg=0, invalid=96777 0419: dt=2.400000, rms=0.511 (0.092%), neg=0, invalid=96777 0420: dt=2.400000, rms=0.510 (0.098%), neg=0, invalid=96777 0421: dt=2.400000, rms=0.510 (0.096%), neg=0, invalid=96777 0422: dt=2.400000, rms=0.509 (0.101%), neg=0, invalid=96777 0423: dt=2.400000, rms=0.509 (0.101%), neg=0, invalid=96777 0424: dt=2.400000, rms=0.508 (0.090%), neg=0, invalid=96777 0425: dt=2.400000, rms=0.508 (0.086%), neg=0, invalid=96777 0426: dt=2.400000, rms=0.507 (0.083%), neg=0, invalid=96777 0427: dt=2.400000, rms=0.507 (0.074%), neg=0, invalid=96777 0428: dt=2.400000, rms=0.507 (0.076%), neg=0, invalid=96777 0429: dt=2.400000, rms=0.506 (0.074%), neg=0, invalid=96777 0430: dt=2.400000, rms=0.506 (0.082%), neg=0, invalid=96777 0431: dt=2.400000, rms=0.505 (0.082%), neg=0, invalid=96777 0432: dt=2.400000, rms=0.505 (0.081%), neg=0, invalid=96777 0433: dt=2.400000, rms=0.505 (0.071%), neg=0, invalid=96777 0434: dt=2.400000, rms=0.504 (0.067%), neg=0, invalid=96777 0435: dt=2.400000, rms=0.504 (0.063%), neg=0, invalid=96777 0436: dt=2.400000, rms=0.504 (0.062%), neg=0, invalid=96777 0437: dt=2.400000, rms=0.503 (0.057%), neg=0, invalid=96777 0438: dt=2.400000, rms=0.503 (0.053%), neg=0, invalid=96777 0439: dt=2.400000, rms=0.503 (0.058%), neg=0, invalid=96777 0440: dt=2.400000, rms=0.502 (0.057%), neg=0, invalid=96777 0441: dt=2.400000, rms=0.502 (0.061%), neg=0, invalid=96777 0442: dt=2.400000, rms=0.502 (0.054%), neg=0, invalid=96777 0443: dt=2.400000, rms=0.502 (0.050%), neg=0, invalid=96777 0444: dt=2.400000, rms=0.501 (0.050%), neg=0, invalid=96777 0445: dt=2.400000, rms=0.501 (0.051%), neg=0, invalid=96777 0446: dt=2.400000, rms=0.501 (0.048%), neg=0, invalid=96777 0447: dt=2.400000, rms=0.501 (0.047%), neg=0, invalid=96777 0448: dt=2.400000, rms=0.500 (0.051%), neg=0, invalid=96777 0449: dt=2.400000, rms=0.500 (0.048%), neg=0, invalid=96777 0450: dt=2.400000, rms=0.500 (0.047%), neg=0, invalid=96777 0451: dt=2.400000, rms=0.500 (0.050%), neg=0, invalid=96777 0452: dt=2.400000, rms=0.499 (0.042%), neg=0, invalid=96777 0453: dt=2.400000, rms=0.499 (0.039%), neg=0, invalid=96777 0454: dt=2.400000, rms=0.499 (0.039%), neg=0, invalid=96777 0455: dt=2.400000, rms=0.499 (0.032%), neg=0, invalid=96777 0456: dt=2.400000, rms=0.499 (0.038%), neg=0, invalid=96777 0457: dt=2.400000, rms=0.499 (0.036%), neg=0, invalid=96777 0458: dt=2.400000, rms=0.498 (0.035%), neg=0, invalid=96777 0459: dt=2.400000, rms=0.498 (0.038%), neg=0, invalid=96777 0460: dt=2.400000, rms=0.498 (0.031%), neg=0, invalid=96777 0461: dt=2.400000, rms=0.498 (0.032%), neg=0, invalid=96777 0462: dt=2.400000, rms=0.498 (0.032%), neg=0, invalid=96777 0463: dt=2.400000, rms=0.498 (0.031%), neg=0, invalid=96777 0464: dt=2.400000, rms=0.497 (0.028%), neg=0, invalid=96777 0465: dt=2.400000, rms=0.497 (0.030%), neg=0, invalid=96777 0466: dt=2.400000, rms=0.497 (0.029%), neg=0, invalid=96777 0467: dt=2.400000, rms=0.497 (0.029%), neg=0, invalid=96777 0468: dt=2.400000, rms=0.497 (0.030%), neg=0, invalid=96777 0469: dt=2.400000, rms=0.497 (0.028%), neg=0, invalid=96777 0470: dt=2.400000, rms=0.497 (0.026%), neg=0, invalid=96777 0471: dt=2.400000, rms=0.496 (0.025%), neg=0, invalid=96777 0472: dt=2.400000, rms=0.496 (0.022%), neg=0, invalid=96777 0473: dt=2.400000, rms=0.496 (0.023%), neg=0, invalid=96777 0474: dt=2.400000, rms=0.496 (0.024%), neg=0, invalid=96777 0475: dt=2.400000, rms=0.496 (0.025%), neg=0, invalid=96777 0476: dt=2.400000, rms=0.496 (0.025%), neg=0, invalid=96777 0477: dt=179.200000, rms=0.495 (0.111%), neg=0, invalid=96777 0478: dt=2.800000, rms=0.495 (0.007%), neg=0, invalid=96777 0479: dt=2.800000, rms=0.495 (0.026%), neg=0, invalid=96777 0480: dt=2.800000, rms=0.495 (0.013%), neg=0, invalid=96777 0481: dt=2.800000, rms=0.495 (0.000%), neg=0, invalid=96777 0482: dt=11.200000, rms=0.495 (0.036%), neg=0, invalid=96777 0483: dt=0.031250, rms=0.495 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0484: dt=11.200000, rms=0.494 (0.170%), neg=0, invalid=96777 0485: dt=44.800000, rms=0.493 (0.295%), neg=0, invalid=96777 0486: dt=5.104762, rms=0.492 (0.041%), neg=0, invalid=96777 0487: dt=5.104762, rms=0.492 (0.040%), neg=0, invalid=96777 0488: dt=5.104762, rms=0.492 (0.016%), neg=0, invalid=96777 0489: dt=5.104762, rms=0.492 (0.026%), neg=0, invalid=96777 0490: dt=5.104762, rms=0.492 (0.027%), neg=0, invalid=96777 0491: dt=5.104762, rms=0.492 (0.017%), neg=0, invalid=96777 0492: dt=5.104762, rms=0.492 (0.014%), neg=0, invalid=96777 0493: dt=11.200000, rms=0.492 (0.008%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.492 (0.024%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.491 (0.022%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.491 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=96777 0497: dt=0.000000, rms=0.514 (0.005%), neg=0, invalid=96777 0498: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=96777 0499: dt=0.000000, rms=0.514 (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=0.560, neg=0, invalid=96777 0500: dt=1.725322, rms=0.555 (0.953%), neg=0, invalid=96777 0501: dt=0.450000, rms=0.555 (0.035%), neg=0, invalid=96777 0502: dt=0.450000, rms=0.555 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0503: dt=1.280000, rms=0.554 (0.199%), neg=0, invalid=96777 0504: dt=0.448000, rms=0.554 (0.011%), neg=0, invalid=96777 0505: dt=0.448000, rms=0.554 (-0.011%), 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=0.509, neg=0, invalid=96777 0506: dt=0.448000, rms=0.493 (3.106%), neg=0, invalid=96777 0507: dt=0.448000, rms=0.490 (0.583%), neg=0, invalid=96777 0508: dt=0.448000, rms=0.488 (0.408%), neg=0, invalid=96777 0509: dt=0.448000, rms=0.487 (0.265%), neg=0, invalid=96777 0510: dt=0.448000, rms=0.486 (0.198%), neg=0, invalid=96777 0511: dt=0.448000, rms=0.485 (0.153%), neg=0, invalid=96777 0512: dt=0.448000, rms=0.484 (0.121%), neg=0, invalid=96777 0513: dt=0.448000, rms=0.484 (0.098%), neg=0, invalid=96777 0514: dt=0.448000, rms=0.483 (0.089%), neg=0, invalid=96777 0515: dt=0.863636, rms=0.483 (0.126%), neg=0, invalid=96777 0516: dt=0.112000, rms=0.483 (0.018%), neg=0, invalid=96777 0517: dt=0.112000, rms=0.483 (0.015%), neg=0, invalid=96777 0518: dt=0.112000, rms=0.483 (0.022%), neg=0, invalid=96777 0519: dt=0.112000, rms=0.482 (0.028%), neg=0, invalid=96777 0520: dt=0.112000, rms=0.482 (0.037%), neg=0, invalid=96777 0521: dt=0.112000, rms=0.482 (0.008%), neg=0, invalid=96777 0522: dt=0.112000, rms=0.482 (0.018%), neg=0, invalid=96777 0523: dt=0.112000, rms=0.482 (0.021%), neg=0, invalid=96777 0524: dt=0.112000, rms=0.482 (0.033%), neg=0, invalid=96777 0525: dt=0.112000, rms=0.482 (0.033%), neg=0, invalid=96777 0526: dt=0.112000, rms=0.481 (0.033%), neg=0, invalid=96777 0527: dt=0.112000, rms=0.481 (0.035%), neg=0, invalid=96777 0528: dt=0.112000, rms=0.481 (0.034%), neg=0, invalid=96777 0529: dt=0.112000, rms=0.481 (0.038%), neg=0, invalid=96777 0530: dt=0.112000, rms=0.481 (0.033%), neg=0, invalid=96777 0531: dt=0.112000, rms=0.481 (0.032%), neg=0, invalid=96777 0532: dt=0.112000, rms=0.481 (0.025%), neg=0, invalid=96777 0533: dt=0.112000, rms=0.480 (0.031%), neg=0, invalid=96777 0534: dt=0.112000, rms=0.480 (0.019%), neg=0, invalid=96777 0535: dt=0.112000, rms=0.480 (0.018%), neg=0, invalid=96777 0536: dt=0.112000, rms=0.480 (0.002%), neg=0, invalid=96777 0537: dt=0.112000, rms=0.480 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=96777 0538: dt=0.448000, rms=0.475 (1.025%), neg=0, invalid=96777 0539: dt=0.256000, rms=0.475 (0.006%), neg=0, invalid=96777 0540: dt=0.256000, rms=0.475 (-0.002%), 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=0.473, neg=0, invalid=96777 0541: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=96777 0542: dt=129.472000, rms=0.472 (0.105%), neg=0, invalid=96777 0543: dt=129.472000, rms=0.472 (0.057%), neg=0, invalid=96777 0544: dt=129.472000, rms=0.472 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0545: dt=36.288000, rms=0.472 (0.084%), neg=0, invalid=96777 0546: dt=36.288000, rms=0.471 (0.064%), neg=0, invalid=96777 0547: dt=36.288000, rms=0.471 (0.065%), neg=0, invalid=96777 0548: dt=36.288000, rms=0.471 (0.064%), neg=0, invalid=96777 0549: dt=36.288000, rms=0.471 (0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 0550: dt=103.680000, rms=0.467 (0.709%), neg=0, invalid=96777 0551: dt=25.920000, rms=0.467 (0.108%), neg=0, invalid=96777 0552: dt=25.920000, rms=0.466 (0.075%), neg=0, invalid=96777 0553: dt=25.920000, rms=0.466 (0.069%), neg=0, invalid=96777 0554: dt=25.920000, rms=0.466 (0.077%), neg=0, invalid=96777 0555: dt=25.920000, rms=0.465 (0.073%), neg=0, invalid=96777 0556: dt=36.288000, rms=0.465 (0.099%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.465 (0.030%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0558: dt=38.400000, rms=0.462 (0.702%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0559: dt=32.000000, rms=0.460 (0.407%), neg=0, invalid=96777 0560: dt=8.115523, rms=0.458 (0.377%), neg=0, invalid=96777 0561: dt=9.600000, rms=0.458 (0.133%), neg=0, invalid=96777 0562: dt=9.600000, rms=0.457 (0.146%), neg=0, invalid=96777 0563: dt=9.600000, rms=0.456 (0.180%), neg=0, invalid=96777 0564: dt=9.600000, rms=0.455 (0.227%), neg=0, invalid=96777 0565: dt=9.600000, rms=0.454 (0.237%), neg=0, invalid=96777 0566: dt=9.600000, rms=0.453 (0.296%), neg=0, invalid=96777 0567: dt=9.600000, rms=0.452 (0.261%), neg=0, invalid=96777 0568: dt=9.600000, rms=0.451 (0.215%), neg=0, invalid=96777 0569: dt=9.600000, rms=0.450 (0.191%), neg=0, invalid=96777 0570: dt=9.600000, rms=0.449 (0.202%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0571: dt=9.600000, rms=0.448 (0.153%), neg=0, invalid=96777 0572: dt=9.600000, rms=0.447 (0.149%), neg=0, invalid=96777 0573: dt=9.600000, rms=0.447 (0.106%), neg=0, invalid=96777 0574: dt=9.600000, rms=0.446 (0.175%), neg=0, invalid=96777 0575: dt=9.600000, rms=0.446 (0.150%), neg=0, invalid=96777 0576: dt=9.600000, rms=0.445 (0.128%), neg=0, invalid=96777 0577: dt=9.600000, rms=0.444 (0.115%), neg=0, invalid=96777 0578: dt=9.600000, rms=0.444 (0.141%), neg=0, invalid=96777 0579: dt=9.600000, rms=0.443 (0.104%), neg=0, invalid=96777 0580: dt=9.600000, rms=0.443 (0.071%), neg=0, invalid=96777 0581: dt=11.200000, rms=0.443 (0.007%), neg=0, invalid=96777 0582: dt=11.200000, rms=0.443 (0.024%), neg=0, invalid=96777 0583: dt=11.200000, rms=0.443 (0.019%), neg=0, invalid=96777 0584: dt=11.200000, rms=0.443 (0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 0585: dt=44.800000, rms=0.439 (0.770%), neg=0, invalid=96777 0586: dt=8.000000, rms=0.439 (0.108%), neg=0, invalid=96777 0587: dt=8.000000, rms=0.438 (0.098%), neg=0, invalid=96777 0588: dt=8.000000, rms=0.438 (0.089%), neg=0, invalid=96777 0589: dt=8.000000, rms=0.438 (0.091%), neg=0, invalid=96777 0590: dt=8.000000, rms=0.437 (0.078%), neg=0, invalid=96777 0591: dt=11.200000, rms=0.437 (0.073%), 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 0592: dt=2.880000, rms=0.445 (0.063%), neg=0, invalid=96777 0593: dt=1.728000, rms=0.445 (0.011%), neg=0, invalid=96777 0594: dt=1.728000, rms=0.445 (0.004%), neg=0, invalid=96777 0595: dt=1.728000, rms=0.445 (-0.039%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=96777 0596: dt=5.904762, rms=0.444 (0.182%), neg=0, invalid=96777 0597: dt=4.032000, rms=0.444 (0.067%), neg=0, invalid=96777 0598: dt=4.032000, rms=0.443 (0.045%), neg=0, invalid=96777 0599: dt=4.032000, rms=0.443 (0.025%), neg=0, invalid=96777 0600: dt=4.032000, rms=0.443 (-0.057%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=96777 0601: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=96777 0602: dt=0.000000, rms=0.450 (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=0.439, neg=0, invalid=96777 iter 0, gcam->neg = 456 after 18 iterations, nbhd size=2, neg = 0 0603: dt=2.074223, rms=0.405 (7.756%), neg=0, invalid=96777 0604: dt=0.000438, rms=0.405 (0.001%), neg=0, invalid=96777 0605: dt=0.000438, 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 0606: dt=0.007000, rms=0.405 (0.005%), neg=0, invalid=96777 0607: dt=0.007000, rms=0.405 (0.001%), neg=0, invalid=96777 0608: dt=0.007000, rms=0.405 (-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=0.388, neg=0, invalid=96777 0609: dt=0.000000, rms=0.388 (-0.174%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 0610: dt=73.984000, rms=0.388 (0.014%), neg=0, invalid=96777 0611: dt=129.472000, rms=0.388 (0.005%), neg=0, invalid=96777 0612: dt=129.472000, rms=0.388 (-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=0.388, neg=0, invalid=96777 0613: dt=0.000000, rms=0.388 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 0614: dt=82.944000, rms=0.388 (0.043%), neg=0, invalid=96777 0615: dt=145.152000, rms=0.388 (0.062%), neg=0, invalid=96777 0616: dt=36.288000, rms=0.388 (0.010%), neg=0, invalid=96777 0617: dt=36.288000, rms=0.388 (0.010%), neg=0, invalid=96777 0618: dt=36.288000, rms=0.388 (0.017%), neg=0, invalid=96777 0619: dt=36.288000, rms=0.388 (0.021%), neg=0, invalid=96777 0620: dt=36.288000, rms=0.388 (0.023%), neg=0, invalid=96777 0621: dt=36.288000, rms=0.388 (0.021%), neg=0, invalid=96777 0622: dt=36.288000, rms=0.388 (0.018%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 0623: dt=8.000000, rms=0.388 (0.023%), neg=0, invalid=96777 0624: dt=2.800000, rms=0.388 (0.002%), neg=0, invalid=96777 0625: dt=2.800000, rms=0.388 (0.001%), neg=0, invalid=96777 0626: dt=2.800000, rms=0.388 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 0627: dt=44.800000, rms=0.386 (0.511%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 13 iterations, nbhd size=2, neg = 0 0628: dt=32.000000, rms=0.386 (0.151%), neg=0, invalid=96777 0629: dt=32.000000, rms=0.385 (0.098%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0630: dt=32.000000, rms=0.385 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 37 iterations, nbhd size=4, neg = 0 0631: dt=32.000000, rms=0.385 (-0.026%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0632: dt=1.826087, rms=0.388 (0.058%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 14 iterations, nbhd size=2, neg = 0 0633: dt=6.250000, rms=0.387 (0.175%), neg=0, invalid=96777 0634: dt=4.032000, rms=0.387 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 13 iterations, nbhd size=2, neg = 0 0635: dt=4.032000, rms=0.387 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 28 after 20 iterations, nbhd size=2, neg = 0 0636: dt=4.032000, rms=0.387 (-0.024%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=96777 iter 0, gcam->neg = 42 after 20 iterations, nbhd size=2, neg = 0 0637: dt=12.271845, rms=0.385 (0.491%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0638: dt=1.008000, rms=0.385 (0.009%), neg=0, invalid=96777 0639: dt=1.008000, rms=0.385 (0.023%), neg=0, invalid=96777 0640: dt=1.008000, rms=0.385 (0.039%), neg=0, invalid=96777 0641: dt=1.008000, rms=0.384 (0.048%), neg=0, invalid=96777 0642: dt=1.008000, rms=0.384 (0.049%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0643: dt=1.008000, rms=0.384 (0.046%), neg=0, invalid=96777 0644: dt=1.008000, rms=0.384 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0645: dt=1.008000, rms=0.384 (0.039%), neg=0, invalid=96777 0646: dt=3.456000, rms=0.384 (0.006%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0647: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0648: dt=0.000000, rms=0.390 (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=0.379, neg=0, invalid=96777 iter 0, gcam->neg = 413 after 27 iterations, nbhd size=3, neg = 0 0649: dt=1.091144, rms=0.367 (3.331%), neg=0, invalid=96777 0650: dt=0.000109, rms=0.367 (0.002%), neg=0, invalid=96777 0651: dt=0.000109, rms=0.367 (0.000%), neg=0, invalid=96777 0652: dt=0.000109, rms=0.367 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.367, neg=0, invalid=96777 0653: dt=0.000438, rms=0.367 (0.000%), neg=0, invalid=96777 0654: dt=0.000000, rms=0.367 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 44 minutes and 23 seconds. #-------------------------------------- #@# CA Reg Inv Fri Nov 6 13:18:26 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Nov 6 13:19:16 EST 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable5_3_0/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... 10833816 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 51 seconds. #-------------------------------------- #@# SkullLTA Fri Nov 6 13:20:08 EST 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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=9.0 skull bounding box = (47, 44, 0) --> (215, 238, 212) using (103, 109, 106) as brain centroid... mean wm in atlas = 126, using box (82,85,80) --> (123, 132,132) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 0.982 -0.028 -0.027 2.198; 0.035 1.010 0.475 -63.510; 0.012 -0.460 0.885 81.976; 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.000 -0.042 0.003 -1.254; 0.034 1.018 0.408 -59.863; -0.018 -0.384 0.897 74.615; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.000 -0.042 0.003 -1.254; 0.034 1.018 0.408 -59.863; -0.018 -0.384 0.897 74.615; 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.003 -0.061 -0.021 2.388; 0.058 1.015 0.407 -61.310; -0.002 -0.385 0.897 72.101; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.001 -0.058 -0.029 3.283; 0.058 1.017 0.408 -61.524; 0.007 -0.386 0.898 71.052; 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 1.00143 -0.05757 -0.02870 3.28260; 0.05810 1.01664 0.40773 -61.52415; 0.00664 -0.38624 0.89768 71.05225; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.00143 -0.05757 -0.02870 3.28260; 0.05810 1.01664 0.40773 -61.52415; 0.00664 -0.38624 0.89768 71.05225; 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: 1.001 -0.058 -0.029 3.283; 0.058 1.017 0.408 -61.524; 0.007 -0.386 0.898 71.052; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-3.9) transform before final EM align: 1.001 -0.058 -0.029 3.283; 0.058 1.017 0.408 -61.524; 0.007 -0.386 0.898 71.052; 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 1.00143 -0.05757 -0.02870 3.28260; 0.05810 1.01664 0.40773 -61.52415; 0.00664 -0.38624 0.89768 71.05225; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.00143 -0.05757 -0.02870 3.28260; 0.05810 1.01664 0.40773 -61.52415; 0.00664 -0.38624 0.89768 71.05225; 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: 008: -log(p) = 4.3 tol 0.000000 final transform: 1.001 -0.058 -0.029 3.283; 0.058 1.017 0.408 -61.524; 0.007 -0.386 0.898 71.052; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 19 minutes and 42 seconds. #-------------------------------------- #@# SubCort Seg Fri Nov 6 13:39:51 EST 2015 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname pyrrha machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects cd /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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 = 0.15122 (21) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (609 voxels, overlap=0.484) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (609 voxels, peak = 22), gca=22.0 gca peak = 0.14982 (20) mri peak = 0.13467 (22) Right_Lateral_Ventricle (43): linear fit = 0.89 x + 0.0 (349 voxels, overlap=0.670) Right_Lateral_Ventricle (43): linear fit = 0.89 x + 0.0 (349 voxels, peak = 18), gca=17.9 gca peak = 0.28003 (97) mri peak = 0.10394 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (276 voxels, overlap=1.016) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (276 voxels, peak = 97), gca=97.5 gca peak = 0.18160 (96) mri peak = 0.10195 (113) Left_Pallidum (13): linear fit = 1.16 x + 0.0 (279 voxels, overlap=0.044) Left_Pallidum (13): linear fit = 1.16 x + 0.0 (279 voxels, peak = 112), gca=111.8 gca peak = 0.27536 (62) mri peak = 0.11010 (70) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (881 voxels, overlap=0.832) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (881 voxels, peak = 69), gca=68.5 gca peak = 0.32745 (63) mri peak = 0.10818 (77) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (730 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (730 voxels, peak = 77), gca=76.5 gca peak = 0.08597 (105) mri peak = 0.08701 (109) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (55769 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (55769 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.08945 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (57591 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (57591 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.05169 (72) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (27476 voxels, overlap=0.693) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (27476 voxels, peak = 69), gca=69.0 gca peak = 0.08598 (64) mri peak = 0.04783 (72) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26185 voxels, overlap=0.491) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26185 voxels, peak = 73), gca=72.6 gca peak = 0.24164 (71) mri peak = 0.13567 (89) Right_Caudate (50): linear fit = 1.20 x + 0.0 (457 voxels, overlap=0.022) Right_Caudate (50): linear fit = 1.20 x + 0.0 (457 voxels, peak = 85), gca=84.8 gca peak = 0.18227 (75) mri peak = 0.12037 (91) Left_Caudate (11): linear fit = 1.15 x + 0.0 (544 voxels, overlap=0.095) Left_Caudate (11): linear fit = 1.15 x + 0.0 (544 voxels, peak = 87), gca=86.6 gca peak = 0.10629 (62) mri peak = 0.04442 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (16332 voxels, overlap=0.237) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (16332 voxels, peak = 76), gca=76.0 gca peak = 0.11668 (59) mri peak = 0.04718 (72) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19235 voxels, overlap=0.425) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19235 voxels, peak = 71), gca=70.5 gca peak = 0.17849 (88) mri peak = 0.10708 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5753 voxels, overlap=0.815) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5753 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.11351 (84) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4738 voxels, overlap=0.979) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4738 voxels, peak = 85), gca=84.7 gca peak = 0.41688 (64) mri peak = 0.11200 (81) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (266 voxels, overlap=0.064) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (266 voxels, peak = 82), gca=81.6 gca peak = 0.42394 (62) mri peak = 0.10032 (74) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (308 voxels, overlap=0.059) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (308 voxels, peak = 73), gca=73.5 gca peak = 0.10041 (96) mri peak = 0.07542 (101) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (4601 voxels, overlap=0.538) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (4601 voxels, peak = 105), gca=105.1 gca peak = 0.13978 (88) mri peak = 0.09021 (93) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (5098 voxels, overlap=0.744) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (5098 voxels, peak = 92), gca=92.0 gca peak = 0.08514 (81) mri peak = 0.07975 (96) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1677 voxels, overlap=0.050) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1677 voxels, peak = 94), gca=93.6 gca peak = 0.09624 (82) mri peak = 0.08919 (90) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1821 voxels, overlap=0.436) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1821 voxels, peak = 89), gca=89.0 gca peak = 0.07543 (88) mri peak = 0.07161 (89) Brain_Stem (16): linear fit = 1.03 x + 0.0 (13172 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (13172 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.07451 (97) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1125 voxels, overlap=0.803) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1125 voxels, peak = 96), gca=96.4 gca peak = 0.17004 (92) mri peak = 0.07927 (97) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (987 voxels, overlap=0.699) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (987 voxels, peak = 97), gca=97.1 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.12572 (16) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (254 voxels, overlap=0.070) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (254 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) 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 1.17 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Left_Pallidum too bright - rescaling by 0.952 (from 1.165) to 106.4 (was 111.8) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17513 (22) mri peak = 0.15122 (21) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (609 voxels, overlap=0.913) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (609 voxels, peak = 21), gca=21.5 gca peak = 0.17553 (18) mri peak = 0.13467 (22) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (349 voxels, overlap=0.819) Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (349 voxels, peak = 18), gca=18.3 gca peak = 0.27796 (98) mri peak = 0.10394 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (276 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (276 voxels, peak = 98), gca=98.5 gca peak = 0.16123 (106) mri peak = 0.10195 (113) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (279 voxels, overlap=0.749) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (279 voxels, peak = 111), gca=110.8 gca peak = 0.23416 (68) mri peak = 0.11010 (70) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (881 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (881 voxels, peak = 68), gca=68.0 gca peak = 0.24640 (81) mri peak = 0.10818 (77) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (730 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (730 voxels, peak = 80), gca=79.8 gca peak = 0.08268 (109) mri peak = 0.08701 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55769 voxels, overlap=0.736) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55769 voxels, peak = 110), gca=109.5 gca peak = 0.08583 (111) mri peak = 0.08945 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (57591 voxels, overlap=0.743) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (57591 voxels, peak = 111), gca=111.0 gca peak = 0.07160 (69) mri peak = 0.05169 (72) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27476 voxels, overlap=0.873) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (27476 voxels, peak = 69), gca=69.0 gca peak = 0.07740 (72) mri peak = 0.04783 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (26185 voxels, overlap=0.860) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (26185 voxels, peak = 72), gca=72.0 gca peak = 0.26841 (88) mri peak = 0.13567 (89) Right_Caudate (50): linear fit = 1.01 x + 0.0 (457 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.01 x + 0.0 (457 voxels, peak = 89), gca=89.3 gca peak = 0.14359 (86) mri peak = 0.12037 (91) Left_Caudate (11): linear fit = 1.01 x + 0.0 (544 voxels, overlap=0.942) Left_Caudate (11): linear fit = 1.01 x + 0.0 (544 voxels, peak = 87), gca=87.3 gca peak = 0.08856 (76) mri peak = 0.04442 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (16332 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (16332 voxels, peak = 75), gca=74.9 gca peak = 0.10664 (71) mri peak = 0.04718 (72) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (19235 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (19235 voxels, peak = 73), gca=73.5 gca peak = 0.17033 (92) mri peak = 0.10708 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5753 voxels, overlap=0.984) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5753 voxels, peak = 92), gca=91.5 gca peak = 0.16690 (85) mri peak = 0.11351 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4738 voxels, overlap=0.968) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4738 voxels, peak = 85), gca=85.0 gca peak = 0.30085 (81) mri peak = 0.11200 (81) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (266 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (266 voxels, peak = 82), gca=82.2 gca peak = 0.36002 (74) mri peak = 0.10032 (74) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (308 voxels, overlap=1.017) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (308 voxels, peak = 73), gca=72.9 gca peak = 0.09438 (103) mri peak = 0.07542 (101) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4601 voxels, overlap=0.961) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4601 voxels, peak = 102), gca=102.5 gca peak = 0.13624 (92) mri peak = 0.09021 (93) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5098 voxels, overlap=0.904) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5098 voxels, peak = 92), gca=92.5 gca peak = 0.08673 (95) mri peak = 0.07975 (96) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1677 voxels, overlap=0.830) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1677 voxels, peak = 97), gca=97.4 gca peak = 0.09968 (82) mri peak = 0.08919 (90) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1821 voxels, overlap=0.833) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1821 voxels, peak = 84), gca=84.0 gca peak = 0.07116 (91) mri peak = 0.07161 (89) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13172 voxels, overlap=0.836) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13172 voxels, peak = 90), gca=89.6 gca peak = 0.14835 (96) mri peak = 0.07451 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1125 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1125 voxels, peak = 96), gca=95.5 gca peak = 0.14955 (97) mri peak = 0.07927 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (987 voxels, peak = 97), gca=97.5 gca peak = 0.21697 (31) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.22371 (20) mri peak = 0.12572 (16) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (254 voxels, overlap=0.634) Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (254 voxels, peak = 15), gca=14.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.22716 (43) gca peak Third_Ventricle = 0.21697 (31) gca peak CSF = 0.26436 (33) gca peak Left_Accumbens_area = 0.40973 (81) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09086 (48) gca peak Right_Inf_Lat_Vent = 0.28428 (35) gca peak Right_Accumbens_area = 0.25706 (86) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (36) gca peak WM_hypointensities = 0.17647 (85) gca peak non_WM_hypointensities = 0.12111 (55) gca peak Optic_Chiasm = 0.34771 (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 0.91 x + 0.0 Left_Pallidum too bright - rescaling by 0.966 (from 1.045) to 107.0 (was 110.8) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 26895 gm and wm labels changed (%19 to gray, %81 to white out of all changed labels) 374 hippocampal voxels changed. 8 amygdala voxels changed. pass 1: 80585 changed. image ll: -2.212, PF=1.000 pass 2: 12026 changed. image ll: -2.209, PF=1.000 pass 3: 3709 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 13 minutes and 21 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/cc_up.lta PBR_CON_010_02 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/norm.mgz 46684 voxels in left wm, 33159 in right wm, xrange [128, 137] searching rotation angles z=[-4 10], y=[-8 6] searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.9 global minimum found at slice 131.4, rotations (-0.74, 3.11) final transformation (x=131.4, yr=-0.743, zr=3.108): 0.998 -0.054 -0.013 4.576; 0.054 0.999 -0.001 -0.881; 0.013 -0.000 1.000 36.303; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 142 117 eigenvectors: -0.001 -0.000 1.000; -0.183 -0.983 -0.001; 0.983 -0.183 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Fri Nov 6 13:53:57 EST 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Nov 6 13:53:57 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/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... 2193 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 75 (75), valley at 32 (32) csf peak at 11, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 76 (76), valley at 32 (32) csf peak at 11, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 16 seconds. #-------------------------------------------- #@# Mask BFS Fri Nov 6 13:57:15 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1807710 voxels in mask (pct= 10.77) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Nov 6 13:57:18 EST 2015 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.2 +- 7.2 [80.0 --> 125.0] GM (75.0) : 74.2 +- 9.5 [30.0 --> 96.0] setting bottom of white matter range to 83.6 setting top of gray matter range to 93.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 7599 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2927 filled 2871 bright non-wm voxels segmented. 4937 diagonally connected voxels added... white matter segmentation took 1.7 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 0.47 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 2101 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35196 voxels turned on, 38211 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+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 28 found - 28 modified | TOTAL: 47 pass 2 (xy-): 0 found - 28 modified | TOTAL: 47 pass 1 (yz+): 24 found - 24 modified | TOTAL: 71 pass 2 (yz+): 0 found - 24 modified | TOTAL: 71 pass 1 (yz-): 30 found - 30 modified | TOTAL: 101 pass 2 (yz-): 0 found - 30 modified | TOTAL: 101 pass 1 (xz+): 21 found - 21 modified | TOTAL: 122 pass 2 (xz+): 0 found - 21 modified | TOTAL: 122 pass 1 (xz-): 38 found - 38 modified | TOTAL: 160 pass 2 (xz-): 0 found - 38 modified | TOTAL: 160 Iteration Number : 1 pass 1 (+++): 14 found - 14 modified | TOTAL: 14 pass 2 (+++): 0 found - 14 modified | TOTAL: 14 pass 1 (+++): 31 found - 31 modified | TOTAL: 45 pass 2 (+++): 0 found - 31 modified | TOTAL: 45 pass 1 (+++): 24 found - 24 modified | TOTAL: 69 pass 2 (+++): 0 found - 24 modified | TOTAL: 69 pass 1 (+++): 32 found - 32 modified | TOTAL: 101 pass 2 (+++): 0 found - 32 modified | TOTAL: 101 Iteration Number : 1 pass 1 (++): 148 found - 148 modified | TOTAL: 148 pass 2 (++): 0 found - 148 modified | TOTAL: 148 pass 1 (+-): 130 found - 130 modified | TOTAL: 278 pass 2 (+-): 1 found - 131 modified | TOTAL: 279 pass 3 (+-): 0 found - 131 modified | TOTAL: 279 pass 1 (--): 175 found - 175 modified | TOTAL: 454 pass 2 (--): 0 found - 175 modified | TOTAL: 454 pass 1 (-+): 135 found - 135 modified | TOTAL: 589 pass 2 (-+): 0 found - 135 modified | TOTAL: 589 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 8 found - 8 modified | TOTAL: 15 pass 2 (xy-): 0 found - 8 modified | TOTAL: 15 pass 1 (yz+): 7 found - 7 modified | TOTAL: 22 pass 2 (yz+): 0 found - 7 modified | TOTAL: 22 pass 1 (yz-): 9 found - 9 modified | TOTAL: 31 pass 2 (yz-): 0 found - 9 modified | TOTAL: 31 pass 1 (xz+): 10 found - 10 modified | TOTAL: 41 pass 2 (xz+): 0 found - 10 modified | TOTAL: 41 pass 1 (xz-): 7 found - 7 modified | TOTAL: 48 pass 2 (xz-): 0 found - 7 modified | TOTAL: 48 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 6 found - 6 modified | TOTAL: 8 pass 2 (+-): 0 found - 6 modified | TOTAL: 8 pass 1 (--): 0 found - 0 modified | TOTAL: 8 pass 1 (-+): 3 found - 3 modified | TOTAL: 11 pass 2 (-+): 0 found - 3 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 911 (out of 711684: 0.128006) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Nov 6 13:59:34 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.982 -0.028 -0.027 2.198; 0.033 1.062 0.355 -58.790; 0.016 -0.324 0.939 58.084; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1042 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (124, 104, 121), TAL = (4.0, -7.0, 24.0) talairach voxel to voxel transform 1.017 0.032 0.017 -1.310; -0.023 0.844 -0.320 68.233; -0.025 0.291 0.954 -38.280; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 104, 121) --> (4.0, -7.0, 24.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (4.00, -7.00, 24.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -7.00, 24.00) SRC: (111.89, 114.79, 104.72) search lh wm seed point around talairach space (-14.00, -7.00, 24.00), SRC: (148.51, 113.95, 103.80) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Nov 6 14:00:15 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 modified | TOTAL: 13 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 2 found - 2 modified | TOTAL: 4 pass 2 (-+): 0 found - 2 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 = 17 (out of 342409: 0.004965) 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 20: 609 vertices, 693 faces slice 30: 8171 vertices, 8561 faces slice 40: 20215 vertices, 20660 faces slice 50: 34384 vertices, 34869 faces slice 60: 49152 vertices, 49608 faces slice 70: 62790 vertices, 63245 faces slice 80: 75512 vertices, 75955 faces slice 90: 88532 vertices, 89013 faces slice 100: 100575 vertices, 101036 faces slice 110: 112493 vertices, 112958 faces slice 120: 124213 vertices, 124678 faces slice 130: 135329 vertices, 135738 faces slice 140: 145440 vertices, 145823 faces slice 150: 154880 vertices, 155218 faces slice 160: 161790 vertices, 162084 faces slice 170: 167525 vertices, 167751 faces slice 180: 171002 vertices, 171141 faces slice 190: 171456 vertices, 171528 faces slice 200: 171456 vertices, 171528 faces slice 210: 171456 vertices, 171528 faces slice 220: 171456 vertices, 171528 faces slice 230: 171456 vertices, 171528 faces slice 240: 171456 vertices, 171528 faces slice 250: 171456 vertices, 171528 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... 171456 voxel in cpt #1: X=-72 [v=171456,e=514584,f=343056] located at (-32.842945, -38.069492, 3.092735) For the whole surface: X=-72 [v=171456,e=514584,f=343056] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Nov 6 14:00:22 EST 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Nov 6 14:00:27 EST 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts avg radius = 50.4 mm, total surface area = 89563 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Nov 6 14:01:01 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.90 +- 0.53 (0.00-->6.54) (max @ vno 99083 --> 99093) face area 0.02 +- 0.03 (-0.19-->0.50) scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.580, avgs=0 005/300: dt: 0.9000, rms radial error=175.322, avgs=0 010/300: dt: 0.9000, rms radial error=174.767, avgs=0 015/300: dt: 0.9000, rms radial error=174.038, avgs=0 020/300: dt: 0.9000, rms radial error=173.208, avgs=0 025/300: dt: 0.9000, rms radial error=172.319, avgs=0 030/300: dt: 0.9000, rms radial error=171.398, avgs=0 035/300: dt: 0.9000, rms radial error=170.459, avgs=0 040/300: dt: 0.9000, rms radial error=169.512, avgs=0 045/300: dt: 0.9000, rms radial error=168.562, avgs=0 050/300: dt: 0.9000, rms radial error=167.612, avgs=0 055/300: dt: 0.9000, rms radial error=166.665, avgs=0 060/300: dt: 0.9000, rms radial error=165.721, avgs=0 065/300: dt: 0.9000, rms radial error=164.781, avgs=0 070/300: dt: 0.9000, rms radial error=163.853, avgs=0 075/300: dt: 0.9000, rms radial error=162.930, avgs=0 080/300: dt: 0.9000, rms radial error=162.012, avgs=0 085/300: dt: 0.9000, rms radial error=161.099, avgs=0 090/300: dt: 0.9000, rms radial error=160.191, avgs=0 095/300: dt: 0.9000, rms radial error=159.287, avgs=0 100/300: dt: 0.9000, rms radial error=158.389, avgs=0 105/300: dt: 0.9000, rms radial error=157.496, avgs=0 110/300: dt: 0.9000, rms radial error=156.608, avgs=0 115/300: dt: 0.9000, rms radial error=155.724, avgs=0 120/300: dt: 0.9000, rms radial error=154.846, avgs=0 125/300: dt: 0.9000, rms radial error=153.975, avgs=0 130/300: dt: 0.9000, rms radial error=153.111, avgs=0 135/300: dt: 0.9000, rms radial error=152.251, avgs=0 140/300: dt: 0.9000, rms radial error=151.397, avgs=0 145/300: dt: 0.9000, rms radial error=150.547, avgs=0 150/300: dt: 0.9000, rms radial error=149.702, avgs=0 155/300: dt: 0.9000, rms radial error=148.861, avgs=0 160/300: dt: 0.9000, rms radial error=148.025, avgs=0 165/300: dt: 0.9000, rms radial error=147.194, avgs=0 170/300: dt: 0.9000, rms radial error=146.368, avgs=0 175/300: dt: 0.9000, rms radial error=145.545, avgs=0 180/300: dt: 0.9000, rms radial error=144.728, avgs=0 185/300: dt: 0.9000, rms radial error=143.914, avgs=0 190/300: dt: 0.9000, rms radial error=143.105, avgs=0 195/300: dt: 0.9000, rms radial error=142.300, avgs=0 200/300: dt: 0.9000, rms radial error=141.500, avgs=0 205/300: dt: 0.9000, rms radial error=140.704, avgs=0 210/300: dt: 0.9000, rms radial error=139.912, avgs=0 215/300: dt: 0.9000, rms radial error=139.125, avgs=0 220/300: dt: 0.9000, rms radial error=138.342, avgs=0 225/300: dt: 0.9000, rms radial error=137.563, avgs=0 230/300: dt: 0.9000, rms radial error=136.788, avgs=0 235/300: dt: 0.9000, rms radial error=136.018, avgs=0 240/300: dt: 0.9000, rms radial error=135.251, avgs=0 245/300: dt: 0.9000, rms radial error=134.490, avgs=0 250/300: dt: 0.9000, rms radial error=133.732, avgs=0 255/300: dt: 0.9000, rms radial error=132.979, avgs=0 260/300: dt: 0.9000, rms radial error=132.230, avgs=0 265/300: dt: 0.9000, rms radial error=131.485, avgs=0 270/300: dt: 0.9000, rms radial error=130.744, avgs=0 275/300: dt: 0.9000, rms radial error=130.007, avgs=0 280/300: dt: 0.9000, rms radial error=129.275, avgs=0 285/300: dt: 0.9000, rms radial error=128.546, avgs=0 290/300: dt: 0.9000, rms radial error=127.822, avgs=0 295/300: dt: 0.9000, rms radial error=127.101, avgs=0 300/300: dt: 0.9000, rms radial error=126.385, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20438.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3565.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 383.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00423 epoch 4 (K=640.0), pass 1, starting sse = 25.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00559 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Nov 6 14:05:21 EST 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 PBR_CON_010_02 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=-72 (nv=171456, nf=343056, ne=514584, 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... 6817 ambiguous faces found in tessellation segmenting defects... 30 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 11 -merging segment 21 into 15 28 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1765 (-4.5882) -vertex loglikelihood: -5.9406 (-2.9703) -normal dot loglikelihood: -3.5902 (-3.5902) -quad curv loglikelihood: -6.3579 (-3.1789) Total Loglikelihood : -25.0651 CORRECTING DEFECT 0 (vertices=66, convex hull=94) After retessellation of defect 0, euler #=-26 (167320,500414,333068) : difference with theory (-25) = 1 CORRECTING DEFECT 1 (vertices=58, convex hull=93) After retessellation of defect 1, euler #=-25 (167359,500569,333185) : difference with theory (-24) = 1 CORRECTING DEFECT 2 (vertices=231, convex hull=204) After retessellation of defect 2, euler #=-24 (167424,500855,333407) : difference with theory (-23) = 1 CORRECTING DEFECT 3 (vertices=6, convex hull=35) After retessellation of defect 3, euler #=-23 (167425,500868,333420) : difference with theory (-22) = 1 CORRECTING DEFECT 4 (vertices=12, convex hull=34) After retessellation of defect 4, euler #=-22 (167429,500892,333441) : difference with theory (-21) = 1 CORRECTING DEFECT 5 (vertices=502, convex hull=334) After retessellation of defect 5, euler #=-21 (167657,501735,334057) : difference with theory (-20) = 1 CORRECTING DEFECT 6 (vertices=20, convex hull=51) After retessellation of defect 6, euler #=-20 (167665,501779,334094) : difference with theory (-19) = 1 CORRECTING DEFECT 7 (vertices=16, convex hull=49) After retessellation of defect 7, euler #=-19 (167672,501819,334128) : difference with theory (-18) = 1 CORRECTING DEFECT 8 (vertices=61, convex hull=82) After retessellation of defect 8, euler #=-18 (167711,501967,334238) : difference with theory (-17) = 1 CORRECTING DEFECT 9 (vertices=207, convex hull=170) After retessellation of defect 9, euler #=-17 (167723,502084,334344) : difference with theory (-16) = 1 CORRECTING DEFECT 10 (vertices=1054, convex hull=862) After retessellation of defect 10, euler #=-16 (168277,504210,335917) : difference with theory (-15) = 1 CORRECTING DEFECT 11 (vertices=35, convex hull=45) After retessellation of defect 11, euler #=-15 (168295,504281,335971) : difference with theory (-14) = 1 CORRECTING DEFECT 12 (vertices=55, convex hull=41) After retessellation of defect 12, euler #=-14 (168301,504316,336001) : difference with theory (-13) = 1 CORRECTING DEFECT 13 (vertices=47, convex hull=58) After retessellation of defect 13, euler #=-13 (168313,504372,336046) : difference with theory (-12) = 1 CORRECTING DEFECT 14 (vertices=296, convex hull=186) After retessellation of defect 14, euler #=-11 (168378,504657,336268) : difference with theory (-11) = 0 CORRECTING DEFECT 15 (vertices=23, convex hull=42) After retessellation of defect 15, euler #=-10 (168382,504686,336294) : difference with theory (-10) = 0 CORRECTING DEFECT 16 (vertices=79, convex hull=46) After retessellation of defect 16, euler #=-9 (168400,504764,336355) : difference with theory (-9) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=58) After retessellation of defect 17, euler #=-8 (168409,504812,336395) : difference with theory (-8) = 0 CORRECTING DEFECT 18 (vertices=866, convex hull=298) After retessellation of defect 18, euler #=-7 (168481,505180,336692) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=11, convex hull=18) After retessellation of defect 19, euler #=-6 (168482,505188,336700) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=35, convex hull=53) After retessellation of defect 20, euler #=-5 (168502,505268,336761) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=11, convex hull=30) After retessellation of defect 21, euler #=-4 (168503,505282,336775) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=64, convex hull=71) After retessellation of defect 22, euler #=-3 (168534,505407,336870) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=11, convex hull=30) After retessellation of defect 23, euler #=-2 (168535,505421,336884) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=55, convex hull=37) After retessellation of defect 24, euler #=-1 (168543,505456,336912) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=64, convex hull=69) After retessellation of defect 25, euler #=0 (168568,505559,336991) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=198, convex hull=226) After retessellation of defect 26, euler #=1 (168664,505956,337293) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=31, convex hull=72) After retessellation of defect 27, euler #=2 (168678,506028,337352) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.05-->16.57) (max @ vno 127916 --> 141859) 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 (0.05-->16.57) (max @ vno 127916 --> 141859) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 122 mutations (36.3%), 214 crossovers (63.7%), 258 vertices were eliminated building final representation... 2778 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=168678, nf=337352, ne=506028, g=0) writing corrected surface to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.5 minutes 0 defective edges removing intersecting faces 000: 290 intersecting 001: 14 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 168678 - 506028 + 337352 = 2 --> 0 holes F =2V-4: 337352 = 337356-4 (0) 2E=3F: 1012056 = 1012056 (0) total defect index = 0 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 66 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Nov 6 14:26:59 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs PBR_CON_010_02 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 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/filled.mgz... reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/wm.mgz... 19362 bright wm thresholded. 2968 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.orig... computing class statistics... border white: 327994 voxels (1.95%) border gray 356685 voxels (2.13%) WM (97.0): 97.7 +- 7.4 [70.0 --> 110.0] GM (85.0) : 83.6 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.1 (was 70) setting MAX_BORDER_WHITE to 113.4 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.2 (was 40) setting MAX_GRAY to 98.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.41) (max @ vno 52045 --> 167604) face area 0.28 +- 0.12 (0.00-->5.97) mean absolute distance = 0.74 +- 0.96 3708 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=106, GM=75 mean inside = 97.4, mean outside = 80.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=84.8, 49 (49) missing vertices, mean dist 0.2 [0.7 (%37.2)->0.8 (%62.8))] %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=pyrrh, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.86) (max @ vno 167738 --> 84294) face area 0.28 +- 0.13 (0.00-->5.43) mean absolute distance = 0.35 +- 0.59 3105 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6073201.0, rms=9.57 001: dt: 0.5000, sse=7048670.0, rms=6.761 (0.000%) 002: dt: 0.5000, sse=7494078.0, rms=4.984 (0.000%) 003: dt: 0.5000, sse=7913992.5, rms=3.930 (0.000%) 004: dt: 0.5000, sse=8289723.5, rms=3.335 (0.000%) 005: dt: 0.5000, sse=8403417.0, rms=3.080 (0.000%) 006: dt: 0.5000, sse=8575801.0, rms=2.932 (0.000%) rms = 2.89, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8533035.0, rms=2.888 (0.000%) 008: dt: 0.2500, sse=5236300.5, rms=1.999 (0.000%) 009: dt: 0.2500, sse=4857157.5, rms=1.793 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=4689955.0, rms=1.751 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=4619388.0, rms=1.715 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.5, 56 (12) missing vertices, mean dist -0.2 [0.4 (%71.2)->0.2 (%28.8))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=pyrrh, 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 (0.04-->5.13) (max @ vno 167738 --> 84294) face area 0.34 +- 0.16 (0.00-->7.05) mean absolute distance = 0.25 +- 0.36 3165 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5248211.5, rms=4.27 012: dt: 0.5000, sse=5662072.5, rms=2.657 (0.000%) 013: dt: 0.5000, sse=6223060.0, rms=2.512 (0.000%) 014: dt: 0.5000, sse=6795867.0, rms=2.433 (0.000%) rms = 2.67, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=5545084.0, rms=1.773 (0.000%) 016: dt: 0.2500, sse=5148655.0, rms=1.480 (0.000%) 017: dt: 0.2500, sse=4979857.0, rms=1.427 (0.000%) rms = 1.43, time step reduction 2 of 3 to 0.125... rms = 1.42, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4948273.5, rms=1.416 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 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=90.1, 44 (4) missing vertices, mean dist -0.2 [0.3 (%75.6)->0.2 (%24.4))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=pyrrh, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.26) (max @ vno 167738 --> 84294) face area 0.33 +- 0.16 (0.00-->7.31) mean absolute distance = 0.19 +- 0.28 3258 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5219698.0, rms=3.35 019: dt: 0.5000, sse=5456582.0, rms=2.247 (0.000%) rms = 2.44, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5141285.0, rms=1.645 (0.000%) 021: dt: 0.2500, sse=5061318.5, rms=1.350 (0.000%) 022: dt: 0.2500, sse=5025551.0, rms=1.293 (0.000%) rms = 1.30, time step reduction 2 of 3 to 0.125... rms = 1.28, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4998717.0, rms=1.281 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.9, 55 (3) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=pyrrh, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5011437.5, rms=1.55 rms = 1.54, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=6291651.0, rms=1.545 (0.000%) 025: dt: 0.2500, sse=5407038.5, rms=1.214 (0.000%) 026: dt: 0.2500, sse=5587301.5, rms=1.064 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5550517.5, rms=1.040 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group generating cortex label... 7 non-cortical segments detected only using segment with 2938 vertices erasing segment 1 (vno[0] = 106272) erasing segment 2 (vno[0] = 108917) erasing segment 3 (vno[0] = 127882) erasing segment 4 (vno[0] = 130069) erasing segment 5 (vno[0] = 131118) erasing segment 6 (vno[0] = 168496) writing cortex label to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/label/lh.cortex.label... writing curvature file /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.area vertex spacing 0.88 +- 0.24 (0.08-->5.21) (max @ vno 167738 --> 84294) face area 0.33 +- 0.15 (0.00-->7.03) refinement took 5.4 minutes #-------------------------------------------- #@# Smooth2 lh Fri Nov 6 14:32:26 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri Nov 6 14:32:31 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 50.7 mm, total surface area = 100488 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.078 (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=0.021 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 232 vertices thresholded to be in k1 ~ [-0.19 0.68], k2 ~ [-0.09 0.07] total integrated curvature = 0.592*4pi (7.435) --> 0 handles ICI = 1.9, FI = 12.9, variation=218.203 135 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 167 vertices thresholded to be in [-0.11 0.28] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.014, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Fri Nov 6 14:34:36 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PBR_CON_010_02 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 [ PBR_CON_010_02/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 [ 303 ] Gb_filter = 0 WARN: S lookup min: -0.435874 WARN: S explicit min: 0.000000 vertex = 20 #-------------------------------------------- #@# Sphere lh Fri Nov 6 14:34:42 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/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 0.279... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=pyrrh, 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 %20.60 pass 1: epoch 2 of 3 starting distance error %20.59 unfolding complete - removing small folds... starting distance error %20.50 removing remaining folds... final distance error %20.51 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.87 hours #-------------------------------------------- #@# Surf Reg lh Fri Nov 6 15:26:57 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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=pyrrh, 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=pyrrh, 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 = 0.573 curvature mean = 0.024, std = 0.933 curvature mean = 0.026, std = 0.826 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 443559.3, tmin=1.0908 d=32.00 min @ (0.00, 8.00, -8.00) sse = 356041.8, tmin=2.1858 d=16.00 min @ (0.00, 0.00, 4.00) sse = 340175.8, tmin=3.2925 d=8.00 min @ (2.00, 0.00, 0.00) sse = 337222.4, tmin=4.4095 d=4.00 min @ (0.00, 0.00, -1.00) sse = 336832.2, tmin=5.5360 d=2.00 min @ (-0.50, 0.50, 1.00) sse = 336593.1, tmin=6.6722 d=1.00 min @ (0.25, -0.25, -0.50) sse = 336433.6, tmin=7.8161 d=0.50 min @ (0.00, 0.12, 0.12) sse = 336431.2, tmin=8.9819 tol=1.0e+00, sigma=0.5, host=pyrrh, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.98 min curvature mean = -0.006, std = 0.933 curvature mean = 0.013, std = 0.923 curvature mean = -0.012, std = 0.943 curvature mean = 0.006, std = 0.963 curvature mean = -0.015, std = 0.942 curvature mean = 0.002, std = 0.983 2 Reading smoothwm curvature mean = -0.023, std = 0.284 curvature mean = 0.002, std = 0.066 curvature mean = 0.070, std = 0.320 curvature mean = 0.002, std = 0.078 curvature mean = 0.034, std = 0.517 curvature mean = 0.003, std = 0.084 curvature mean = 0.019, std = 0.669 curvature mean = 0.003, std = 0.085 curvature mean = 0.005, std = 0.788 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Nov 6 15:57:11 EST 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Nov 6 15:57:14 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Nov 6 15:57:17 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBR_CON_010_02 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/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... 1642 labels changed using aseg relabeling using gibbs priors... 000: 3468 changed, 168678 examined... 001: 792 changed, 14672 examined... 002: 216 changed, 4330 examined... 003: 71 changed, 1276 examined... 004: 30 changed, 417 examined... 005: 13 changed, 190 examined... 006: 10 changed, 89 examined... 007: 7 changed, 59 examined... 008: 2 changed, 41 examined... 009: 2 changed, 10 examined... 010: 3 changed, 13 examined... 011: 0 changed, 12 examined... 253 labels changed using aseg 000: 132 total segments, 86 labels (252 vertices) changed 001: 48 total segments, 4 labels (11 vertices) changed 002: 44 total segments, 1 labels (4 vertices) changed 003: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1902 vertices marked for relabeling... 1902 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Nov 6 15:58:08 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs PBR_CON_010_02 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 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/filled.mgz... reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/wm.mgz... 19362 bright wm thresholded. 2968 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.orig... computing class statistics... border white: 327994 voxels (1.95%) border gray 356685 voxels (2.13%) WM (97.0): 97.7 +- 7.4 [70.0 --> 110.0] GM (85.0) : 83.6 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.1 (was 70) setting MAX_BORDER_WHITE to 113.4 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.2 (was 40) setting MAX_GRAY to 98.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106, GM=75 mean inside = 97.4, mean outside = 80.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.41) (max @ vno 52045 --> 167604) face area 0.28 +- 0.12 (0.00-->5.97) mean absolute distance = 0.74 +- 0.96 3794 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 581 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=84.8, 49 (49) missing vertices, mean dist 0.2 [0.7 (%37.3)->0.8 (%62.7))] %63 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=pyrrh, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->4.86) (max @ vno 167738 --> 84294) face area 0.28 +- 0.13 (0.00-->5.43) mean absolute distance = 0.35 +- 0.60 3182 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6083395.5, rms=9.56 001: dt: 0.5000, sse=7071710.5, rms=6.753 (0.000%) 002: dt: 0.5000, sse=7515043.5, rms=4.978 (0.000%) 003: dt: 0.5000, sse=7937038.5, rms=3.927 (0.000%) 004: dt: 0.5000, sse=8316452.0, rms=3.331 (0.000%) 005: dt: 0.5000, sse=8430382.0, rms=3.078 (0.000%) 006: dt: 0.5000, sse=8605615.0, rms=2.930 (0.000%) rms = 2.89, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8560877.0, rms=2.886 (0.000%) 008: dt: 0.2500, sse=5252565.0, rms=1.998 (0.000%) 009: dt: 0.2500, sse=4872439.5, rms=1.793 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=4705224.5, rms=1.751 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=4634438.0, rms=1.715 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 4 with 396 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 61 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 89 points - only 59.55% unknown deleting segment 11 with 19 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=87.5, 63 (13) missing vertices, mean dist -0.2 [0.4 (%71.1)->0.2 (%28.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=pyrrh, 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 +- 0.24 (0.04-->5.13) (max @ vno 167738 --> 84294) face area 0.34 +- 0.16 (0.00-->7.05) mean absolute distance = 0.25 +- 0.36 3190 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5274134.5, rms=4.27 012: dt: 0.5000, sse=5692730.0, rms=2.655 (0.000%) 013: dt: 0.5000, sse=6267261.5, rms=2.508 (0.000%) 014: dt: 0.5000, sse=6830341.0, rms=2.431 (0.000%) rms = 2.67, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=5575881.0, rms=1.772 (0.000%) 016: dt: 0.2500, sse=5180276.5, rms=1.484 (0.000%) 017: dt: 0.2500, sse=5010442.5, rms=1.432 (0.000%) rms = 1.44, time step reduction 2 of 3 to 0.125... rms = 1.42, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4978767.5, rms=1.422 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 407 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 115 points - only 0.00% unknown deleting segment 7 with 34 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=90.1, 51 (6) missing vertices, mean dist -0.2 [0.3 (%75.5)->0.2 (%24.5))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=pyrrh, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.07-->5.26) (max @ vno 167738 --> 84294) face area 0.33 +- 0.16 (0.00-->7.31) mean absolute distance = 0.20 +- 0.28 3295 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5244113.5, rms=3.34 019: dt: 0.5000, sse=5483813.0, rms=2.253 (0.000%) rms = 2.45, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5167973.5, rms=1.653 (0.000%) 021: dt: 0.2500, sse=5088537.0, rms=1.355 (0.000%) 022: dt: 0.2500, sse=5053359.0, rms=1.295 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... rms = 1.28, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5026077.0, rms=1.284 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 421 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 143 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 48 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=90.9, 62 (5) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=pyrrh, 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=5038708.0, rms=1.55 rms = 1.55, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=6325883.0, rms=1.547 (0.000%) 025: dt: 0.2500, sse=5429987.0, rms=1.217 (0.000%) 026: dt: 0.2500, sse=5617184.5, rms=1.069 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5579440.5, rms=1.044 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=65.1, 93 (93) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.3 (%100.0))] %23 local maxima, %43 large gradients and %30 min vals, 1564 gradients ignored tol=1.0e-04, sigma=2.0, host=pyrrh, 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=25604780.0, rms=26.23 001: dt: 0.5000, sse=19822064.0, rms=22.566 (0.000%) 002: dt: 0.5000, sse=15482949.0, rms=19.417 (0.000%) 003: dt: 0.5000, sse=12369170.0, rms=16.769 (0.000%) 004: dt: 0.5000, sse=10356365.0, rms=14.571 (0.000%) 005: dt: 0.5000, sse=9127780.0, rms=12.786 (0.000%) 006: dt: 0.5000, sse=8399245.0, rms=11.316 (0.000%) 007: dt: 0.5000, sse=7988533.0, rms=9.992 (0.000%) 008: dt: 0.5000, sse=7725082.5, rms=8.807 (0.000%) 009: dt: 0.5000, sse=7641804.0, rms=7.658 (0.000%) 010: dt: 0.5000, sse=7588993.5, rms=6.564 (0.000%) 011: dt: 0.5000, sse=7645764.0, rms=5.626 (0.000%) 012: dt: 0.5000, sse=7789623.0, rms=4.970 (0.000%) 013: dt: 0.5000, sse=7993092.5, rms=4.569 (0.000%) 014: dt: 0.5000, sse=8100075.0, rms=4.350 (0.000%) 015: dt: 0.5000, sse=8208797.5, rms=4.208 (0.000%) 016: dt: 0.5000, sse=8229042.5, rms=4.119 (0.000%) 017: dt: 0.5000, sse=8274717.5, rms=4.058 (0.000%) rms = 4.01, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8303072.0, rms=4.015 (0.000%) 019: dt: 0.2500, sse=5615781.5, rms=3.194 (0.000%) 020: dt: 0.2500, sse=5368262.5, rms=2.950 (0.000%) rms = 2.92, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5231706.0, rms=2.924 (0.000%) 022: dt: 0.1250, sse=4923589.5, rms=2.726 (0.000%) rms = 2.70, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4886580.0, rms=2.698 (0.000%) positioning took 2.5 minutes mean border=62.1, 1442 (21) missing vertices, mean dist 0.2 [0.2 (%39.0)->0.5 (%61.0))] %41 local maxima, %30 large gradients and %24 min vals, 639 gradients ignored tol=1.0e-04, sigma=1.0, host=pyrrh, 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=5850448.0, rms=5.42 024: dt: 0.5000, sse=5899373.5, rms=4.012 (0.000%) rms = 4.12, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5450570.0, rms=3.263 (0.000%) 026: dt: 0.2500, sse=5538797.5, rms=2.974 (0.000%) 027: dt: 0.2500, sse=5496598.5, rms=2.871 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5558940.5, rms=2.844 (0.000%) 029: dt: 0.1250, sse=5273168.5, rms=2.600 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5259255.0, rms=2.555 (0.000%) positioning took 0.9 minutes mean border=60.2, 1732 (16) missing vertices, mean dist 0.1 [0.2 (%33.0)->0.3 (%67.0))] %55 local maxima, %17 large gradients and %24 min vals, 688 gradients ignored tol=1.0e-04, sigma=0.5, host=pyrrh, 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=5506731.0, rms=3.68 rms = 4.04, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=5263950.0, rms=3.038 (0.000%) 032: dt: 0.2500, sse=5284225.5, rms=2.742 (0.000%) rms = 2.71, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=5507936.0, rms=2.706 (0.000%) 034: dt: 0.1250, sse=5316792.0, rms=2.513 (0.000%) rms = 2.48, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5326403.0, rms=2.482 (0.000%) positioning took 0.6 minutes mean border=59.4, 3380 (15) missing vertices, mean dist 0.0 [0.2 (%41.2)->0.2 (%58.8))] %58 local maxima, %13 large gradients and %24 min vals, 583 gradients ignored tol=1.0e-04, sigma=0.2, host=pyrrh, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5366284.0, rms=2.73 rms = 3.49, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5268412.0, rms=2.524 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5508024.5, rms=2.479 (0.000%) 038: dt: 0.1250, sse=5387417.5, rms=2.413 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5428932.5, rms=2.390 (0.000%) positioning took 0.5 minutes writing curvature file /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.area.pial vertex spacing 0.98 +- 0.40 (0.06-->8.07) (max @ vno 167738 --> 84294) face area 0.38 +- 0.28 (0.00-->9.53) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 168678 vertices processed 25000 of 168678 vertices processed 50000 of 168678 vertices processed 75000 of 168678 vertices processed 100000 of 168678 vertices processed 125000 of 168678 vertices processed 150000 of 168678 vertices processed 0 of 168678 vertices processed 25000 of 168678 vertices processed 50000 of 168678 vertices processed 75000 of 168678 vertices processed 100000 of 168678 vertices processed 125000 of 168678 vertices processed 150000 of 168678 vertices processed thickness calculation complete, 186:509 truncations. 41820 vertices at 0 distance 121047 vertices at 1 distance 104637 vertices at 2 distance 40499 vertices at 3 distance 12175 vertices at 4 distance 3483 vertices at 5 distance 1122 vertices at 6 distance 330 vertices at 7 distance 114 vertices at 8 distance 37 vertices at 9 distance 30 vertices at 10 distance 21 vertices at 11 distance 17 vertices at 12 distance 21 vertices at 13 distance 12 vertices at 14 distance 26 vertices at 15 distance 16 vertices at 16 distance 9 vertices at 17 distance 8 vertices at 18 distance 4 vertices at 19 distance 6 vertices at 20 distance writing curvature file /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/lh.thickness positioning took 10.9 minutes #-------------------------------------------- #@# Surf Volume lh Fri Nov 6 16:09:02 EST 2015 /autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf mris_calc -o lh.area.mid lh.area add lh.area.pial WARNING: # of slices=-106 in header - assuming 124... read_signa(/autofs/cluster/hookerlab/Users/Nicole/Autism/FS/subjects/PBR_CON_010_02/surf/I.001): could not open file No such file or directory mris_calc: could not establish read access to 'lh.area'. No such file or directory Linux pyrrha 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PBR_CON_010_02 exited with ERRORS at Fri Nov 6 16:09:03 EST 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting